diff --git a/.eslintignore b/.eslintignore index d5d3bde528..0708397ceb 100644 --- a/.eslintignore +++ b/.eslintignore @@ -13,7 +13,7 @@ products/jbrowse-web/scripts/** /products/jbrowse-web/config/ products/jbrowse-desktop/public/electron.js products/jbrowse-desktop/public/generateFastaIndex.js -/demos/ +/embedded_demos/ webpack.config.js craco.config.js packages/core/util/QuickLRU.js diff --git a/.eslintrc.json b/.eslintrc.json index dae65d0917..b4d8f26cb3 100644 --- a/.eslintrc.json +++ b/.eslintrc.json @@ -25,10 +25,9 @@ "@typescript-eslint/explicit-module-boundary-types": "off", "@typescript-eslint/no-empty-function": "off", "@typescript-eslint/no-unused-vars": ["warn"], + "@typescript-eslint/no-floating-promises": "error", "@typescript-eslint/no-unused-expressions": "off", - "@typescript-eslint/no-use-before-define": "off", "@typescript-eslint/no-var-requires": "off", - "@typescript-eslint/no-redeclare": "off", "no-use-before-define": "off", "curly": "error", diff --git a/.github/workflows/desktop_build_linux.yml b/.github/workflows/desktop_build_linux.yml index 8de297b59c..d570d1bb9a 100644 --- a/.github/workflows/desktop_build_linux.yml +++ b/.github/workflows/desktop_build_linux.yml @@ -18,7 +18,7 @@ jobs: uses: bahmutov/npm-install@v1 - name: Install build deps run: | - sudo apt install -y python make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev + sudo apt install -y python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev - name: Build app env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/desktop_build_win.yml b/.github/workflows/desktop_build_win.yml index ade11a3c23..4a49e898a7 100644 --- a/.github/workflows/desktop_build_win.yml +++ b/.github/workflows/desktop_build_win.yml @@ -22,7 +22,7 @@ jobs: apt install --yes wine wine32 wine64 libwine libwine:i386 fonts-wine - name: Install build deps run: | - apt install --yes python make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev + apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev - name: Build app env: WIN_CSC_LINK: ${{ secrets.WIN_CSC_LINK }} diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index f32b52f260..034561cf66 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -30,3 +30,12 @@ jobs: uses: bahmutov/npm-install@v1 - name: Check codebase format run: yarn prettier --check . + + spellcheck: + name: Spell check + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v2 + - name: Check spelling + uses: crate-ci/typos@master diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml index 35084f8d03..5e7d99c98b 100644 --- a/.github/workflows/push.yml +++ b/.github/workflows/push.yml @@ -91,8 +91,8 @@ jobs: aws-region: us-east-1 - name: Copy branch build to S3 run: | - cp products/jbrowse-web/build/test_data/config.json products/jbrowse-web/build/config.json cd products/jbrowse-web/build && zip -r "jbrowse-web-$(echo ${{github.ref}} | cut -d '/' -f3-).zip" . && cd - + cp products/jbrowse-web/build/test_data/config.json products/jbrowse-web/build/config.json aws s3 sync --delete products/jbrowse-web/build s3://jbrowse.org/code/jb2/$(echo ${{github.ref}} | cut -d "/" -f3-) storybook_lgv: name: Build and deploy static linear genome view Storybook site to AWS S3 diff --git a/.ignore b/.ignore new file mode 100644 index 0000000000..760dca67d9 --- /dev/null +++ b/.ignore @@ -0,0 +1,21 @@ +*.ix +test_data/large.chrom.sizes +packages/core/ui/react-colorful.js +plugins/legacy-jbrowse/test_data +plugins/data-management/src/ucsc-trackhub/ucscAssemblies.ts +plugins/circular-view/test_data/circos_example_content.txt +plugins/circular-view/test_data/circos_example.svg +products/jbrowse-web/src/tests/Loader.test.tsx +test_data/yeast_synteny/ +test_data/hg38_aliases.txt +test_data/config_honeybee.json +test_data/amel_hav3.1.chrom.sizes +plugins/wiggle/src/util.ts +plugins/protein/src/ProteinReferenceSequenceRenderer/aminoAcids.js +plugins/spreadsheet-view/src/SpreadsheetView/test_data/starfusion_example.fusion_predictions.tsv +products/jbrowse-aws-lambda-functions/ +products/jbrowse-desktop/src/JBrowse.test.tsx +test_data/volvox/names/ +products/jbrowse-web/src/sessionSharing.ts +website/docs/models/ +*.snap diff --git a/.prettierignore b/.prettierignore index eab850fa9f..5c05c6e36e 100644 --- a/.prettierignore +++ b/.prettierignore @@ -15,3 +15,4 @@ # JSON files we don't want to format **/*nclist*/**/*.json **/ensembl_genes/**/*.json +**/storybook-static/* diff --git a/.prettierrc.json b/.prettierrc.json index 97b711153a..c3e9304027 100644 --- a/.prettierrc.json +++ b/.prettierrc.json @@ -2,5 +2,6 @@ "semi": false, "singleQuote": true, "trailingComma": "all", - "arrowParens": "avoid" + "arrowParens": "avoid", + "proseWrap": "always" } diff --git a/CHANGELOG.md b/CHANGELOG.md index 8eb407da69..02d5959a40 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,502 @@ +## 2.3.2 (2022-12-20) + +
Packages in this release +

+ +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

+
+ +#### :rocket: Enhancement + +- `core` + - [#3422](https://github.com/GMOD/jbrowse-components/pull/3422) Auto-adjust + height of reference sequence track to current settings + ([@cmdcolin](https://github.com/cmdcolin)) +- Other + - [#3421](https://github.com/GMOD/jbrowse-components/pull/3421) Add ability to + revcomp sequence in the "Get sequence" dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3413](https://github.com/GMOD/jbrowse-components/pull/3413) Add a "base" + set of tracks and assemblies for the embedded demos + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- [#3419](https://github.com/GMOD/jbrowse-components/pull/3419) Fix rendering + base-level alignments on synteny visualizations, especially in inverted + regions ([@cmdcolin](https://github.com/cmdcolin)) +- [#3416](https://github.com/GMOD/jbrowse-components/pull/3416) Fix rendering + alignment arcs on files that need refname renaming and add jitter setting + ([@cmdcolin](https://github.com/cmdcolin)) +- [#3415](https://github.com/GMOD/jbrowse-components/pull/3415) Fix circular + view being rendered as a blank area if tab is opened in the background + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) + +
Packages in this release +

+ +| Package | Download | +| ----------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | + +

+
+ +## 2.3.0 (2022-12-15) + +
Packages in this release +

+ +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/text-indexing | | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-arc | | +| @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-breakpoint-split-view | | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-hic | | +| @jbrowse/plugin-jobs-management | | +| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-menus | | +| @jbrowse/plugin-protein | | +| @jbrowse/plugin-rdf | | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-sv-inspector | | +| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | +| @jbrowse/plugin-text-indexing | | +| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

+
+ +#### :rocket: Enhancement + +- Other + - [#3403](https://github.com/GMOD/jbrowse-components/pull/3403) Reduce + overplotting on dotplot grid lines and other misc improvements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3381](https://github.com/GMOD/jbrowse-components/pull/3381) Add method for + cache busting requests to the config file in jbrowse-web + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3384](https://github.com/GMOD/jbrowse-components/pull/3384) Add method to + more easily create compact view of alignments + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3391](https://github.com/GMOD/jbrowse-components/pull/3391) Allow arc + display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3387](https://github.com/GMOD/jbrowse-components/pull/3387) Small UI + tweaks for add track workflow ([@cmdcolin](https://github.com/cmdcolin)) + - [#3358](https://github.com/GMOD/jbrowse-components/pull/3358) Create new + "arc" display type to show long range connections between paired-end and + split-reads ([@cmdcolin](https://github.com/cmdcolin)) +- `text-indexing` + - [#3385](https://github.com/GMOD/jbrowse-components/pull/3385) Optimize + prefix size for text indexing automatically + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- Other + - [#3407](https://github.com/GMOD/jbrowse-components/pull/3407) Remove + trackhub registry plugin from core plugins, moved to plugin store + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3406](https://github.com/GMOD/jbrowse-components/pull/3406) Fix loading + connection tracks from connections that don't specify assemblyNames in + config ([@cmdcolin](https://github.com/cmdcolin)) + - [#3390](https://github.com/GMOD/jbrowse-components/pull/3390) Fix + positioning within large alignments for query->target LGV synteny navigation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3388](https://github.com/GMOD/jbrowse-components/pull/3388) Fix search + result that matches synonyms that matches multiple locations + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3404](https://github.com/GMOD/jbrowse-components/pull/3404) Fix + double-render of some synteny features + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3401](https://github.com/GMOD/jbrowse-components/pull/3401) Remove + y-scalebar rendering placeholder values in blank and loading states + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3389](https://github.com/GMOD/jbrowse-components/pull/3389) Fix issue + where snackbar would not show up when same error message is triggered + multiple times ([@cmdcolin](https://github.com/cmdcolin)) + +#### :memo: Documentation + +- `core` + - [#3396](https://github.com/GMOD/jbrowse-components/pull/3396) Use prettier + to word wrap markdown prose ([@cmdcolin](https://github.com/cmdcolin)) +- Other + - [#3383](https://github.com/GMOD/jbrowse-components/pull/3383) Add note to + user guide about variant callers that can be used for SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- `__mocks__`, `core`, `text-indexing` + - [#3400](https://github.com/GMOD/jbrowse-components/pull/3400) Reduce + peerDependency warnings from installing dev environment + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3394](https://github.com/GMOD/jbrowse-components/pull/3394) Simplify RPC + watchWorker ([@cmdcolin](https://github.com/cmdcolin)) + - [#3386](https://github.com/GMOD/jbrowse-components/pull/3386) Fix warning + when rendering circular chord displays with web worker RPC + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) + +## 2.2.2 (2022-12-06) + +
Packages in this release +

+ +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/text-indexing | | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-arc | | +| @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-breakpoint-split-view | | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-hic | | +| @jbrowse/plugin-jobs-management | | +| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-lollipop | | +| @jbrowse/plugin-menus | | +| @jbrowse/plugin-protein | | +| @jbrowse/plugin-rdf | | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-sv-inspector | | +| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | +| @jbrowse/plugin-text-indexing | | +| @jbrowse/plugin-trackhub-registry | | +| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

+
+ +#### :rocket: Enhancement + +- Other + - [#3350](https://github.com/GMOD/jbrowse-components/pull/3350) Retain feature + labels in compact display mode for SVG features, and allow turning off + keeping feature description without feature label + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3357](https://github.com/GMOD/jbrowse-components/pull/3357) Allow holding + shift key to create rubberband selection on LGV + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3363](https://github.com/GMOD/jbrowse-components/pull/3363) Create + remove-track CLI command ([@cmdcolin](https://github.com/cmdcolin)) + - [#3341](https://github.com/GMOD/jbrowse-components/pull/3341) Add BEDPE + adapter type ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3359](https://github.com/GMOD/jbrowse-components/pull/3359) Fix typos in + codebase using typos-cli ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- Other + - [#3377](https://github.com/GMOD/jbrowse-components/pull/3377) Fix rendering + and clicking synteny features when using MainThreadRpc + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3375](https://github.com/GMOD/jbrowse-components/pull/3375) Fix + `jbrowse upgrade` CLI command overwriting config.json with --branch or + --nightly options ([@cmdcolin](https://github.com/cmdcolin)) + - [#3370](https://github.com/GMOD/jbrowse-components/pull/3370) Fix error with + SNPCoverage not rendering MM tag modifications in some cases + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3366](https://github.com/GMOD/jbrowse-components/pull/3366) Fix ability to + use LGV synteny track on inverted alignments + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3348](https://github.com/GMOD/jbrowse-components/pull/3348) Fix for + breakpoint split view and circular view issues with `` type entries in + v2.2.1 ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3369](https://github.com/GMOD/jbrowse-components/pull/3369) Fix uncaught + promise errors and add lint rule for catching these + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :memo: Documentation + +- [#3347](https://github.com/GMOD/jbrowse-components/pull/3347) Reduce number of + quickstart guides ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- `core` + - [#3368](https://github.com/GMOD/jbrowse-components/pull/3368) Create base + "Dialog" component to standardize dialogs across codebase + ([@cmdcolin](https://github.com/cmdcolin)) +- `text-indexing` + - [#3344](https://github.com/GMOD/jbrowse-components/pull/3344) fix yarn build + error in Windows ([@Lilas-w](https://github.com/Lilas-w)) + +#### Committers: 2 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) +- [@Lilas-w](https://github.com/Lilas-w) + +## 2.2.1 (2022-11-21) + +
Packages in this release +

+ +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-breakpoint-split-view | | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-rdf | | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

+
+ +#### :rocket: Enhancement + +- Other + - [#3277](https://github.com/GMOD/jbrowse-components/pull/3277) Create new + "Add track workflow" that allows pasting JSON track configs + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3328](https://github.com/GMOD/jbrowse-components/pull/3328) Add GC content + display type to the reference sequence track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3316](https://github.com/GMOD/jbrowse-components/pull/3316) Add LGV + typescripting to @jbrowse/react-linear-genome-view + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3298](https://github.com/GMOD/jbrowse-components/pull/3298) Add + authentication plugin to embedded components + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3329](https://github.com/GMOD/jbrowse-components/pull/3329) Add ability to + minimize/collapse tracks and views and move views up/down in view stack + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3308](https://github.com/GMOD/jbrowse-components/pull/3308) Add ability to + display synteny track in a normal LGV showing regions of synteny as features + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3317](https://github.com/GMOD/jbrowse-components/pull/3317) Move + ErrorBoundary so that tracks/views that have crashed can be closed more + easily ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- Other + - [#3342](https://github.com/GMOD/jbrowse-components/pull/3342) Fix CRAM + mismatches calculation regression in v2.2.0 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3319](https://github.com/GMOD/jbrowse-components/pull/3319) Fix pileup + "sort by" setting being lost on zoom level change + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3340](https://github.com/GMOD/jbrowse-components/pull/3340) Fix linear + genome view import form going into infinite loading state changing + assemblies with same refnames ([@cmdcolin](https://github.com/cmdcolin)) + - [#3339](https://github.com/GMOD/jbrowse-components/pull/3339) Fix force flag + for drawing large regions and node-fetch polyfill for node 18 fix in + @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 2 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) +- Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) + +## 2.2.0 (2022-11-04) + +
Packages in this release +

+ +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/text-indexing | | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-arc | | +| @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-hic | | +| @jbrowse/plugin-jobs-management | | +| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-menus | | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | +| @jbrowse/plugin-text-indexing | | +| @jbrowse/plugin-trackhub-registry | | +| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

+
+ +#### :rocket: Enhancement + +- Other + - [#3296](https://github.com/GMOD/jbrowse-components/pull/3296) Add option to + use OAuth "state" param in internet accounts + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3285](https://github.com/GMOD/jbrowse-components/pull/3285) Use typescript + version of @gmod/cram ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3299](https://github.com/GMOD/jbrowse-components/pull/3299) Add ability to + open a synteny track directly from the dotplot/linear synteny view import + forms ([@cmdcolin](https://github.com/cmdcolin)) + - [#3287](https://github.com/GMOD/jbrowse-components/pull/3287) Lazy-load + assemblies on demand instead of all at app startup + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3279](https://github.com/GMOD/jbrowse-components/pull/3279) Remove + unnecessary expanded region query and small refactors + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- `core` + - [#3309](https://github.com/GMOD/jbrowse-components/pull/3309) Fix animated + "Loading..." message keyframes ([@cmdcolin](https://github.com/cmdcolin)) + - [#3306](https://github.com/GMOD/jbrowse-components/pull/3306) Fix the + RefNameAutocomplete displaying a stale value for chromosome names + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3302](https://github.com/GMOD/jbrowse-components/pull/3302) Improve + rubberband zooming across elided regions + ([@cmdcolin](https://github.com/cmdcolin)) +- Other + - [#3293](https://github.com/GMOD/jbrowse-components/pull/3293) Fix CRAM + plotting for data files that encode insertions in uncommon way + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :memo: Documentation + +- `core`, `text-indexing` + - [#3278](https://github.com/GMOD/jbrowse-components/pull/3278) Auto-generate + docs ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- [#3310](https://github.com/GMOD/jbrowse-components/pull/3310) Remove + CacheProvider emotion cache ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 3 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) +- Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) +- Scott Cain ([@scottcain](https://github.com/scottcain)) + ## 2.1.7 (2022-10-20)
Packages in this release @@ -14,7 +513,9 @@ #### :bug: Bug Fix -- [#3282](https://github.com/GMOD/jbrowse-components/pull/3282) Fix for embedded build with webpack 4 failing with v2.1.6 ([@cmdcolin](https://github.com/cmdcolin)) +- [#3282](https://github.com/GMOD/jbrowse-components/pull/3282) Fix for embedded + build with webpack 4 failing with v2.1.6 + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 @@ -74,34 +575,55 @@ #### :rocket: Enhancement - Other - - [#3272](https://github.com/GMOD/jbrowse-components/pull/3272) Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff ([@cmdcolin](https://github.com/cmdcolin)) - - [#3254](https://github.com/GMOD/jbrowse-components/pull/3254) Use tick labels that correspond to the overview's larger zoom level ([@cmdcolin](https://github.com/cmdcolin)) + - [#3272](https://github.com/GMOD/jbrowse-components/pull/3272) Disable + resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3254](https://github.com/GMOD/jbrowse-components/pull/3254) Use tick + labels that correspond to the overview's larger zoom level + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3230](https://github.com/GMOD/jbrowse-components/pull/3230) Add ability to customize About dialog with callbacks and optionally hide links to data ([@cmdcolin](https://github.com/cmdcolin)) - - [#3275](https://github.com/GMOD/jbrowse-components/pull/3275) Add help dialog for feature sequence panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#3250](https://github.com/GMOD/jbrowse-components/pull/3250) Handle alternate line endings ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3252](https://github.com/GMOD/jbrowse-components/pull/3252) Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types ([@cmdcolin](https://github.com/cmdcolin)) + - [#3230](https://github.com/GMOD/jbrowse-components/pull/3230) Add ability to + customize About dialog with callbacks and optionally hide links to data + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3275](https://github.com/GMOD/jbrowse-components/pull/3275) Add help + dialog for feature sequence panel ([@cmdcolin](https://github.com/cmdcolin)) + - [#3250](https://github.com/GMOD/jbrowse-components/pull/3250) Handle + alternate line endings + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3252](https://github.com/GMOD/jbrowse-components/pull/3252) Fix gene + sequence fetching in embedded, and allow fetching genomic sequence for other + feature types ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `text-indexing` - - [#3276](https://github.com/GMOD/jbrowse-components/pull/3276) Allow using web worker RPC on embedded LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#3276](https://github.com/GMOD/jbrowse-components/pull/3276) Allow using + web worker RPC on embedded LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#3266](https://github.com/GMOD/jbrowse-components/pull/3266) Fix relative path loading of plugins ([@cmdcolin](https://github.com/cmdcolin)) - - [#3269](https://github.com/GMOD/jbrowse-components/pull/3269) Fix ability to rename session in web/desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#3256](https://github.com/GMOD/jbrowse-components/pull/3256) Fix tracks hanging in safari and polyfill for bigwig tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#3266](https://github.com/GMOD/jbrowse-components/pull/3266) Fix relative + path loading of plugins ([@cmdcolin](https://github.com/cmdcolin)) + - [#3269](https://github.com/GMOD/jbrowse-components/pull/3269) Fix ability to + rename session in web/desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#3256](https://github.com/GMOD/jbrowse-components/pull/3256) Fix tracks + hanging in safari and polyfill for bigwig tracks + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3274](https://github.com/GMOD/jbrowse-components/pull/3274) Update bbi-js for bugfix on webpack 4 ([@cmdcolin](https://github.com/cmdcolin)) - - [#3259](https://github.com/GMOD/jbrowse-components/pull/3259) Fix issue with breakpoint split view using view before initialized ([@cmdcolin](https://github.com/cmdcolin)) + - [#3274](https://github.com/GMOD/jbrowse-components/pull/3274) Update bbi-js + for bugfix on webpack 4 ([@cmdcolin](https://github.com/cmdcolin)) + - [#3259](https://github.com/GMOD/jbrowse-components/pull/3259) Fix issue with + breakpoint split view using view before initialized + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#3255](https://github.com/GMOD/jbrowse-components/pull/3255) Add more docs about color callbacks ([@cmdcolin](https://github.com/cmdcolin)) +- [#3255](https://github.com/GMOD/jbrowse-components/pull/3255) Add more docs + about color callbacks ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#3261](https://github.com/GMOD/jbrowse-components/pull/3261) Fix for flaky test ([@cmdcolin](https://github.com/cmdcolin)) + - [#3261](https://github.com/GMOD/jbrowse-components/pull/3261) Fix for flaky + test ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -147,46 +669,89 @@ #### :rocket: Enhancement - Other - - [#3200](https://github.com/GMOD/jbrowse-components/pull/3200) Use Alert component for track messages ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3229](https://github.com/GMOD/jbrowse-components/pull/3229) Allow user to select local assembly to add tracks to for trackhub registry ([@cmdcolin](https://github.com/cmdcolin)) - - [#3220](https://github.com/GMOD/jbrowse-components/pull/3220) Improve error reporting on SV inspector/spreadsheet view on import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#3198](https://github.com/GMOD/jbrowse-components/pull/3198) Improve error reporting on jbrowse-web start screen when user attempts to open a broken recent session ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#3200](https://github.com/GMOD/jbrowse-components/pull/3200) Use Alert + component for track messages + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3229](https://github.com/GMOD/jbrowse-components/pull/3229) Allow user to + select local assembly to add tracks to for trackhub registry + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3220](https://github.com/GMOD/jbrowse-components/pull/3220) Improve error + reporting on SV inspector/spreadsheet view on import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3198](https://github.com/GMOD/jbrowse-components/pull/3198) Improve error + reporting on jbrowse-web start screen when user attempts to open a broken + recent session + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - `core` - - [#3223](https://github.com/GMOD/jbrowse-components/pull/3223) Allow adding session tracks to embedded react component along with disableAddTracks option if unwanted ([@cmdcolin](https://github.com/cmdcolin)) - - [#3227](https://github.com/GMOD/jbrowse-components/pull/3227) Add infrastructure for creating linear-genome-view sub-classes ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#3215](https://github.com/GMOD/jbrowse-components/pull/3215) Add error boundary on view, track, and drawer widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#3216](https://github.com/GMOD/jbrowse-components/pull/3216) Add ability to set number of bp to fetch up/down stream/inside intron in feature details ([@cmdcolin](https://github.com/cmdcolin)) + - [#3223](https://github.com/GMOD/jbrowse-components/pull/3223) Allow adding + session tracks to embedded react component along with disableAddTracks + option if unwanted ([@cmdcolin](https://github.com/cmdcolin)) + - [#3227](https://github.com/GMOD/jbrowse-components/pull/3227) Add + infrastructure for creating linear-genome-view sub-classes + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#3215](https://github.com/GMOD/jbrowse-components/pull/3215) Add error + boundary on view, track, and drawer widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3216](https://github.com/GMOD/jbrowse-components/pull/3216) Add ability to + set number of bp to fetch up/down stream/inside intron in feature details + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3241](https://github.com/GMOD/jbrowse-components/pull/3241) Fix local session failing to load copying between tabs in some cases ([@cmdcolin](https://github.com/cmdcolin)) - - [#3234](https://github.com/GMOD/jbrowse-components/pull/3234) Fix circular embedded view failing to load in v2.1.3 and v2.1.4 ([@cmdcolin](https://github.com/cmdcolin)) - - [#3233](https://github.com/GMOD/jbrowse-components/pull/3233) Fix legend being cutoff on multiwiggle tracks with wide window ([@cmdcolin](https://github.com/cmdcolin)) - - [#3217](https://github.com/GMOD/jbrowse-components/pull/3217) Fix loading tracks from connection using assembly alias ([@cmdcolin](https://github.com/cmdcolin)) - - [#3214](https://github.com/GMOD/jbrowse-components/pull/3214) Fix trackhub registry failing to load in 2.x.y versions of jbrowse ([@cmdcolin](https://github.com/cmdcolin)) - - [#3204](https://github.com/GMOD/jbrowse-components/pull/3204) Fix authentication configuration on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#3241](https://github.com/GMOD/jbrowse-components/pull/3241) Fix local + session failing to load copying between tabs in some cases + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3234](https://github.com/GMOD/jbrowse-components/pull/3234) Fix circular + embedded view failing to load in v2.1.3 and v2.1.4 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3233](https://github.com/GMOD/jbrowse-components/pull/3233) Fix legend + being cutoff on multiwiggle tracks with wide window + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3217](https://github.com/GMOD/jbrowse-components/pull/3217) Fix loading + tracks from connection using assembly alias + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3214](https://github.com/GMOD/jbrowse-components/pull/3214) Fix trackhub + registry failing to load in 2.x.y versions of jbrowse + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3204](https://github.com/GMOD/jbrowse-components/pull/3204) Fix + authentication configuration on jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3231](https://github.com/GMOD/jbrowse-components/pull/3231) Fix theme coloring for components that use overrides e.g. accordion summary ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3231](https://github.com/GMOD/jbrowse-components/pull/3231) Fix theme + coloring for components that use overrides e.g. accordion summary + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation -- [#3193](https://github.com/GMOD/jbrowse-components/pull/3193) Add desktop specific plugin tutorial ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#3193](https://github.com/GMOD/jbrowse-components/pull/3193) Add desktop + specific plugin tutorial + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - Other - - [#3243](https://github.com/GMOD/jbrowse-components/pull/3243) Add component test for circular genome view ([@cmdcolin](https://github.com/cmdcolin)) - - [#3242](https://github.com/GMOD/jbrowse-components/pull/3242) Fix flaky test in plugins/linear-genome-view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3243](https://github.com/GMOD/jbrowse-components/pull/3243) Add component + test for circular genome view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3242](https://github.com/GMOD/jbrowse-components/pull/3242) Fix flaky test + in plugins/linear-genome-view ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3228](https://github.com/GMOD/jbrowse-components/pull/3228) Improve TypeScript for queueDialog ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3224](https://github.com/GMOD/jbrowse-components/pull/3224) More typescripting of plain js files ([@cmdcolin](https://github.com/cmdcolin)) - - [#3207](https://github.com/GMOD/jbrowse-components/pull/3207) Hardcoded block width of 800px on static blocks ([@cmdcolin](https://github.com/cmdcolin)) - - [#3197](https://github.com/GMOD/jbrowse-components/pull/3197) Use "temporaryAssemblies" to store read vs ref assemblies, and allow selecting "sessionAssemblies" in dropdown ([@cmdcolin](https://github.com/cmdcolin)) + - [#3228](https://github.com/GMOD/jbrowse-components/pull/3228) Improve + TypeScript for queueDialog + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3224](https://github.com/GMOD/jbrowse-components/pull/3224) More + typescripting of plain js files ([@cmdcolin](https://github.com/cmdcolin)) + - [#3207](https://github.com/GMOD/jbrowse-components/pull/3207) Hardcoded + block width of 800px on static blocks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3197](https://github.com/GMOD/jbrowse-components/pull/3197) Use + "temporaryAssemblies" to store read vs ref assemblies, and allow selecting + "sessionAssemblies" in dropdown ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) @@ -206,7 +771,9 @@ #### :bug: Bug Fix -- [#3191](https://github.com/GMOD/jbrowse-components/pull/3191) Fix the UMD build of the react embedded components ([@cmdcolin](https://github.com/cmdcolin)) +- [#3191](https://github.com/GMOD/jbrowse-components/pull/3191) Fix the UMD + build of the react embedded components + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 @@ -246,53 +813,109 @@ #### :rocket: Enhancement - Other - - [#3188](https://github.com/GMOD/jbrowse-components/pull/3188) Add 'Open saved session' button to start screen on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#3187](https://github.com/GMOD/jbrowse-components/pull/3187) Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table ([@cmdcolin](https://github.com/cmdcolin)) - - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target ([@cmdcolin](https://github.com/cmdcolin)) - - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability for CLI to recognize plaintext BED files ([@cmdcolin](https://github.com/cmdcolin)) - - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about dialog with version number for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user to wait before re-launching app on desktop update ([@cmdcolin](https://github.com/cmdcolin)) - - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target ([@cmdcolin](https://github.com/cmdcolin)) - - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability for CLI to recognize plaintext BED files ([@cmdcolin](https://github.com/cmdcolin)) - - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about dialog with version number for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user to wait before re-launching app on desktop update ([@cmdcolin](https://github.com/cmdcolin)) + - [#3188](https://github.com/GMOD/jbrowse-components/pull/3188) Add 'Open + saved session' button to start screen on desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3187](https://github.com/GMOD/jbrowse-components/pull/3187) Add mouseover + tooltip descriptions to the header of the VariantFeatureDetails + sample/genotype table ([@cmdcolin](https://github.com/cmdcolin)) + - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add + extendSession extension point to web and desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y + assemblies of dotplot or top/bottom selection of synteny views to be either + query or target ([@cmdcolin](https://github.com/cmdcolin)) + - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability + for CLI to recognize plaintext BED files + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about + dialog with version number for embedded components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user + to wait before re-launching app on desktop update + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add + extendSession extension point to web and desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y + assemblies of dotplot or top/bottom selection of synteny views to be either + query or target ([@cmdcolin](https://github.com/cmdcolin)) + - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability + for CLI to recognize plaintext BED files + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about + dialog with version number for embedded components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user + to wait before re-launching app on desktop update + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3180](https://github.com/GMOD/jbrowse-components/pull/3180) Improve adding assemblies internally, and use the assembly displayName in more places in the UI ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3180](https://github.com/GMOD/jbrowse-components/pull/3180) Improve adding + assemblies internally, and use the assembly displayName in more places in + the UI ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make + pluginManager param to getFetcher optional + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make + pluginManager param to getFetcher optional + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - `core` - - [#3168](https://github.com/GMOD/jbrowse-components/pull/3168) Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead state tree node" error by creating snapshots of parent region for block calculations ([@cmdcolin](https://github.com/cmdcolin)) - - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead state tree node" error by creating snapshots of parent region for block calculations ([@cmdcolin](https://github.com/cmdcolin)) + - [#3168](https://github.com/GMOD/jbrowse-components/pull/3168) Fix search + behavior when there are multiple matches in LGV header and when feature + description matched in import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead + state tree node" error by creating snapshots of parent region for block + calculations ([@cmdcolin](https://github.com/cmdcolin)) + - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead + state tree node" error by creating snapshots of parent region for block + calculations ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing inverted CIGAR segments on dotplot ([@cmdcolin](https://github.com/cmdcolin)) - - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing inverted CIGAR segments on dotplot ([@cmdcolin](https://github.com/cmdcolin)) + - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing + inverted CIGAR segments on dotplot + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing + inverted CIGAR segments on dotplot + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) -- [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation + overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation + overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - Other - - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3165](https://github.com/GMOD/jbrowse-components/pull/3165) Use more defaults in rollup plugins ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add + extendSession extension point to web and desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add + extendSession extension point to web and desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3165](https://github.com/GMOD/jbrowse-components/pull/3165) Use more + defaults in rollup plugins + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) - - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) + - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make + pluginManager param to getFetcher optional + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the + QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) + - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make + pluginManager param to getFetcher optional + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the + QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) @@ -393,25 +1016,50 @@ #### :rocket: Enhancement - Other - - [#3152](https://github.com/GMOD/jbrowse-components/pull/3152) Render CSQ and ANN fields in VCF feature details as data grids ([@cmdcolin](https://github.com/cmdcolin)) - - [#3137](https://github.com/GMOD/jbrowse-components/pull/3137) Make ideogram menu item similar to others ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3152](https://github.com/GMOD/jbrowse-components/pull/3152) Render CSQ and + ANN fields in VCF feature details as data grids + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3137](https://github.com/GMOD/jbrowse-components/pull/3137) Make ideogram + menu item similar to others + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3159](https://github.com/GMOD/jbrowse-components/pull/3159) Sequence search track ([@cmdcolin](https://github.com/cmdcolin)) - - [#3132](https://github.com/GMOD/jbrowse-components/pull/3132) Extend theme with module augmentation ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3159](https://github.com/GMOD/jbrowse-components/pull/3159) Sequence + search track ([@cmdcolin](https://github.com/cmdcolin)) + - [#3132](https://github.com/GMOD/jbrowse-components/pull/3132) Extend theme + with module augmentation + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#3157](https://github.com/GMOD/jbrowse-components/pull/3157) Support the "name" field on multi-wiggle adapter subadapters instead of source ([@cmdcolin](https://github.com/cmdcolin)) - - [#3154](https://github.com/GMOD/jbrowse-components/pull/3154) Use the union of all the subadapter refNames for the MultiWiggleAdapter getRefNames ([@cmdcolin](https://github.com/cmdcolin)) - - [#3156](https://github.com/GMOD/jbrowse-components/pull/3156) Fix for mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode ([@cmdcolin](https://github.com/cmdcolin)) - - [#3151](https://github.com/GMOD/jbrowse-components/pull/3151) Fix ability to click and drag overview scale bar dragging right to left ([@cmdcolin](https://github.com/cmdcolin)) - - [#3133](https://github.com/GMOD/jbrowse-components/pull/3133) Update the ref name box when assembly is changed in LGV import form ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3131](https://github.com/GMOD/jbrowse-components/pull/3131) Use "code" instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3119](https://github.com/GMOD/jbrowse-components/pull/3119) Use es2015 setting for commonjs builds of packages to fix @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) - - [#3142](https://github.com/GMOD/jbrowse-components/pull/3142) Fix unicode arrow icon not rendering with some fonts in configuration editor ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3157](https://github.com/GMOD/jbrowse-components/pull/3157) Support the + "name" field on multi-wiggle adapter subadapters instead of source + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3154](https://github.com/GMOD/jbrowse-components/pull/3154) Use the union + of all the subadapter refNames for the MultiWiggleAdapter getRefNames + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3156](https://github.com/GMOD/jbrowse-components/pull/3156) Fix for + mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3151](https://github.com/GMOD/jbrowse-components/pull/3151) Fix ability to + click and drag overview scale bar dragging right to left + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3133](https://github.com/GMOD/jbrowse-components/pull/3133) Update the ref + name box when assembly is changed in LGV import form + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3131](https://github.com/GMOD/jbrowse-components/pull/3131) Use "code" + instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3119](https://github.com/GMOD/jbrowse-components/pull/3119) Use es2015 + setting for commonjs builds of packages to fix @jbrowse/img + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3142](https://github.com/GMOD/jbrowse-components/pull/3142) Fix unicode + arrow icon not rendering with some fonts in configuration editor + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3120](https://github.com/GMOD/jbrowse-components/pull/3120) Fix menu items for changing display type from track menu ([@cmdcolin](https://github.com/cmdcolin)) + - [#3120](https://github.com/GMOD/jbrowse-components/pull/3120) Fix menu items + for changing display type from track menu + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 @@ -455,26 +1103,47 @@ #### :rocket: Enhancement - `core` - - [#3111](https://github.com/GMOD/jbrowse-components/pull/3111) Create undo manager in jbrowse-web and jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#3115](https://github.com/GMOD/jbrowse-components/pull/3115) Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - - [#3102](https://github.com/GMOD/jbrowse-components/pull/3102) Allow creating alternative "add track workflows" from within the "Add track" widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#3043](https://github.com/GMOD/jbrowse-components/pull/3043) Create MultiWiggle track type, adapter, and renderers ([@cmdcolin](https://github.com/cmdcolin)) + - [#3111](https://github.com/GMOD/jbrowse-components/pull/3111) Create undo + manager in jbrowse-web and jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3115](https://github.com/GMOD/jbrowse-components/pull/3115) Add warning + when dotplot renders outside of it's boundaries, and create click-and-drag + panning of dotplot view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3102](https://github.com/GMOD/jbrowse-components/pull/3102) Allow creating + alternative "add track workflows" from within the "Add track" widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3043](https://github.com/GMOD/jbrowse-components/pull/3043) Create + MultiWiggle track type, adapter, and renderers + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3113](https://github.com/GMOD/jbrowse-components/pull/3113) Improve SVG performance by avoiding re-render when feature is clicked ([@cmdcolin](https://github.com/cmdcolin)) - - [#3110](https://github.com/GMOD/jbrowse-components/pull/3110) Remove TSDX from plugin development tools ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3106](https://github.com/GMOD/jbrowse-components/pull/3106) Add "emphasis" mode for no fill/scatterplot mode in XYPlot type renderings ([@cmdcolin](https://github.com/cmdcolin)) + - [#3113](https://github.com/GMOD/jbrowse-components/pull/3113) Improve SVG + performance by avoiding re-render when feature is clicked + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3110](https://github.com/GMOD/jbrowse-components/pull/3110) Remove TSDX + from plugin development tools + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3106](https://github.com/GMOD/jbrowse-components/pull/3106) Add "emphasis" + mode for no fill/scatterplot mode in XYPlot type renderings + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3109](https://github.com/GMOD/jbrowse-components/pull/3109) Better support for developing plugins from within yarn 2+ workspaces (include \_\_virtual folder in build) ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3109](https://github.com/GMOD/jbrowse-components/pull/3109) Better support + for developing plugins from within yarn 2+ workspaces (include \_\_virtual + folder in build) ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3095](https://github.com/GMOD/jbrowse-components/pull/3095) Add MUI exports to re-exports list ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3092](https://github.com/GMOD/jbrowse-components/pull/3092) Fix use of embedded components with vite 3.0 using tsc to compile @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) + - [#3095](https://github.com/GMOD/jbrowse-components/pull/3095) Add MUI + exports to re-exports list + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3092](https://github.com/GMOD/jbrowse-components/pull/3092) Fix use of + embedded components with vite 3.0 using tsc to compile @jbrowse/core + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#3116](https://github.com/GMOD/jbrowse-components/pull/3116) Add docs for multi-wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) +- [#3116](https://github.com/GMOD/jbrowse-components/pull/3116) Add docs for + multi-wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 @@ -533,21 +1202,38 @@ #### :rocket: Enhancement - `core` - - [#3089](https://github.com/GMOD/jbrowse-components/pull/3089) Clarify error message when adapter has no features ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3084](https://github.com/GMOD/jbrowse-components/pull/3084) Show a descriptive error if an adapter doesn't provide a sequence ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3071](https://github.com/GMOD/jbrowse-components/pull/3071) Add ability to mouseover/click on synteny feature polygons in the linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3089](https://github.com/GMOD/jbrowse-components/pull/3089) Clarify error + message when adapter has no features + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3084](https://github.com/GMOD/jbrowse-components/pull/3084) Show a + descriptive error if an adapter doesn't provide a sequence + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3071](https://github.com/GMOD/jbrowse-components/pull/3071) Add ability to + mouseover/click on synteny feature polygons in the linear synteny view + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3081](https://github.com/GMOD/jbrowse-components/pull/3081) Add ability to toggle gridlines on the LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#3081](https://github.com/GMOD/jbrowse-components/pull/3081) Add ability to + toggle gridlines on the LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3088](https://github.com/GMOD/jbrowse-components/pull/3088) Fix labels being cut-off in SVG features by rendering feature labels on main thread ([@cmdcolin](https://github.com/cmdcolin)) - - [#3085](https://github.com/GMOD/jbrowse-components/pull/3085) Fix zoom to behavior being inaccurate with many displayed regions visible ([@cmdcolin](https://github.com/cmdcolin)) - - [#3082](https://github.com/GMOD/jbrowse-components/pull/3082) Fix negative strand CIGAR renderings on linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#3077](https://github.com/GMOD/jbrowse-components/pull/3077) Fix crash opening multiple synteny track selectors launched from dotplot view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3088](https://github.com/GMOD/jbrowse-components/pull/3088) Fix labels + being cut-off in SVG features by rendering feature labels on main thread + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3085](https://github.com/GMOD/jbrowse-components/pull/3085) Fix zoom to + behavior being inaccurate with many displayed regions visible + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3082](https://github.com/GMOD/jbrowse-components/pull/3082) Fix negative + strand CIGAR renderings on linear synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3077](https://github.com/GMOD/jbrowse-components/pull/3077) Fix crash + opening multiple synteny track selectors launched from dotplot view + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3086](https://github.com/GMOD/jbrowse-components/pull/3086) Fix pxToBp and bpToPx calculations when there are many displayed regions ([@cmdcolin](https://github.com/cmdcolin)) + - [#3086](https://github.com/GMOD/jbrowse-components/pull/3086) Fix pxToBp and + bpToPx calculations when there are many displayed regions + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 @@ -607,27 +1293,46 @@ #### :rocket: Enhancement - Other - - [#3001](https://github.com/GMOD/jbrowse-components/pull/3001) Draw SNPs in modifications/methylation views ([@cmdcolin](https://github.com/cmdcolin)) - - [#3068](https://github.com/GMOD/jbrowse-components/pull/3068) Allow HTML in feature tooltips, remove react-simple-code-editor ([@cmdcolin](https://github.com/cmdcolin)) - - [#3065](https://github.com/GMOD/jbrowse-components/pull/3065) Allow changing between xyplot,line,density for linear wiggle tracks and other small fixes ([@cmdcolin](https://github.com/cmdcolin)) + - [#3001](https://github.com/GMOD/jbrowse-components/pull/3001) Draw SNPs in + modifications/methylation views ([@cmdcolin](https://github.com/cmdcolin)) + - [#3068](https://github.com/GMOD/jbrowse-components/pull/3068) Allow HTML in + feature tooltips, remove react-simple-code-editor + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3065](https://github.com/GMOD/jbrowse-components/pull/3065) Allow changing + between xyplot,line,density for linear wiggle tracks and other small fixes + ([@cmdcolin](https://github.com/cmdcolin)) - `text-indexing` - - [#3058](https://github.com/GMOD/jbrowse-components/pull/3058) Improve bundle size and code splitting on embedded builds (v2) ([@cmdcolin](https://github.com/cmdcolin)) + - [#3058](https://github.com/GMOD/jbrowse-components/pull/3058) Improve bundle + size and code splitting on embedded builds (v2) + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core`, `text-indexing` - - [#2949](https://github.com/GMOD/jbrowse-components/pull/2949) Upgrade to MUI v5, mobx-state-tree v5, mobx-react v6, mobx-react v7 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2949](https://github.com/GMOD/jbrowse-components/pull/2949) Upgrade to MUI + v5, mobx-state-tree v5, mobx-react v6, mobx-react v7 + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3072](https://github.com/GMOD/jbrowse-components/pull/3072) Fix the display of inversions for MCScan alignments ([@cmdcolin](https://github.com/cmdcolin)) - - [#3057](https://github.com/GMOD/jbrowse-components/pull/3057) Fix export SVG crash on some BigWig tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#3052](https://github.com/GMOD/jbrowse-components/pull/3052) Fix negative value quantitative display in svg exports ([@cmdcolin](https://github.com/cmdcolin)) + - [#3072](https://github.com/GMOD/jbrowse-components/pull/3072) Fix the + display of inversions for MCScan alignments + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3057](https://github.com/GMOD/jbrowse-components/pull/3057) Fix export SVG + crash on some BigWig tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#3052](https://github.com/GMOD/jbrowse-components/pull/3052) Fix negative + value quantitative display in svg exports + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3064](https://github.com/GMOD/jbrowse-components/pull/3064) Fix opening link in new tab by default in feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#3053](https://github.com/GMOD/jbrowse-components/pull/3053) Avoid displaying [object Object] on deeply nested data in base feature details ([@cmdcolin](https://github.com/cmdcolin)) + - [#3064](https://github.com/GMOD/jbrowse-components/pull/3064) Fix opening + link in new tab by default in feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3053](https://github.com/GMOD/jbrowse-components/pull/3053) Avoid + displaying [object Object] on deeply nested data in base feature details + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#3067](https://github.com/GMOD/jbrowse-components/pull/3067) Typescriptify some integration tests ([@cmdcolin](https://github.com/cmdcolin)) +- [#3067](https://github.com/GMOD/jbrowse-components/pull/3067) Typescriptify + some integration tests ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 @@ -688,27 +1393,43 @@ #### :rocket: Enhancement - `core` - - [#3044](https://github.com/GMOD/jbrowse-components/pull/3044) Remove node-canvas from @jbrowse/core dependencies ([@cmdcolin](https://github.com/cmdcolin)) - - [#3041](https://github.com/GMOD/jbrowse-components/pull/3041) Fix ability to search and load data files using lower case refName aliases ([@cmdcolin](https://github.com/cmdcolin)) + - [#3044](https://github.com/GMOD/jbrowse-components/pull/3044) Remove + node-canvas from @jbrowse/core dependencies + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3041](https://github.com/GMOD/jbrowse-components/pull/3041) Fix ability to + search and load data files using lower case refName aliases + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3042](https://github.com/GMOD/jbrowse-components/pull/3042) Add fetch with proxy support to jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#3038](https://github.com/GMOD/jbrowse-components/pull/3038) Display coordinates in overview scalebar when no cytoband available ([@cmdcolin](https://github.com/cmdcolin)) - - [#3015](https://github.com/GMOD/jbrowse-components/pull/3015) Add plaintext bed support with BedAdapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#3042](https://github.com/GMOD/jbrowse-components/pull/3042) Add fetch with + proxy support to jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) + - [#3038](https://github.com/GMOD/jbrowse-components/pull/3038) Display + coordinates in overview scalebar when no cytoband available + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3015](https://github.com/GMOD/jbrowse-components/pull/3015) Add plaintext + bed support with BedAdapter ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#3049](https://github.com/GMOD/jbrowse-components/pull/3049) Fix ability to use callbacks for the linear arc renderer ([@cmdcolin](https://github.com/cmdcolin)) +- [#3049](https://github.com/GMOD/jbrowse-components/pull/3049) Fix ability to + use callbacks for the linear arc renderer + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2831](https://github.com/GMOD/jbrowse-components/pull/2831) Update commands for sorting GFF3 for tabix ([@cmdcolin](https://github.com/cmdcolin)) -- [#3018](https://github.com/GMOD/jbrowse-components/pull/3018) Add desktop specific plugin example ([@cmdcolin](https://github.com/cmdcolin)) -- [#3022](https://github.com/GMOD/jbrowse-components/pull/3022) Add example using embedded components with next.js ([@cmdcolin](https://github.com/cmdcolin)) +- [#2831](https://github.com/GMOD/jbrowse-components/pull/2831) Update commands + for sorting GFF3 for tabix ([@cmdcolin](https://github.com/cmdcolin)) +- [#3018](https://github.com/GMOD/jbrowse-components/pull/3018) Add desktop + specific plugin example ([@cmdcolin](https://github.com/cmdcolin)) +- [#3022](https://github.com/GMOD/jbrowse-components/pull/3022) Add example + using embedded components with next.js + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#3035](https://github.com/GMOD/jbrowse-components/pull/3035) Add typescripting to hierarchical track selector ([@cmdcolin](https://github.com/cmdcolin)) + - [#3035](https://github.com/GMOD/jbrowse-components/pull/3035) Add + typescripting to hierarchical track selector + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 @@ -748,35 +1469,70 @@ #### :rocket: Enhancement - Other - - [#3025](https://github.com/GMOD/jbrowse-components/pull/3025) Add dotplot session spec ([@cmdcolin](https://github.com/cmdcolin)) - - [#2975](https://github.com/GMOD/jbrowse-components/pull/2975) Add simplified URL format for loading synteny views ([@cmdcolin](https://github.com/cmdcolin)) - - [#3023](https://github.com/GMOD/jbrowse-components/pull/3023) Add error handling in case of invalid OAuth2 configuration used. ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) - - [#3020](https://github.com/GMOD/jbrowse-components/pull/3020) Allow choosing trackId when using text-index with --file with --fileId ([@cmdcolin](https://github.com/cmdcolin)) - - [#3016](https://github.com/GMOD/jbrowse-components/pull/3016) Allow whitespace separated refname,start,end type locstring ([@cmdcolin](https://github.com/cmdcolin)) - - [#3006](https://github.com/GMOD/jbrowse-components/pull/3006) Add string array configuration slot UI improvements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2998](https://github.com/GMOD/jbrowse-components/pull/2998) Avoid rendering offscreen contents in pileup renderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#3000](https://github.com/GMOD/jbrowse-components/pull/3000) Add reference base and correct percentage calculations to tooltip on SNPCoverage display ([@cmdcolin](https://github.com/cmdcolin)) -- `core` - - [#2981](https://github.com/GMOD/jbrowse-components/pull/2981) Add simplified URL format for loading spreadsheet and SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#2990](https://github.com/GMOD/jbrowse-components/pull/2990) Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#3003](https://github.com/GMOD/jbrowse-components/pull/3003) Add ability to run field formatters on the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#3017](https://github.com/GMOD/jbrowse-components/pull/3017) Add button to copy track config in About track dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2999](https://github.com/GMOD/jbrowse-components/pull/2999) Generate clickable links to track data in about track dialog ([@cmdcolin](https://github.com/cmdcolin)) + - [#3025](https://github.com/GMOD/jbrowse-components/pull/3025) Add dotplot + session spec ([@cmdcolin](https://github.com/cmdcolin)) + - [#2975](https://github.com/GMOD/jbrowse-components/pull/2975) Add simplified + URL format for loading synteny views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3023](https://github.com/GMOD/jbrowse-components/pull/3023) Add error + handling in case of invalid OAuth2 configuration used. + ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) + - [#3020](https://github.com/GMOD/jbrowse-components/pull/3020) Allow choosing + trackId when using text-index with --file with --fileId + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3016](https://github.com/GMOD/jbrowse-components/pull/3016) Allow + whitespace separated refname,start,end type locstring + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3006](https://github.com/GMOD/jbrowse-components/pull/3006) Add string + array configuration slot UI improvements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2998](https://github.com/GMOD/jbrowse-components/pull/2998) Avoid + rendering offscreen contents in pileup renderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3000](https://github.com/GMOD/jbrowse-components/pull/3000) Add reference + base and correct percentage calculations to tooltip on SNPCoverage display + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#2981](https://github.com/GMOD/jbrowse-components/pull/2981) Add simplified + URL format for loading spreadsheet and SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2990](https://github.com/GMOD/jbrowse-components/pull/2990) Use shortened + megabases (M) display when zoomed out, and option to hide the "open track + selector" button + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#3003](https://github.com/GMOD/jbrowse-components/pull/3003) Add ability to + run field formatters on the feature details panel + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3017](https://github.com/GMOD/jbrowse-components/pull/3017) Add button to + copy track config in About track dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2999](https://github.com/GMOD/jbrowse-components/pull/2999) Generate + clickable links to track data in about track dialog + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - - [#3005](https://github.com/GMOD/jbrowse-components/pull/3005) Use cascading menu helper library for track menu to avoid menu going offscreen ([@cmdcolin](https://github.com/cmdcolin)) + - [#3005](https://github.com/GMOD/jbrowse-components/pull/3005) Use cascading + menu helper library for track menu to avoid menu going offscreen + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3021](https://github.com/GMOD/jbrowse-components/pull/3021) Fix mouseover display of read name to alignments track ([@cmdcolin](https://github.com/cmdcolin)) - - [#3012](https://github.com/GMOD/jbrowse-components/pull/3012) Small fix to rankSearchResults logic ([@cmdcolin](https://github.com/cmdcolin)) - - [#3009](https://github.com/GMOD/jbrowse-components/pull/3009) Add jsdom to jbrowse-img to fix --noRasterize option ([@cmdcolin](https://github.com/cmdcolin)) + - [#3021](https://github.com/GMOD/jbrowse-components/pull/3021) Fix mouseover + display of read name to alignments track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3012](https://github.com/GMOD/jbrowse-components/pull/3012) Small fix to + rankSearchResults logic ([@cmdcolin](https://github.com/cmdcolin)) + - [#3009](https://github.com/GMOD/jbrowse-components/pull/3009) Add jsdom to + jbrowse-img to fix --noRasterize option + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3007](https://github.com/GMOD/jbrowse-components/pull/3007) Fix read vs ref dotplot view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3007](https://github.com/GMOD/jbrowse-components/pull/3007) Fix read vs + ref dotplot view ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - [@andrzejgrzelak](https://github.com/andrzejgrzelak) @@ -810,23 +1566,36 @@ #### :rocket: Enhancement - `core` - - [#2991](https://github.com/GMOD/jbrowse-components/pull/2991) Use canvas2svg for SVG export, fixes non-rasterized usage of bezier, arcs, and more ([@cmdcolin](https://github.com/cmdcolin)) - - [#2483](https://github.com/GMOD/jbrowse-components/pull/2483) Add setting to color by query score per alignment for dotplot, support HTML in config slot descriptions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2983](https://github.com/GMOD/jbrowse-components/pull/2983) Set target=\_blank by default in user HTML links ([@cmdcolin](https://github.com/cmdcolin)) + - [#2991](https://github.com/GMOD/jbrowse-components/pull/2991) Use canvas2svg + for SVG export, fixes non-rasterized usage of bezier, arcs, and more + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2483](https://github.com/GMOD/jbrowse-components/pull/2483) Add setting to + color by query score per alignment for dotplot, support HTML in config slot + descriptions ([@cmdcolin](https://github.com/cmdcolin)) + - [#2983](https://github.com/GMOD/jbrowse-components/pull/2983) Set + target=\_blank by default in user HTML links + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2994](https://github.com/GMOD/jbrowse-components/pull/2994) Allow choosing filename for svg export ([@cmdcolin](https://github.com/cmdcolin)) + - [#2994](https://github.com/GMOD/jbrowse-components/pull/2994) Allow choosing + filename for svg export ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#2989](https://github.com/GMOD/jbrowse-components/pull/2989) Fix bezierCurveTo ponyfill on firefox ([@cmdcolin](https://github.com/cmdcolin)) + - [#2989](https://github.com/GMOD/jbrowse-components/pull/2989) Fix + bezierCurveTo ponyfill on firefox ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2977](https://github.com/GMOD/jbrowse-components/pull/2977) Respect --indexFile option when adding VCF and BED tracks ([@heavywatal](https://github.com/heavywatal)) - - [#2974](https://github.com/GMOD/jbrowse-components/pull/2974) Fix track indexing being ignored after first add track widget usage ([@teresam856](https://github.com/teresam856)) + - [#2977](https://github.com/GMOD/jbrowse-components/pull/2977) Respect + --indexFile option when adding VCF and BED tracks + ([@heavywatal](https://github.com/heavywatal)) + - [#2974](https://github.com/GMOD/jbrowse-components/pull/2974) Fix track + indexing being ignored after first add track widget usage + ([@teresam856](https://github.com/teresam856)) #### :house: Internal -- [#2980](https://github.com/GMOD/jbrowse-components/pull/2980) Remove errors related to test coverage in CI ([@cmdcolin](https://github.com/cmdcolin)) +- [#2980](https://github.com/GMOD/jbrowse-components/pull/2980) Remove errors + related to test coverage in CI ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 @@ -859,28 +1628,48 @@ #### :rocket: Enhancement -- [#2970](https://github.com/GMOD/jbrowse-components/pull/2970) Draw indels in modifications/methylation mode ([@cmdcolin](https://github.com/cmdcolin)) -- [#2961](https://github.com/GMOD/jbrowse-components/pull/2961) Add more visible pileup mismatches when zoomed out ([@cmdcolin](https://github.com/cmdcolin)) -- [#2960](https://github.com/GMOD/jbrowse-components/pull/2960) Avoid performing a text index search if input looks like a locstring ([@cmdcolin](https://github.com/cmdcolin)) -- [#2954](https://github.com/GMOD/jbrowse-components/pull/2954) Support in-memory GFF3 and GTF in JBrowse 1 connection ([@garrettjstevens](https://github.com/garrettjstevens)) -- [#2947](https://github.com/GMOD/jbrowse-components/pull/2947) Optimization for SNPCoverageAdapter and CRAM parsing ([@cmdcolin](https://github.com/cmdcolin)) +- [#2970](https://github.com/GMOD/jbrowse-components/pull/2970) Draw indels in + modifications/methylation mode ([@cmdcolin](https://github.com/cmdcolin)) +- [#2961](https://github.com/GMOD/jbrowse-components/pull/2961) Add more visible + pileup mismatches when zoomed out ([@cmdcolin](https://github.com/cmdcolin)) +- [#2960](https://github.com/GMOD/jbrowse-components/pull/2960) Avoid performing + a text index search if input looks like a locstring + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2954](https://github.com/GMOD/jbrowse-components/pull/2954) Support + in-memory GFF3 and GTF in JBrowse 1 connection + ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2947](https://github.com/GMOD/jbrowse-components/pull/2947) Optimization for + SNPCoverageAdapter and CRAM parsing ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#2969](https://github.com/GMOD/jbrowse-components/pull/2969) Fix link on yeast synteny demo and fix CIGAR rendering on dotplot ([@cmdcolin](https://github.com/cmdcolin)) -- [#2964](https://github.com/GMOD/jbrowse-components/pull/2964) Fix crash displaying modifications called on softclipped regions of reads ([@cmdcolin](https://github.com/cmdcolin)) -- [#2965](https://github.com/GMOD/jbrowse-components/pull/2965) Fix filter functionality on pileup tracks ([@cmdcolin](https://github.com/cmdcolin)) -- [#2953](https://github.com/GMOD/jbrowse-components/pull/2953) Fix "Open" button on LGV ImportForm ([@cmdcolin](https://github.com/cmdcolin)) -- [#2952](https://github.com/GMOD/jbrowse-components/pull/2952) Fix read vs ref not finding primary alignment on certain CRAM files ([@cmdcolin](https://github.com/cmdcolin)) -- [#2951](https://github.com/GMOD/jbrowse-components/pull/2951) Fix viewing soft/hardclip indicator in some regions ([@cmdcolin](https://github.com/cmdcolin)) +- [#2969](https://github.com/GMOD/jbrowse-components/pull/2969) Fix link on + yeast synteny demo and fix CIGAR rendering on dotplot + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2964](https://github.com/GMOD/jbrowse-components/pull/2964) Fix crash + displaying modifications called on softclipped regions of reads + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2965](https://github.com/GMOD/jbrowse-components/pull/2965) Fix filter + functionality on pileup tracks ([@cmdcolin](https://github.com/cmdcolin)) +- [#2953](https://github.com/GMOD/jbrowse-components/pull/2953) Fix "Open" + button on LGV ImportForm ([@cmdcolin](https://github.com/cmdcolin)) +- [#2952](https://github.com/GMOD/jbrowse-components/pull/2952) Fix read vs ref + not finding primary alignment on certain CRAM files + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2951](https://github.com/GMOD/jbrowse-components/pull/2951) Fix viewing + soft/hardclip indicator in some regions + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2946](https://github.com/GMOD/jbrowse-components/pull/2946) Small doc updates ([@cmdcolin](https://github.com/cmdcolin)) +- [#2946](https://github.com/GMOD/jbrowse-components/pull/2946) Small doc + updates ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#2955](https://github.com/GMOD/jbrowse-components/pull/2955) Re-enable eslint autofix for prettier rules ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2955](https://github.com/GMOD/jbrowse-components/pull/2955) Re-enable eslint + autofix for prettier rules + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 @@ -907,12 +1696,15 @@ #### :bug: Bug Fix -- [#2941](https://github.com/GMOD/jbrowse-components/pull/2941) Fix linear read vs ref hanging in v1.7.5 ([@cmdcolin](https://github.com/cmdcolin)) +- [#2941](https://github.com/GMOD/jbrowse-components/pull/2941) Fix linear read + vs ref hanging in v1.7.5 ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2944](https://github.com/GMOD/jbrowse-components/pull/2944) Avoid stalling on undefined assemblyName during ref name renaming ([@cmdcolin](https://github.com/cmdcolin)) + - [#2944](https://github.com/GMOD/jbrowse-components/pull/2944) Avoid stalling + on undefined assemblyName during ref name renaming + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 @@ -932,7 +1724,9 @@ #### :bug: Bug Fix -- [#2939](https://github.com/GMOD/jbrowse-components/pull/2939) Fix loading CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) +- [#2939](https://github.com/GMOD/jbrowse-components/pull/2939) Fix loading + CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse + desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 @@ -973,19 +1767,32 @@ #### :rocket: Enhancement - `core` - - [#2885](https://github.com/GMOD/jbrowse-components/pull/2885) Reduce serialization overhead on alignments tracks and access feature details asynchronously ([@cmdcolin](https://github.com/cmdcolin)) + - [#2885](https://github.com/GMOD/jbrowse-components/pull/2885) Reduce + serialization overhead on alignments tracks and access feature details + asynchronously ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2935](https://github.com/GMOD/jbrowse-components/pull/2935) Use the name "Read Sequence" for the read vs ref view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2916](https://github.com/GMOD/jbrowse-components/pull/2916) Add vite setup to our embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) - - [#2927](https://github.com/GMOD/jbrowse-components/pull/2927) Optimize gtf by only parsing lazily per-refName ([@cmdcolin](https://github.com/cmdcolin)) - - [#2928](https://github.com/GMOD/jbrowse-components/pull/2928) Add vanillajs/script tag loading embedded components demos ([@cmdcolin](https://github.com/cmdcolin)) + - [#2935](https://github.com/GMOD/jbrowse-components/pull/2935) Use the name + "Read Sequence" for the read vs ref view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2916](https://github.com/GMOD/jbrowse-components/pull/2916) Add vite setup + to our embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) + - [#2927](https://github.com/GMOD/jbrowse-components/pull/2927) Optimize gtf + by only parsing lazily per-refName + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2928](https://github.com/GMOD/jbrowse-components/pull/2928) Add + vanillajs/script tag loading embedded components demos + ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `text-indexing` - - [#2684](https://github.com/GMOD/jbrowse-components/pull/2684) Text-indexing in desktop ([@teresam856](https://github.com/teresam856)) + - [#2684](https://github.com/GMOD/jbrowse-components/pull/2684) Text-indexing + in desktop ([@teresam856](https://github.com/teresam856)) #### :bug: Bug Fix -- [#2863](https://github.com/GMOD/jbrowse-components/pull/2863) Render gene with CDS subfeatures properly ([@cmdcolin](https://github.com/cmdcolin)) -- [#2934](https://github.com/GMOD/jbrowse-components/pull/2934) Bump @gmod/trix to fix prefix size calculation and searching first word in index ([@cmdcolin](https://github.com/cmdcolin)) +- [#2863](https://github.com/GMOD/jbrowse-components/pull/2863) Render gene with + CDS subfeatures properly ([@cmdcolin](https://github.com/cmdcolin)) +- [#2934](https://github.com/GMOD/jbrowse-components/pull/2934) Bump @gmod/trix + to fix prefix size calculation and searching first word in index + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -1043,9 +1850,13 @@ #### :bug: Bug Fix - Other - - [#2925](https://github.com/GMOD/jbrowse-components/pull/2925) Fix embedded vanillaJS/script tag usage of embedded components ([@cmdcolin](https://github.com/cmdcolin)) + - [#2925](https://github.com/GMOD/jbrowse-components/pull/2925) Fix embedded + vanillaJS/script tag usage of embedded components + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2923](https://github.com/GMOD/jbrowse-components/pull/2923) Add babel/runtime to dependencies ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2923](https://github.com/GMOD/jbrowse-components/pull/2923) Add + babel/runtime to dependencies + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 @@ -1127,13 +1938,18 @@ #### :bug: Bug Fix - `core` - - [#2917](https://github.com/GMOD/jbrowse-components/pull/2917) Create tsconfig.build.json to add types to plugins/embedded components ([@cmdcolin](https://github.com/cmdcolin)) + - [#2917](https://github.com/GMOD/jbrowse-components/pull/2917) Create + tsconfig.build.json to add types to plugins/embedded components + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2914](https://github.com/GMOD/jbrowse-components/pull/2914) Manually polyfill fetch in @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) + - [#2914](https://github.com/GMOD/jbrowse-components/pull/2914) Manually + polyfill fetch in @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2903](https://github.com/GMOD/jbrowse-components/pull/2903) Add download link for jbrowse web on downloads page ([@cmdcolin](https://github.com/cmdcolin)) +- [#2903](https://github.com/GMOD/jbrowse-components/pull/2903) Add download + link for jbrowse web on downloads page + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 @@ -1190,45 +2006,86 @@ #### :rocket: Enhancement - Other - - [#2909](https://github.com/GMOD/jbrowse-components/pull/2909) Add --prefixSize flag to @jbrowse/cli text-index ([@cmdcolin](https://github.com/cmdcolin)) - - [#2887](https://github.com/GMOD/jbrowse-components/pull/2887) Optimize filtering on alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2879](https://github.com/GMOD/jbrowse-components/pull/2879) Multi-level synteny rubberband ([@cmdcolin](https://github.com/cmdcolin)) - - [#2874](https://github.com/GMOD/jbrowse-components/pull/2874) Optimizations for rendering long syntenic alignments e.g. CHM13 vs GRCh38 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2872](https://github.com/GMOD/jbrowse-components/pull/2872) Better connection between paired-end alignments in breakpoint split view and optimizations ([@cmdcolin](https://github.com/cmdcolin)) + - [#2909](https://github.com/GMOD/jbrowse-components/pull/2909) Add + --prefixSize flag to @jbrowse/cli text-index + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2887](https://github.com/GMOD/jbrowse-components/pull/2887) Optimize + filtering on alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2879](https://github.com/GMOD/jbrowse-components/pull/2879) Multi-level + synteny rubberband ([@cmdcolin](https://github.com/cmdcolin)) + - [#2874](https://github.com/GMOD/jbrowse-components/pull/2874) Optimizations + for rendering long syntenic alignments e.g. CHM13 vs GRCh38 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2872](https://github.com/GMOD/jbrowse-components/pull/2872) Better + connection between paired-end alignments in breakpoint split view and + optimizations ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2902](https://github.com/GMOD/jbrowse-components/pull/2902) Standardize heights of widgets in LGV import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#2781](https://github.com/GMOD/jbrowse-components/pull/2781) Add floating labels to SVG features ([@cmdcolin](https://github.com/cmdcolin)) - - [#2875](https://github.com/GMOD/jbrowse-components/pull/2875) Make assembly selector remember your last selected assembly ([@cmdcolin](https://github.com/cmdcolin)) - - [#2860](https://github.com/GMOD/jbrowse-components/pull/2860) Avoid performing many peekTransferables to optimize RPC serialization ([@rbuels](https://github.com/rbuels)) + - [#2902](https://github.com/GMOD/jbrowse-components/pull/2902) Standardize + heights of widgets in LGV import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2781](https://github.com/GMOD/jbrowse-components/pull/2781) Add floating + labels to SVG features ([@cmdcolin](https://github.com/cmdcolin)) + - [#2875](https://github.com/GMOD/jbrowse-components/pull/2875) Make assembly + selector remember your last selected assembly + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2860](https://github.com/GMOD/jbrowse-components/pull/2860) Avoid + performing many peekTransferables to optimize RPC serialization + ([@rbuels](https://github.com/rbuels)) #### :bug: Bug Fix - Other - - [#2908](https://github.com/GMOD/jbrowse-components/pull/2908) Fix AboutDialog under vite for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#2900](https://github.com/GMOD/jbrowse-components/pull/2900) Fix the 'Open assembly' menu item in jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2882](https://github.com/GMOD/jbrowse-components/pull/2882) Add padding at the bottom of the configuration editor to help color editing popup being cutoff ([@cmdcolin](https://github.com/cmdcolin)) - - [#2877](https://github.com/GMOD/jbrowse-components/pull/2877) Fix strand on arrows in horizontally flipped mode ([@cmdcolin](https://github.com/cmdcolin)) + - [#2908](https://github.com/GMOD/jbrowse-components/pull/2908) Fix + AboutDialog under vite for embedded components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2900](https://github.com/GMOD/jbrowse-components/pull/2900) Fix the 'Open + assembly' menu item in jbrowse desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2882](https://github.com/GMOD/jbrowse-components/pull/2882) Add padding at + the bottom of the configuration editor to help color editing popup being + cutoff ([@cmdcolin](https://github.com/cmdcolin)) + - [#2877](https://github.com/GMOD/jbrowse-components/pull/2877) Fix strand on + arrows in horizontally flipped mode + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components ([@cmdcolin](https://github.com/cmdcolin)) + - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a + user-supplied fetchESM callback to import ESM plugins to fix 'Critical + dependency...' errors from embedded components + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2894](https://github.com/GMOD/jbrowse-components/pull/2894) Add create-react-app v5 embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) -- [#2830](https://github.com/GMOD/jbrowse-components/pull/2830) Documentation comparing main app with embedded components ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#2894](https://github.com/GMOD/jbrowse-components/pull/2894) Add + create-react-app v5 embedded component demos + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2830](https://github.com/GMOD/jbrowse-components/pull/2830) Documentation + comparing main app with embedded components + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - `core` - - [#2904](https://github.com/GMOD/jbrowse-components/pull/2904) Use a user-supplied fetchCJS callback to import CJS plugins ([@cmdcolin](https://github.com/cmdcolin)) - - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#2857](https://github.com/GMOD/jbrowse-components/pull/2857) Refactor and improve types of OffscreenCanvas shim and ponyfill ([@rbuels](https://github.com/rbuels)) + - [#2904](https://github.com/GMOD/jbrowse-components/pull/2904) Use a + user-supplied fetchCJS callback to import CJS plugins + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a + user-supplied fetchESM callback to import ESM plugins to fix 'Critical + dependency...' errors from embedded components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2857](https://github.com/GMOD/jbrowse-components/pull/2857) Refactor and + improve types of OffscreenCanvas shim and ponyfill + ([@rbuels](https://github.com/rbuels)) - `__mocks__`, `core` - - [#2905](https://github.com/GMOD/jbrowse-components/pull/2905) Use react-use-measure instead of react-use-dimensions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2646](https://github.com/GMOD/jbrowse-components/pull/2646) Upgrade repository to use webpack 5/CRA 5 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2905](https://github.com/GMOD/jbrowse-components/pull/2905) Use + react-use-measure instead of react-use-dimensions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2646](https://github.com/GMOD/jbrowse-components/pull/2646) Upgrade + repository to use webpack 5/CRA 5 ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Robert Buels ([@rbuels](https://github.com/rbuels)) @@ -1289,30 +2146,58 @@ #### :rocket: Enhancement - Other - - [#2847](https://github.com/GMOD/jbrowse-components/pull/2847) Add option to color all the letters on all the reads to the pileup renderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#2849](https://github.com/GMOD/jbrowse-components/pull/2849) Avoid drawing intron subfeatures for gene glyphs ([@cmdcolin](https://github.com/cmdcolin)) - - [#2835](https://github.com/GMOD/jbrowse-components/pull/2835) Hide add track and connection menu items when using embedded component ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2836](https://github.com/GMOD/jbrowse-components/pull/2836) Display low-quality modifications in SNPCoverage renderer for MM tag ([@cmdcolin](https://github.com/cmdcolin)) + - [#2847](https://github.com/GMOD/jbrowse-components/pull/2847) Add option to + color all the letters on all the reads to the pileup renderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2849](https://github.com/GMOD/jbrowse-components/pull/2849) Avoid drawing + intron subfeatures for gene glyphs + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2835](https://github.com/GMOD/jbrowse-components/pull/2835) Hide add track + and connection menu items when using embedded component + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2836](https://github.com/GMOD/jbrowse-components/pull/2836) Display + low-quality modifications in SNPCoverage renderer for MM tag + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2809](https://github.com/GMOD/jbrowse-components/pull/2809) Optimizations for alignments tracks and BAM parsing ([@cmdcolin](https://github.com/cmdcolin)) - - [#2828](https://github.com/GMOD/jbrowse-components/pull/2828) Change calculation for number of webworkers for web/desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to specify number of workers ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2775](https://github.com/GMOD/jbrowse-components/pull/2775) New SVG gene glyph with directional arrows ([@cmdcolin](https://github.com/cmdcolin)) + - [#2809](https://github.com/GMOD/jbrowse-components/pull/2809) Optimizations + for alignments tracks and BAM parsing + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2828](https://github.com/GMOD/jbrowse-components/pull/2828) Change + calculation for number of webworkers for web/desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to + specify number of workers + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2775](https://github.com/GMOD/jbrowse-components/pull/2775) New SVG gene + glyph with directional arrows ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2852](https://github.com/GMOD/jbrowse-components/pull/2852) Fix misaligned features under breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2844](https://github.com/GMOD/jbrowse-components/pull/2844) Fix layout of small features without labels for SvgFeatureRenderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#2839](https://github.com/GMOD/jbrowse-components/pull/2839) Fix the drawing of SNP height when the SNPCoverage track is using log scale ([@cmdcolin](https://github.com/cmdcolin)) - - [#2825](https://github.com/GMOD/jbrowse-components/pull/2825) Fix tracklabels positioning not updating in UI after user selection ([@cmdcolin](https://github.com/cmdcolin)) + - [#2852](https://github.com/GMOD/jbrowse-components/pull/2852) Fix misaligned + features under breakpoint split view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2844](https://github.com/GMOD/jbrowse-components/pull/2844) Fix layout of + small features without labels for SvgFeatureRenderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2839](https://github.com/GMOD/jbrowse-components/pull/2839) Fix the + drawing of SNP height when the SNPCoverage track is using log scale + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2825](https://github.com/GMOD/jbrowse-components/pull/2825) Fix + tracklabels positioning not updating in UI after user selection + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2841](https://github.com/GMOD/jbrowse-components/pull/2841) Fix alignments tracks loading excessive data on chromosomes where no features exist ([@cmdcolin](https://github.com/cmdcolin)) - - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to specify number of workers ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2841](https://github.com/GMOD/jbrowse-components/pull/2841) Fix alignments + tracks loading excessive data on chromosomes where no features exist + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to + specify number of workers + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) @@ -1344,12 +2229,17 @@ #### :rocket: Enhancement -- [#2820](https://github.com/GMOD/jbrowse-components/pull/2820) Add optimization for BAM and unzip operations ([@cmdcolin](https://github.com/cmdcolin)) +- [#2820](https://github.com/GMOD/jbrowse-components/pull/2820) Add optimization + for BAM and unzip operations ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#2821](https://github.com/GMOD/jbrowse-components/pull/2821) Fixup scroll on wiggle tracks with trackLabels->offset ([@cmdcolin](https://github.com/cmdcolin)) -- [#2819](https://github.com/GMOD/jbrowse-components/pull/2819) Fix bug in desktop where first track gets stuck loading ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2821](https://github.com/GMOD/jbrowse-components/pull/2821) Fixup scroll on + wiggle tracks with trackLabels->offset + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2819](https://github.com/GMOD/jbrowse-components/pull/2819) Fix bug in + desktop where first track gets stuck loading + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 @@ -1408,40 +2298,83 @@ #### :rocket: Enhancement - `core` - - [#2796](https://github.com/GMOD/jbrowse-components/pull/2796) Add collapsible accordion sections in configuration editor ([@cmdcolin](https://github.com/cmdcolin)) - - [#2791](https://github.com/GMOD/jbrowse-components/pull/2791) Add new coloring options for dotplot and ability to "rectangularize" dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2741](https://github.com/GMOD/jbrowse-components/pull/2741) Allow ability to enter a space-separated locstring to open a list of regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2725](https://github.com/GMOD/jbrowse-components/pull/2725) Refactor InternetAccounts, add standard getFetcher ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2787](https://github.com/GMOD/jbrowse-components/pull/2787) Display the total bp viewed in the header of the dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2767](https://github.com/GMOD/jbrowse-components/pull/2767) Wiggle and SNPCoverage look and feel improvements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2746](https://github.com/GMOD/jbrowse-components/pull/2746) Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view ([@cmdcolin](https://github.com/cmdcolin)) + - [#2796](https://github.com/GMOD/jbrowse-components/pull/2796) Add + collapsible accordion sections in configuration editor + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2791](https://github.com/GMOD/jbrowse-components/pull/2791) Add new + coloring options for dotplot and ability to "rectangularize" dotplot view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2741](https://github.com/GMOD/jbrowse-components/pull/2741) Allow ability + to enter a space-separated locstring to open a list of regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2725](https://github.com/GMOD/jbrowse-components/pull/2725) Refactor + InternetAccounts, add standard getFetcher + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2787](https://github.com/GMOD/jbrowse-components/pull/2787) Display the + total bp viewed in the header of the dotplot view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2767](https://github.com/GMOD/jbrowse-components/pull/2767) Wiggle and + SNPCoverage look and feel improvements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2746](https://github.com/GMOD/jbrowse-components/pull/2746) Add .delta and + .chain format adapters, fix ref name aliasing in synteny/dotplot views, and + optimize very long CIGAR string in synteny view + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2799](https://github.com/GMOD/jbrowse-components/pull/2799) Exit process after rendering to speed up jb2export ([@cmdcolin](https://github.com/cmdcolin)) - - [#2793](https://github.com/GMOD/jbrowse-components/pull/2793) Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2761](https://github.com/GMOD/jbrowse-components/pull/2761) Add a --clean argument to `jbrowse upgrade` to clean up old files ([@cmdcolin](https://github.com/cmdcolin)) - - [#2760](https://github.com/GMOD/jbrowse-components/pull/2760) Make a configurable refNameColumn in RefNameAliasAdapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#2799](https://github.com/GMOD/jbrowse-components/pull/2799) Exit process + after rendering to speed up jb2export + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2793](https://github.com/GMOD/jbrowse-components/pull/2793) Add + abortcontroller polyfill to jbrowse-img to allow it to run under node 14 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2761](https://github.com/GMOD/jbrowse-components/pull/2761) Add a --clean + argument to `jbrowse upgrade` to clean up old files + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2760](https://github.com/GMOD/jbrowse-components/pull/2760) Make a + configurable refNameColumn in RefNameAliasAdapter + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#2798](https://github.com/GMOD/jbrowse-components/pull/2798) Fix bug where web worker would sometimes be called before it was ready ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2798](https://github.com/GMOD/jbrowse-components/pull/2798) Fix bug where + web worker would sometimes be called before it was ready + ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - - [#2797](https://github.com/GMOD/jbrowse-components/pull/2797) Fix crash plotting methylation in sparse regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2782](https://github.com/GMOD/jbrowse-components/pull/2782) Fix display of cytobands when horizontally flipped ([@cmdcolin](https://github.com/cmdcolin)) - - [#2678](https://github.com/GMOD/jbrowse-components/pull/2678) Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads ([@cmdcolin](https://github.com/cmdcolin)) - - [#2774](https://github.com/GMOD/jbrowse-components/pull/2774) Fix overwriting broken symlink with --force in add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2773](https://github.com/GMOD/jbrowse-components/pull/2773) Fix using global stats autoscale on wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2766](https://github.com/GMOD/jbrowse-components/pull/2766) Add a check for empty content blocks to fix rare empty stats estimation ([@cmdcolin](https://github.com/cmdcolin)) + - [#2797](https://github.com/GMOD/jbrowse-components/pull/2797) Fix crash + plotting methylation in sparse regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2782](https://github.com/GMOD/jbrowse-components/pull/2782) Fix display of + cytobands when horizontally flipped + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2678](https://github.com/GMOD/jbrowse-components/pull/2678) Preserve + double border line when using trackLabel offset and use smaller gap between + snpcoverage and reads ([@cmdcolin](https://github.com/cmdcolin)) + - [#2774](https://github.com/GMOD/jbrowse-components/pull/2774) Fix + overwriting broken symlink with --force in add-track CLI + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2773](https://github.com/GMOD/jbrowse-components/pull/2773) Fix using + global stats autoscale on wiggle tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2766](https://github.com/GMOD/jbrowse-components/pull/2766) Add a check + for empty content blocks to fix rare empty stats estimation + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2804](https://github.com/GMOD/jbrowse-components/pull/2804) Add note about additional pre-requisites to README ([@cmdcolin](https://github.com/cmdcolin)) -- [#2762](https://github.com/GMOD/jbrowse-components/pull/2762) Add bookmark widget docs to user guide ([@cmdcolin](https://github.com/cmdcolin)) +- [#2804](https://github.com/GMOD/jbrowse-components/pull/2804) Add note about + additional pre-requisites to README ([@cmdcolin](https://github.com/cmdcolin)) +- [#2762](https://github.com/GMOD/jbrowse-components/pull/2762) Add bookmark + widget docs to user guide ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#2813](https://github.com/GMOD/jbrowse-components/pull/2813) Create codeVerifierPKCE only when needed ([@garrettjstevens](https://github.com/garrettjstevens)) -- [#2808](https://github.com/GMOD/jbrowse-components/pull/2808) Polyfill window.crypto.getRandomValues in tests ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2813](https://github.com/GMOD/jbrowse-components/pull/2813) Create + codeVerifierPKCE only when needed + ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2808](https://github.com/GMOD/jbrowse-components/pull/2808) Polyfill + window.crypto.getRandomValues in tests + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 @@ -1481,36 +2414,70 @@ #### :rocket: Enhancement -- [#2736](https://github.com/GMOD/jbrowse-components/pull/2736) Add better display of error state in dotplot view and load gzipped PAF files ([@cmdcolin](https://github.com/cmdcolin)) -- [#2705](https://github.com/GMOD/jbrowse-components/pull/2705) Increase admin-server payload limit ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2736](https://github.com/GMOD/jbrowse-components/pull/2736) Add better + display of error state in dotplot view and load gzipped PAF files + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2705](https://github.com/GMOD/jbrowse-components/pull/2705) Increase + admin-server payload limit + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#2758](https://github.com/GMOD/jbrowse-components/pull/2758) Use VariantTrack for plaintext VCF type ([@cmdcolin](https://github.com/cmdcolin)) - - [#2738](https://github.com/GMOD/jbrowse-components/pull/2738) Add better catch for XS and TS tag detection from CRAM ([@cmdcolin](https://github.com/cmdcolin)) - - [#2733](https://github.com/GMOD/jbrowse-components/pull/2733) Use sparse array for alignments coverage to fix bug viewing large sparse regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2734](https://github.com/GMOD/jbrowse-components/pull/2734) Use node fetch instead of follow-redirects in cli ([@cmdcolin](https://github.com/cmdcolin)) - - [#2726](https://github.com/GMOD/jbrowse-components/pull/2726) Handle .bgz file extension for text-index ([@cmdcolin](https://github.com/cmdcolin)) - - [#2727](https://github.com/GMOD/jbrowse-components/pull/2727) Add engines 16 to @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) - - [#2723](https://github.com/GMOD/jbrowse-components/pull/2723) Make jbrowse desktop more robust to errors when reading recent sessions file ([@cmdcolin](https://github.com/cmdcolin)) - - [#2715](https://github.com/GMOD/jbrowse-components/pull/2715) Change --target to --root for jbrowse CLI admin-server ([@cmdcolin](https://github.com/cmdcolin)) + - [#2758](https://github.com/GMOD/jbrowse-components/pull/2758) Use + VariantTrack for plaintext VCF type + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2738](https://github.com/GMOD/jbrowse-components/pull/2738) Add better + catch for XS and TS tag detection from CRAM + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2733](https://github.com/GMOD/jbrowse-components/pull/2733) Use sparse + array for alignments coverage to fix bug viewing large sparse regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2734](https://github.com/GMOD/jbrowse-components/pull/2734) Use node fetch + instead of follow-redirects in cli + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2726](https://github.com/GMOD/jbrowse-components/pull/2726) Handle .bgz + file extension for text-index ([@cmdcolin](https://github.com/cmdcolin)) + - [#2727](https://github.com/GMOD/jbrowse-components/pull/2727) Add engines 16 + to @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) + - [#2723](https://github.com/GMOD/jbrowse-components/pull/2723) Make jbrowse + desktop more robust to errors when reading recent sessions file + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2715](https://github.com/GMOD/jbrowse-components/pull/2715) Change + --target to --root for jbrowse CLI admin-server + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2757](https://github.com/GMOD/jbrowse-components/pull/2757) Fix type confusion with stats estimation causing BAM files to fail byte size calculation ([@cmdcolin](https://github.com/cmdcolin)) - - [#2750](https://github.com/GMOD/jbrowse-components/pull/2750) Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox ([@cmdcolin](https://github.com/cmdcolin)) - - [#2719](https://github.com/GMOD/jbrowse-components/pull/2719) Avoid uninitialized state during stats estimation ([@cmdcolin](https://github.com/cmdcolin)) - - [#2707](https://github.com/GMOD/jbrowse-components/pull/2707) Fix ability to use authenticated assembly files ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2695](https://github.com/GMOD/jbrowse-components/pull/2695) Fix disabled state on the linear genome view track labels dropdown menu ([@cmdcolin](https://github.com/cmdcolin)) + - [#2757](https://github.com/GMOD/jbrowse-components/pull/2757) Fix type + confusion with stats estimation causing BAM files to fail byte size + calculation ([@cmdcolin](https://github.com/cmdcolin)) + - [#2750](https://github.com/GMOD/jbrowse-components/pull/2750) Add + bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in + alignments track in webkit and firefox + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2719](https://github.com/GMOD/jbrowse-components/pull/2719) Avoid + uninitialized state during stats estimation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2707](https://github.com/GMOD/jbrowse-components/pull/2707) Fix ability to + use authenticated assembly files + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2695](https://github.com/GMOD/jbrowse-components/pull/2695) Fix disabled + state on the linear genome view track labels dropdown menu + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2716](https://github.com/GMOD/jbrowse-components/pull/2716) Update to node12 requirement for @jbrowse/cli ([@cmdcolin](https://github.com/cmdcolin)) -- [#2605](https://github.com/GMOD/jbrowse-components/pull/2605) Developer guide reorganization and create new API document ([@cmdcolin](https://github.com/cmdcolin)) +- [#2716](https://github.com/GMOD/jbrowse-components/pull/2716) Update to node12 + requirement for @jbrowse/cli ([@cmdcolin](https://github.com/cmdcolin)) +- [#2605](https://github.com/GMOD/jbrowse-components/pull/2605) Developer guide + reorganization and create new API document + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2664](https://github.com/GMOD/jbrowse-components/pull/2664) Use babel config from core in root ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2664](https://github.com/GMOD/jbrowse-components/pull/2664) Use babel + config from core in root + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 @@ -1615,40 +2582,74 @@ #### :rocket: Enhancement - `core` - - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations and usability improvements to synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) - - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to display curved lines and to square the dotplot and synteny views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot plot rendering ([@cmdcolin](https://github.com/cmdcolin)) + - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations + and usability improvements to synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user + settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats + estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to + display curved lines and to square the dotplot and synteny views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot + plot rendering ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error handling on jbrowse desktop open sequence dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap PAF support ([@cmdcolin](https://github.com/cmdcolin)) - - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of deletion on reads in alignments track ([@cmdcolin](https://github.com/cmdcolin)) + - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error + handling on jbrowse desktop open sequence dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap + PAF support ([@cmdcolin](https://github.com/cmdcolin)) + - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of + deletion on reads in alignments track + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to create new sessions solely from a "session spec" in the URL ([@cmdcolin](https://github.com/cmdcolin)) + - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to + create new sessions solely from a "session spec" in the URL + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix adapterType dropdown in add track widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken @jbrowse/img by adding babel config back to core ([@cmdcolin](https://github.com/cmdcolin)) + - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix + adapterType dropdown in add track widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken + @jbrowse/img by adding babel config back to core + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use path.resolve to fix --load symlink in jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom glyphs to apply to features without subfeatures ([@bbimber](https://github.com/bbimber)) - - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" of embedded React views ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use + path.resolve to fix --load symlink in jbrowse CLI + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom + glyphs to apply to features without subfeatures + ([@bbimber](https://github.com/bbimber)) + - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" + of embedded React views + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation -- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add documentation for URL params and session spec ([@cmdcolin](https://github.com/cmdcolin)) -- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG 2022 youtube tutorial on demos page and course archive ([@cmdcolin](https://github.com/cmdcolin)) +- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add + documentation for URL params and session spec + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG + 2022 youtube tutorial on demos page and course archive + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress test of package that uses embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid console.warns in tests due to writing to MST nodes that are not alive ([@cmdcolin](https://github.com/cmdcolin)) + - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress + test of package that uses embedded components + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid + console.warns in tests due to writing to MST nodes that are not alive + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload using yarn resolution on react-error-overlay ([@cmdcolin](https://github.com/cmdcolin)) + - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload + using yarn resolution on react-error-overlay + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -1697,40 +2698,74 @@ #### :rocket: Enhancement - `core` - - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations and usability improvements to synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) - - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to display curved lines and to square the dotplot and synteny views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot plot rendering ([@cmdcolin](https://github.com/cmdcolin)) + - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations + and usability improvements to synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user + settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats + estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to + display curved lines and to square the dotplot and synteny views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot + plot rendering ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error handling on jbrowse desktop open sequence dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap PAF support ([@cmdcolin](https://github.com/cmdcolin)) - - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of deletion on reads in alignments track ([@cmdcolin](https://github.com/cmdcolin)) + - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error + handling on jbrowse desktop open sequence dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap + PAF support ([@cmdcolin](https://github.com/cmdcolin)) + - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of + deletion on reads in alignments track + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to create new sessions solely from a "session spec" in the URL ([@cmdcolin](https://github.com/cmdcolin)) + - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to + create new sessions solely from a "session spec" in the URL + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix adapterType dropdown in add track widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken @jbrowse/img by adding babel config back to core ([@cmdcolin](https://github.com/cmdcolin)) + - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix + adapterType dropdown in add track widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken + @jbrowse/img by adding babel config back to core + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use path.resolve to fix --load symlink in jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom glyphs to apply to features without subfeatures ([@bbimber](https://github.com/bbimber)) - - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" of embedded React views ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use + path.resolve to fix --load symlink in jbrowse CLI + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom + glyphs to apply to features without subfeatures + ([@bbimber](https://github.com/bbimber)) + - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" + of embedded React views + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation -- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add documentation for URL params and session spec ([@cmdcolin](https://github.com/cmdcolin)) -- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG 2022 youtube tutorial on demos page and course archive ([@cmdcolin](https://github.com/cmdcolin)) +- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add + documentation for URL params and session spec + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG + 2022 youtube tutorial on demos page and course archive + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress test of package that uses embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid console.warns in tests due to writing to MST nodes that are not alive ([@cmdcolin](https://github.com/cmdcolin)) + - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress + test of package that uses embedded components + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid + console.warns in tests due to writing to MST nodes that are not alive + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload using yarn resolution on react-error-overlay ([@cmdcolin](https://github.com/cmdcolin)) + - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload + using yarn resolution on react-error-overlay + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -1779,40 +2814,74 @@ #### :rocket: Enhancement - `core` - - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations and usability improvements to synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) - - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to display curved lines and to square the dotplot and synteny views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot plot rendering ([@cmdcolin](https://github.com/cmdcolin)) + - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations + and usability improvements to synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user + settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats + estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to + display curved lines and to square the dotplot and synteny views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot + plot rendering ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error handling on jbrowse desktop open sequence dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap PAF support ([@cmdcolin](https://github.com/cmdcolin)) - - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of deletion on reads in alignments track ([@cmdcolin](https://github.com/cmdcolin)) + - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error + handling on jbrowse desktop open sequence dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap + PAF support ([@cmdcolin](https://github.com/cmdcolin)) + - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of + deletion on reads in alignments track + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to create new sessions solely from a "session spec" in the URL ([@cmdcolin](https://github.com/cmdcolin)) + - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to + create new sessions solely from a "session spec" in the URL + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix adapterType dropdown in add track widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken @jbrowse/img by adding babel config back to core ([@cmdcolin](https://github.com/cmdcolin)) + - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix + adapterType dropdown in add track widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken + @jbrowse/img by adding babel config back to core + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use path.resolve to fix --load symlink in jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom glyphs to apply to features without subfeatures ([@bbimber](https://github.com/bbimber)) - - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" of embedded React views ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use + path.resolve to fix --load symlink in jbrowse CLI + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom + glyphs to apply to features without subfeatures + ([@bbimber](https://github.com/bbimber)) + - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" + of embedded React views + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation -- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add documentation for URL params and session spec ([@cmdcolin](https://github.com/cmdcolin)) -- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG 2022 youtube tutorial on demos page and course archive ([@cmdcolin](https://github.com/cmdcolin)) +- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add + documentation for URL params and session spec + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG + 2022 youtube tutorial on demos page and course archive + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress test of package that uses embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid console.warns in tests due to writing to MST nodes that are not alive ([@cmdcolin](https://github.com/cmdcolin)) + - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress + test of package that uses embedded components + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid + console.warns in tests due to writing to MST nodes that are not alive + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload using yarn resolution on react-error-overlay ([@cmdcolin](https://github.com/cmdcolin)) + - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload + using yarn resolution on react-error-overlay + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -1839,7 +2908,9 @@ #### :bug: Bug Fix -- [#2645](https://github.com/GMOD/jbrowse-components/pull/2645) Fix core by not using absolute runtime in babel ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2645](https://github.com/GMOD/jbrowse-components/pull/2645) Fix core by not + using absolute runtime in babel + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 1 @@ -1876,7 +2947,8 @@ #### :rocket: Enhancement -- [#2632](https://github.com/GMOD/jbrowse-components/pull/2632) Add vertical resize handle to dotplot view ([@cmdcolin](https://github.com/cmdcolin)) +- [#2632](https://github.com/GMOD/jbrowse-components/pull/2632) Add vertical + resize handle to dotplot view ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 @@ -1903,7 +2975,9 @@ #### :rocket: Enhancement - `core` - - [#2629](https://github.com/GMOD/jbrowse-components/pull/2629) Add ability to get parent feature in jexl syntax with either parent(feature) or get(feature,'parent') ([@cmdcolin](https://github.com/cmdcolin)) + - [#2629](https://github.com/GMOD/jbrowse-components/pull/2629) Add ability to + get parent feature in jexl syntax with either parent(feature) or + get(feature,'parent') ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 @@ -1968,28 +3042,44 @@ #### :rocket: Enhancement - Other - - [#2601](https://github.com/GMOD/jbrowse-components/pull/2601) Allow opening multiple sequences from the desktop start screen ([@cmdcolin](https://github.com/cmdcolin)) + - [#2601](https://github.com/GMOD/jbrowse-components/pull/2601) Allow opening + multiple sequences from the desktop start screen + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2623](https://github.com/GMOD/jbrowse-components/pull/2623) Adjust label width on base feature detail to enforce better alignment ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2623](https://github.com/GMOD/jbrowse-components/pull/2623) Adjust label + width on base feature detail to enforce better alignment + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :bug: Bug Fix - Other - - [#2612](https://github.com/GMOD/jbrowse-components/pull/2612) Fix ability to remove plugins ([@cmdcolin](https://github.com/cmdcolin)) - - [#2622](https://github.com/GMOD/jbrowse-components/pull/2622) Fix GUI color editor rgba string format ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2607](https://github.com/GMOD/jbrowse-components/pull/2607) Fix wiggle tooltip crash on non-numerical inputs ([@cmdcolin](https://github.com/cmdcolin)) + - [#2612](https://github.com/GMOD/jbrowse-components/pull/2612) Fix ability to + remove plugins ([@cmdcolin](https://github.com/cmdcolin)) + - [#2622](https://github.com/GMOD/jbrowse-components/pull/2622) Fix GUI color + editor rgba string format + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2607](https://github.com/GMOD/jbrowse-components/pull/2607) Fix wiggle + tooltip crash on non-numerical inputs + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2626](https://github.com/GMOD/jbrowse-components/pull/2626) Fix bad layout resulting in features being unable to be clicked in embedded mode ([@cmdcolin](https://github.com/cmdcolin)) + - [#2626](https://github.com/GMOD/jbrowse-components/pull/2626) Fix bad layout + resulting in features being unable to be clicked in embedded mode + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2595](https://github.com/GMOD/jbrowse-components/pull/2595) Use some newly available TypeScript types ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2576](https://github.com/GMOD/jbrowse-components/pull/2576) Use TypeScript parameter properties ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2595](https://github.com/GMOD/jbrowse-components/pull/2595) Use some newly + available TypeScript types + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2576](https://github.com/GMOD/jbrowse-components/pull/2576) Use TypeScript + parameter properties + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) @@ -2008,7 +3098,9 @@ #### :bug: Bug Fix - `development-tools` - - [#2600](https://github.com/GMOD/jbrowse-components/pull/2600) Fix broken published build of jbrowse/development-tools ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2600](https://github.com/GMOD/jbrowse-components/pull/2600) Fix broken + published build of jbrowse/development-tools + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 1 @@ -2057,55 +3149,115 @@ #### :rocket: Enhancement - Other - - [#2579](https://github.com/GMOD/jbrowse-components/pull/2579) Add help text and help dialog for the RefNameAutocomplete ([@cmdcolin](https://github.com/cmdcolin)) - - [#2553](https://github.com/GMOD/jbrowse-components/pull/2553) Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display ([@cmdcolin](https://github.com/cmdcolin)) - - [#2552](https://github.com/GMOD/jbrowse-components/pull/2552) Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill ([@cmdcolin](https://github.com/cmdcolin)) - - [#2509](https://github.com/GMOD/jbrowse-components/pull/2509) Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer ([@hextraza](https://github.com/hextraza)) - - [#2485](https://github.com/GMOD/jbrowse-components/pull/2485) Only use one button, "Go", in text search ambiguous results dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2501](https://github.com/GMOD/jbrowse-components/pull/2501) Add a tooltip to desktop session path so you can see the full path if it's cut off ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2579](https://github.com/GMOD/jbrowse-components/pull/2579) Add help text + and help dialog for the RefNameAutocomplete + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2553](https://github.com/GMOD/jbrowse-components/pull/2553) Add + sashimi-style arcs for RNA-seq type skips on SNPCoverage display + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2552](https://github.com/GMOD/jbrowse-components/pull/2552) Change border + on non-cytoband OverviewScaleBar visible region back to blue and cytoband + OverviewScaleBar to a little lighter fill + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2509](https://github.com/GMOD/jbrowse-components/pull/2509) Implement prop + interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer + ([@hextraza](https://github.com/hextraza)) + - [#2485](https://github.com/GMOD/jbrowse-components/pull/2485) Only use one + button, "Go", in text search ambiguous results dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2501](https://github.com/GMOD/jbrowse-components/pull/2501) Add a tooltip + to desktop session path so you can see the full path if it's cut off + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2580](https://github.com/GMOD/jbrowse-components/pull/2580) Make core snackbar notifications module with auto-dismissing info/success level notifications ([@cmdcolin](https://github.com/cmdcolin)) - - [#2534](https://github.com/GMOD/jbrowse-components/pull/2534) New display type for drawing arcs ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2590](https://github.com/GMOD/jbrowse-components/pull/2590) Add more exports that can be used by plugins ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2578](https://github.com/GMOD/jbrowse-components/pull/2578) Add layouts code to core re-exports ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2523](https://github.com/GMOD/jbrowse-components/pull/2523) Performance optimizations for alignments tracks, particularly those with many short reads ([@cmdcolin](https://github.com/cmdcolin)) - - [#2500](https://github.com/GMOD/jbrowse-components/pull/2500) Add RenderProps to core/pluggableElementTypes export ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2580](https://github.com/GMOD/jbrowse-components/pull/2580) Make core + snackbar notifications module with auto-dismissing info/success level + notifications ([@cmdcolin](https://github.com/cmdcolin)) + - [#2534](https://github.com/GMOD/jbrowse-components/pull/2534) New display + type for drawing arcs + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2590](https://github.com/GMOD/jbrowse-components/pull/2590) Add more + exports that can be used by plugins + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2578](https://github.com/GMOD/jbrowse-components/pull/2578) Add layouts + code to core re-exports + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2523](https://github.com/GMOD/jbrowse-components/pull/2523) Performance + optimizations for alignments tracks, particularly those with many short + reads ([@cmdcolin](https://github.com/cmdcolin)) + - [#2500](https://github.com/GMOD/jbrowse-components/pull/2500) Add + RenderProps to core/pluggableElementTypes export + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core`, `development-tools` - - [#2487](https://github.com/GMOD/jbrowse-components/pull/2487) Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2487](https://github.com/GMOD/jbrowse-components/pull/2487) Add support + for additional types of plugin formats (commonjs, esm) to allow access to + node modules on jbrowse desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#2594](https://github.com/GMOD/jbrowse-components/pull/2594) Fix infinite loop bug while searching certain strings and handle multi-word searches better ([@cmdcolin](https://github.com/cmdcolin)) - - [#2589](https://github.com/GMOD/jbrowse-components/pull/2589) Fix occasional failures observed from running text-index command ([@cmdcolin](https://github.com/cmdcolin)) - - [#2583](https://github.com/GMOD/jbrowse-components/pull/2583) Fix for alignments track base modifications display regarding skipped bases on Mm tag ([@cmdcolin](https://github.com/cmdcolin)) - - [#2556](https://github.com/GMOD/jbrowse-components/pull/2556) Fix ability to access BigWig tracks on http basic auth for some cases ([@cmdcolin](https://github.com/cmdcolin)) - - [#2577](https://github.com/GMOD/jbrowse-components/pull/2577) Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2521](https://github.com/GMOD/jbrowse-components/pull/2521) Fix ability to search for tracks with parentheses in tracklist ([@cmdcolin](https://github.com/cmdcolin)) - - [#2512](https://github.com/GMOD/jbrowse-components/pull/2512) Fix [object Window] issue in alignment read vs reference dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2499](https://github.com/GMOD/jbrowse-components/pull/2499) Add missing dependency to CLI ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2594](https://github.com/GMOD/jbrowse-components/pull/2594) Fix infinite + loop bug while searching certain strings and handle multi-word searches + better ([@cmdcolin](https://github.com/cmdcolin)) + - [#2589](https://github.com/GMOD/jbrowse-components/pull/2589) Fix occasional + failures observed from running text-index command + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2583](https://github.com/GMOD/jbrowse-components/pull/2583) Fix for + alignments track base modifications display regarding skipped bases on Mm + tag ([@cmdcolin](https://github.com/cmdcolin)) + - [#2556](https://github.com/GMOD/jbrowse-components/pull/2556) Fix ability to + access BigWig tracks on http basic auth for some cases + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2577](https://github.com/GMOD/jbrowse-components/pull/2577) Fix ability to + use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, + GTF support to add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) + - [#2521](https://github.com/GMOD/jbrowse-components/pull/2521) Fix ability to + search for tracks with parentheses in tracklist + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2512](https://github.com/GMOD/jbrowse-components/pull/2512) Fix [object + Window] issue in alignment read vs reference dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2499](https://github.com/GMOD/jbrowse-components/pull/2499) Add missing + dependency to CLI ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2585](https://github.com/GMOD/jbrowse-components/pull/2585) Fix ability to use "Color by methylation" on files that require refname renaming ([@cmdcolin](https://github.com/cmdcolin)) - - [#2517](https://github.com/GMOD/jbrowse-components/pull/2517) Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state ([@cmdcolin](https://github.com/cmdcolin)) - - [#2564](https://github.com/GMOD/jbrowse-components/pull/2564) Start looking for parents with parent, not self in findParentThat ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2563](https://github.com/GMOD/jbrowse-components/pull/2563) Restore ability to load plugins from relative URL ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2533](https://github.com/GMOD/jbrowse-components/pull/2533) Fix drawer widget minimized button being unclickable when overlapping with a view ([@cmdcolin](https://github.com/cmdcolin)) + - [#2585](https://github.com/GMOD/jbrowse-components/pull/2585) Fix ability to + use "Color by methylation" on files that require refname renaming + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2517](https://github.com/GMOD/jbrowse-components/pull/2517) Remove + aborting on adapter loading process to fix some tracks getting stuck in + infinite loading state ([@cmdcolin](https://github.com/cmdcolin)) + - [#2564](https://github.com/GMOD/jbrowse-components/pull/2564) Start looking + for parents with parent, not self in findParentThat + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2563](https://github.com/GMOD/jbrowse-components/pull/2563) Restore + ability to load plugins from relative URL + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2533](https://github.com/GMOD/jbrowse-components/pull/2533) Fix drawer + widget minimized button being unclickable when overlapping with a view + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2522](https://github.com/GMOD/jbrowse-components/pull/2522) Add circular genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) -- [#2508](https://github.com/GMOD/jbrowse-components/pull/2508) Update docs for embedded components ([@teresam856](https://github.com/teresam856)) -- [#2495](https://github.com/GMOD/jbrowse-components/pull/2495) Improve organization on docs landing page ([@cmdcolin](https://github.com/cmdcolin)) +- [#2522](https://github.com/GMOD/jbrowse-components/pull/2522) Add circular + genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) +- [#2508](https://github.com/GMOD/jbrowse-components/pull/2508) Update docs for + embedded components ([@teresam856](https://github.com/teresam856)) +- [#2495](https://github.com/GMOD/jbrowse-components/pull/2495) Improve + organization on docs landing page ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2597](https://github.com/GMOD/jbrowse-components/pull/2597) Fix flaky tests related to auth and canvas image snapshots ([@cmdcolin](https://github.com/cmdcolin)) - - [#2504](https://github.com/GMOD/jbrowse-components/pull/2504) Spreadsheet change jbrequire to es6 imports ([@cmdcolin](https://github.com/cmdcolin)) + - [#2597](https://github.com/GMOD/jbrowse-components/pull/2597) Fix flaky + tests related to auth and canvas image snapshots + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2504](https://github.com/GMOD/jbrowse-components/pull/2504) Spreadsheet + change jbrequire to es6 imports ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 6 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) @@ -2154,48 +3306,91 @@ #### :rocket: Enhancement - `core` - - [#2488](https://github.com/GMOD/jbrowse-components/pull/2488) Improve usability of the search result autocomplete when typing in via keyboard ([@cmdcolin](https://github.com/cmdcolin)) - - [#2267](https://github.com/GMOD/jbrowse-components/pull/2267) Add cytoband to overview scale bar in LGV ([@cmdcolin](https://github.com/cmdcolin)) - - [#2447](https://github.com/GMOD/jbrowse-components/pull/2447) Drawer widget tooltips and use position: fixed on fab ([@cmdcolin](https://github.com/cmdcolin)) - - [#2299](https://github.com/GMOD/jbrowse-components/pull/2299) Add new pluggable element type and properties to adapter type for registering adapter association with 'add track' workflow ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2488](https://github.com/GMOD/jbrowse-components/pull/2488) Improve + usability of the search result autocomplete when typing in via keyboard + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2267](https://github.com/GMOD/jbrowse-components/pull/2267) Add cytoband + to overview scale bar in LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2447](https://github.com/GMOD/jbrowse-components/pull/2447) Drawer widget + tooltips and use position: fixed on fab + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2299](https://github.com/GMOD/jbrowse-components/pull/2299) Add new + pluggable element type and properties to adapter type for registering + adapter association with 'add track' workflow + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Other - - [#2484](https://github.com/GMOD/jbrowse-components/pull/2484) "Add custom plugin" dialog improvements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2389](https://github.com/GMOD/jbrowse-components/pull/2389) Create plaintext GtfAdapter in plugins/gtf ([@teresam856](https://github.com/teresam856)) - - [#2443](https://github.com/GMOD/jbrowse-components/pull/2443) Support plaintext fasta on desktop by dynamically creating a FAI file on the fly ([@cmdcolin](https://github.com/cmdcolin)) - - [#2479](https://github.com/GMOD/jbrowse-components/pull/2479) Allow gzipped Gff3Adapter input and use 512MB limit ([@cmdcolin](https://github.com/cmdcolin)) - - [#2467](https://github.com/GMOD/jbrowse-components/pull/2467) Set default session dialog redesign ([@cmdcolin](https://github.com/cmdcolin)) - - [#2461](https://github.com/GMOD/jbrowse-components/pull/2461) Add assembly manager back into tools menu on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2442](https://github.com/GMOD/jbrowse-components/pull/2442) Add simple loading screen for LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2484](https://github.com/GMOD/jbrowse-components/pull/2484) "Add custom + plugin" dialog improvements ([@cmdcolin](https://github.com/cmdcolin)) + - [#2389](https://github.com/GMOD/jbrowse-components/pull/2389) Create + plaintext GtfAdapter in plugins/gtf + ([@teresam856](https://github.com/teresam856)) + - [#2443](https://github.com/GMOD/jbrowse-components/pull/2443) Support + plaintext fasta on desktop by dynamically creating a FAI file on the fly + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2479](https://github.com/GMOD/jbrowse-components/pull/2479) Allow gzipped + Gff3Adapter input and use 512MB limit + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2467](https://github.com/GMOD/jbrowse-components/pull/2467) Set default + session dialog redesign ([@cmdcolin](https://github.com/cmdcolin)) + - [#2461](https://github.com/GMOD/jbrowse-components/pull/2461) Add assembly + manager back into tools menu on jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2442](https://github.com/GMOD/jbrowse-components/pull/2442) Add simple + loading screen for LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2494](https://github.com/GMOD/jbrowse-components/pull/2494) Add polyfill for text-index compatibility with node 10 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2492](https://github.com/GMOD/jbrowse-components/pull/2492) Fix ability to open breakpoint split view from a BEDPE row in SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#2480](https://github.com/GMOD/jbrowse-components/pull/2480) Fix refName renaming on VcfAdapter for files that don't have ##contig lines ([@cmdcolin](https://github.com/cmdcolin)) - - [#2469](https://github.com/GMOD/jbrowse-components/pull/2469) Fix embedded crash when opening dialogs ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2451](https://github.com/GMOD/jbrowse-components/pull/2451) Fix issue with intermittent text-index failures and improve speed ([@cmdcolin](https://github.com/cmdcolin)) - - [#2439](https://github.com/GMOD/jbrowse-components/pull/2439) Fix adding plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2426](https://github.com/GMOD/jbrowse-components/pull/2426) Fix CLI create/upgrade failing to find the latest release ([@cmdcolin](https://github.com/cmdcolin)) + - [#2494](https://github.com/GMOD/jbrowse-components/pull/2494) Add polyfill + for text-index compatibility with node 10 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2492](https://github.com/GMOD/jbrowse-components/pull/2492) Fix ability to + open breakpoint split view from a BEDPE row in SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2480](https://github.com/GMOD/jbrowse-components/pull/2480) Fix refName + renaming on VcfAdapter for files that don't have ##contig lines + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2469](https://github.com/GMOD/jbrowse-components/pull/2469) Fix embedded + crash when opening dialogs + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2451](https://github.com/GMOD/jbrowse-components/pull/2451) Fix issue with + intermittent text-index failures and improve speed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2439](https://github.com/GMOD/jbrowse-components/pull/2439) Fix adding + plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#2426](https://github.com/GMOD/jbrowse-components/pull/2426) Fix CLI + create/upgrade failing to find the latest release + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2457](https://github.com/GMOD/jbrowse-components/pull/2457) Fix linear synteny view import form failure ([@cmdcolin](https://github.com/cmdcolin)) - - [#2444](https://github.com/GMOD/jbrowse-components/pull/2444) Fix crash when chromSizesLocation not specified when loading TwoBitAdapter in GUI ([@cmdcolin](https://github.com/cmdcolin)) + - [#2457](https://github.com/GMOD/jbrowse-components/pull/2457) Fix linear + synteny view import form failure ([@cmdcolin](https://github.com/cmdcolin)) + - [#2444](https://github.com/GMOD/jbrowse-components/pull/2444) Fix crash when + chromSizesLocation not specified when loading TwoBitAdapter in GUI + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2446](https://github.com/GMOD/jbrowse-components/pull/2446) Improve some CLI --help messages ([@cmdcolin](https://github.com/cmdcolin)) -- [#2437](https://github.com/GMOD/jbrowse-components/pull/2437) Add example of defining and using a plugin with the embedded component ([@cmdcolin](https://github.com/cmdcolin)) -- [#2430](https://github.com/GMOD/jbrowse-components/pull/2430) Website optimize for less layout shift ([@cmdcolin](https://github.com/cmdcolin)) +- [#2446](https://github.com/GMOD/jbrowse-components/pull/2446) Improve some CLI + --help messages ([@cmdcolin](https://github.com/cmdcolin)) +- [#2437](https://github.com/GMOD/jbrowse-components/pull/2437) Add example of + defining and using a plugin with the embedded component + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2430](https://github.com/GMOD/jbrowse-components/pull/2430) Website optimize + for less layout shift ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2445](https://github.com/GMOD/jbrowse-components/pull/2445) Create core snapshot error message component ([@cmdcolin](https://github.com/cmdcolin)) - - [#2288](https://github.com/GMOD/jbrowse-components/pull/2288) Add extra re-exports for default modules ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2445](https://github.com/GMOD/jbrowse-components/pull/2445) Create core + snapshot error message component ([@cmdcolin](https://github.com/cmdcolin)) + - [#2288](https://github.com/GMOD/jbrowse-components/pull/2288) Add extra + re-exports for default modules + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 4 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) @@ -2247,50 +3442,98 @@ #### :rocket: Enhancement - `core` - - [#2413](https://github.com/GMOD/jbrowse-components/pull/2413) Bundle size savings ([@cmdcolin](https://github.com/cmdcolin)) - - [#2390](https://github.com/GMOD/jbrowse-components/pull/2390) Support plain text (non-tabix'ed) GFF files with new Gff3Adapter ([@teresam856](https://github.com/teresam856)) - - [#2384](https://github.com/GMOD/jbrowse-components/pull/2384) Allow docking the drawer on the left side of the screen ([@cmdcolin](https://github.com/cmdcolin)) - - [#2387](https://github.com/GMOD/jbrowse-components/pull/2387) Add bulk delete of sessions on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2279](https://github.com/GMOD/jbrowse-components/pull/2279) Add ability to access authenticated resources using pluggable internet accounts framework ([@peterkxie](https://github.com/peterkxie)) + - [#2413](https://github.com/GMOD/jbrowse-components/pull/2413) Bundle size + savings ([@cmdcolin](https://github.com/cmdcolin)) + - [#2390](https://github.com/GMOD/jbrowse-components/pull/2390) Support plain + text (non-tabix'ed) GFF files with new Gff3Adapter + ([@teresam856](https://github.com/teresam856)) + - [#2384](https://github.com/GMOD/jbrowse-components/pull/2384) Allow docking + the drawer on the left side of the screen + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2387](https://github.com/GMOD/jbrowse-components/pull/2387) Add bulk + delete of sessions on jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2279](https://github.com/GMOD/jbrowse-components/pull/2279) Add ability to + access authenticated resources using pluggable internet accounts framework + ([@peterkxie](https://github.com/peterkxie)) - Other - - [#2388](https://github.com/GMOD/jbrowse-components/pull/2388) Create "quickstart list" on jbrowse-desktop which users can add to ([@cmdcolin](https://github.com/cmdcolin)) - - [#2385](https://github.com/GMOD/jbrowse-components/pull/2385) Ensure all dependencies are properly specified in package.json files using eslint-plugin-import ([@cmdcolin](https://github.com/cmdcolin)) - - [#2373](https://github.com/GMOD/jbrowse-components/pull/2373) Add auto update functionality for jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2369](https://github.com/GMOD/jbrowse-components/pull/2369) Add tooltip with track description to track selector ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2258](https://github.com/GMOD/jbrowse-components/pull/2258) Update admin-server to accept value from ?config= so that multiple configs could be edited ([@cmdcolin](https://github.com/cmdcolin)) - - [#2321](https://github.com/GMOD/jbrowse-components/pull/2321) Add show descriptions toggle box to most feature tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2388](https://github.com/GMOD/jbrowse-components/pull/2388) Create + "quickstart list" on jbrowse-desktop which users can add to + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2385](https://github.com/GMOD/jbrowse-components/pull/2385) Ensure all + dependencies are properly specified in package.json files using + eslint-plugin-import ([@cmdcolin](https://github.com/cmdcolin)) + - [#2373](https://github.com/GMOD/jbrowse-components/pull/2373) Add auto + update functionality for jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2369](https://github.com/GMOD/jbrowse-components/pull/2369) Add tooltip + with track description to track selector + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2258](https://github.com/GMOD/jbrowse-components/pull/2258) Update + admin-server to accept value from ?config= so that multiple configs could be + edited ([@cmdcolin](https://github.com/cmdcolin)) + - [#2321](https://github.com/GMOD/jbrowse-components/pull/2321) Add show + descriptions toggle box to most feature tracks + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2355](https://github.com/GMOD/jbrowse-components/pull/2355) Allow prefix and exact matches jb1 text search ([@cmdcolin](https://github.com/cmdcolin)) - - [#2348](https://github.com/GMOD/jbrowse-components/pull/2348) Fix ability to use JB1 backcompat text search adapter ([@teresam856](https://github.com/teresam856)) - - [#2322](https://github.com/GMOD/jbrowse-components/pull/2322) Fix install plugin workflow and error handling on desktop, update to electron 15 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2329](https://github.com/GMOD/jbrowse-components/pull/2329) Fix bugs preventing embedded circular genome view from rendering in some circumstances ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2355](https://github.com/GMOD/jbrowse-components/pull/2355) Allow prefix + and exact matches jb1 text search ([@cmdcolin](https://github.com/cmdcolin)) + - [#2348](https://github.com/GMOD/jbrowse-components/pull/2348) Fix ability to + use JB1 backcompat text search adapter + ([@teresam856](https://github.com/teresam856)) + - [#2322](https://github.com/GMOD/jbrowse-components/pull/2322) Fix install + plugin workflow and error handling on desktop, update to electron 15 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2329](https://github.com/GMOD/jbrowse-components/pull/2329) Fix bugs + preventing embedded circular genome view from rendering in some + circumstances ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2352](https://github.com/GMOD/jbrowse-components/pull/2352) Better keyboard navigations on text search autocomplete component ([@cmdcolin](https://github.com/cmdcolin)) - - [#2332](https://github.com/GMOD/jbrowse-components/pull/2332) Fix ability to use LocalFile on nodejs-based apps e.g. @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) + - [#2352](https://github.com/GMOD/jbrowse-components/pull/2352) Better + keyboard navigations on text search autocomplete component + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2332](https://github.com/GMOD/jbrowse-components/pull/2332) Fix ability to + use LocalFile on nodejs-based apps e.g. @jbrowse/img + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2407](https://github.com/GMOD/jbrowse-components/pull/2407) Update website for jbrowse-desktop release ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) -- [#2328](https://github.com/GMOD/jbrowse-components/pull/2328) Use ../ for all doc links and use trailing slash to fix links ([@cmdcolin](https://github.com/cmdcolin)) +- [#2407](https://github.com/GMOD/jbrowse-components/pull/2407) Update website + for jbrowse-desktop release + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#2328](https://github.com/GMOD/jbrowse-components/pull/2328) Use ../ for all + doc links and use trailing slash to fix links + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#2382](https://github.com/GMOD/jbrowse-components/pull/2382) Export RefNameAutocomplete and ViewModel from LinearGenomeView for downstream usage ([@hextraza](https://github.com/hextraza)) - - [#2336](https://github.com/GMOD/jbrowse-components/pull/2336) Add jbrowse-img to monorepo ([@cmdcolin](https://github.com/cmdcolin)) - - [#2324](https://github.com/GMOD/jbrowse-components/pull/2324) Remove unused wrapForRpc functionality ([@cmdcolin](https://github.com/cmdcolin)) + - [#2382](https://github.com/GMOD/jbrowse-components/pull/2382) Export + RefNameAutocomplete and ViewModel from LinearGenomeView for downstream usage + ([@hextraza](https://github.com/hextraza)) + - [#2336](https://github.com/GMOD/jbrowse-components/pull/2336) Add + jbrowse-img to monorepo ([@cmdcolin](https://github.com/cmdcolin)) + - [#2324](https://github.com/GMOD/jbrowse-components/pull/2324) Remove unused + wrapForRpc functionality ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2379](https://github.com/GMOD/jbrowse-components/pull/2379) Bump typescript to 4.4.3 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2363](https://github.com/GMOD/jbrowse-components/pull/2363) Add some typescripting of some MST models and components ([@cmdcolin](https://github.com/cmdcolin)) - - [#2351](https://github.com/GMOD/jbrowse-components/pull/2351) Use main "module" field instead of "browser" from dependency package json files electron builds ([@cmdcolin](https://github.com/cmdcolin)) - - [#2323](https://github.com/GMOD/jbrowse-components/pull/2323) Remove session related menu items from jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#2379](https://github.com/GMOD/jbrowse-components/pull/2379) Bump + typescript to 4.4.3 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2363](https://github.com/GMOD/jbrowse-components/pull/2363) Add some + typescripting of some MST models and components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2351](https://github.com/GMOD/jbrowse-components/pull/2351) Use main + "module" field instead of "browser" from dependency package json files + electron builds ([@cmdcolin](https://github.com/cmdcolin)) + - [#2323](https://github.com/GMOD/jbrowse-components/pull/2323) Remove session + related menu items from jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 6 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) @@ -2332,35 +3575,66 @@ #### :rocket: Enhancement - Other - - [#2287](https://github.com/GMOD/jbrowse-components/pull/2287) Use react-popper to reduce tooltip lag on pages with many elements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2294](https://github.com/GMOD/jbrowse-components/pull/2294) Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2272](https://github.com/GMOD/jbrowse-components/pull/2272) Auto adjust box RefNameAutocomplete width based on refName length ([@cmdcolin](https://github.com/cmdcolin)) - - [#2243](https://github.com/GMOD/jbrowse-components/pull/2243) Import bookmarks functionality for grid bookmark widget ([@cmdcolin](https://github.com/cmdcolin)) + - [#2287](https://github.com/GMOD/jbrowse-components/pull/2287) Use + react-popper to reduce tooltip lag on pages with many elements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2294](https://github.com/GMOD/jbrowse-components/pull/2294) Don't rely on + SVTYPE=BND for breakend split view options and thicker mouseover chords on + circular views ([@cmdcolin](https://github.com/cmdcolin)) + - [#2272](https://github.com/GMOD/jbrowse-components/pull/2272) Auto adjust + box RefNameAutocomplete width based on refName length + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2243](https://github.com/GMOD/jbrowse-components/pull/2243) Import + bookmarks functionality for grid bookmark widget + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2247](https://github.com/GMOD/jbrowse-components/pull/2247) New jbrowse-desktop start screen design ([@cmdcolin](https://github.com/cmdcolin)) - - [#2254](https://github.com/GMOD/jbrowse-components/pull/2254) Better error reporting from web worker and chrom sizes adapter errors ([@cmdcolin](https://github.com/cmdcolin)) - - [#1881](https://github.com/GMOD/jbrowse-components/pull/1881) Add new text searching functionality to core, with `jbrowse text-index` CLI command to generate trix index ([@teresam856](https://github.com/teresam856)) + - [#2247](https://github.com/GMOD/jbrowse-components/pull/2247) New + jbrowse-desktop start screen design + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2254](https://github.com/GMOD/jbrowse-components/pull/2254) Better error + reporting from web worker and chrom sizes adapter errors + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1881](https://github.com/GMOD/jbrowse-components/pull/1881) Add new text + searching functionality to core, with `jbrowse text-index` CLI command to + generate trix index ([@teresam856](https://github.com/teresam856)) #### :bug: Bug Fix - `core` - - [#2320](https://github.com/GMOD/jbrowse-components/pull/2320) Fix issue where add track widget doesn't infer adapters on second usage ([@cmdcolin](https://github.com/cmdcolin)) - - [#2250](https://github.com/GMOD/jbrowse-components/pull/2250) Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available ([@cmdcolin](https://github.com/cmdcolin)) + - [#2320](https://github.com/GMOD/jbrowse-components/pull/2320) Fix issue + where add track widget doesn't infer adapters on second usage + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2250](https://github.com/GMOD/jbrowse-components/pull/2250) Prevent the + ToggleButton for the FileSelector toggling to local file when only URL + should be available ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2309](https://github.com/GMOD/jbrowse-components/pull/2309) Fix mouseover selection appearing across unrelated blocks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2283](https://github.com/GMOD/jbrowse-components/pull/2283) Fix ability for the variant detail panel to create breakpoint split view for elements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2268](https://github.com/GMOD/jbrowse-components/pull/2268) Fix autocomplete height on small displays ([@cmdcolin](https://github.com/cmdcolin)) + - [#2309](https://github.com/GMOD/jbrowse-components/pull/2309) Fix mouseover + selection appearing across unrelated blocks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2283](https://github.com/GMOD/jbrowse-components/pull/2283) Fix ability + for the variant detail panel to create breakpoint split view for + elements ([@cmdcolin](https://github.com/cmdcolin)) + - [#2268](https://github.com/GMOD/jbrowse-components/pull/2268) Fix + autocomplete height on small displays + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2300](https://github.com/GMOD/jbrowse-components/pull/2300) Release announcement draft v1.4.0 ([@teresam856](https://github.com/teresam856)) -- [#2310](https://github.com/GMOD/jbrowse-components/pull/2310) Add cancer demos to the demos page on website ([@cmdcolin](https://github.com/cmdcolin)) -- [#2253](https://github.com/GMOD/jbrowse-components/pull/2253) Add note about legacy-peer-deps to embedded component readme ([@cmdcolin](https://github.com/cmdcolin)) -- [#2262](https://github.com/GMOD/jbrowse-components/pull/2262) Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks ([@cmdcolin](https://github.com/cmdcolin)) +- [#2300](https://github.com/GMOD/jbrowse-components/pull/2300) Release + announcement draft v1.4.0 ([@teresam856](https://github.com/teresam856)) +- [#2310](https://github.com/GMOD/jbrowse-components/pull/2310) Add cancer demos + to the demos page on website ([@cmdcolin](https://github.com/cmdcolin)) +- [#2253](https://github.com/GMOD/jbrowse-components/pull/2253) Add note about + legacy-peer-deps to embedded component readme + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2262](https://github.com/GMOD/jbrowse-components/pull/2262) Add more MDX + documentation pages to @jbrowse/react-linear-genome-view storybooks + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#2263](https://github.com/GMOD/jbrowse-components/pull/2263) Force publish all packages on release ([@cmdcolin](https://github.com/cmdcolin)) +- [#2263](https://github.com/GMOD/jbrowse-components/pull/2263) Force publish + all packages on release ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -2432,47 +3706,89 @@ Broken releases missing some packages #### :rocket: Enhancement - Other - - [#2163](https://github.com/GMOD/jbrowse-components/pull/2163) Add new embeddable React Circular Genome View ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2229](https://github.com/GMOD/jbrowse-components/pull/2229) Use extendPluggableElement for context menu items ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2233](https://github.com/GMOD/jbrowse-components/pull/2233) Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs ([@cmdcolin](https://github.com/cmdcolin)) - - [#2199](https://github.com/GMOD/jbrowse-components/pull/2199) Make the BED parser not interpret general tab delimited data as BED12 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2241](https://github.com/GMOD/jbrowse-components/pull/2241) Restore previous window location when re-opening on desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2203](https://github.com/GMOD/jbrowse-components/pull/2203) Add a helpful message if there is a 404 on config.json error ([@cmdcolin](https://github.com/cmdcolin)) - - [#2204](https://github.com/GMOD/jbrowse-components/pull/2204) Hide reads with unmapped flag by default in alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2198](https://github.com/GMOD/jbrowse-components/pull/2198) Add better inversion visualization to read vs reference visualizations ([@cmdcolin](https://github.com/cmdcolin)) - - [#2154](https://github.com/GMOD/jbrowse-components/pull/2154) Add UMD build of react-linear-genome-view for plain-js use ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2163](https://github.com/GMOD/jbrowse-components/pull/2163) Add new + embeddable React Circular Genome View + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2229](https://github.com/GMOD/jbrowse-components/pull/2229) Use + extendPluggableElement for context menu items + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2233](https://github.com/GMOD/jbrowse-components/pull/2233) Add optional + chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files + with many refseqs ([@cmdcolin](https://github.com/cmdcolin)) + - [#2199](https://github.com/GMOD/jbrowse-components/pull/2199) Make the BED + parser not interpret general tab delimited data as BED12 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2241](https://github.com/GMOD/jbrowse-components/pull/2241) Restore + previous window location when re-opening on desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2203](https://github.com/GMOD/jbrowse-components/pull/2203) Add a helpful + message if there is a 404 on config.json error + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2204](https://github.com/GMOD/jbrowse-components/pull/2204) Hide reads + with unmapped flag by default in alignments tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2198](https://github.com/GMOD/jbrowse-components/pull/2198) Add better + inversion visualization to read vs reference visualizations + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2154](https://github.com/GMOD/jbrowse-components/pull/2154) Add UMD build + of react-linear-genome-view for plain-js use + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2236](https://github.com/GMOD/jbrowse-components/pull/2236) Detect assembly loading error and encapsulate error instead of failing at app level ([@cmdcolin](https://github.com/cmdcolin)) - - [#2029](https://github.com/GMOD/jbrowse-components/pull/2029) Polish desktop builds ([@elliothershberg](https://github.com/elliothershberg)) - - [#2140](https://github.com/GMOD/jbrowse-components/pull/2140) New core plugin that adds a "bookmarked regions" list widget, new extension points system ([@elliothershberg](https://github.com/elliothershberg)) + - [#2236](https://github.com/GMOD/jbrowse-components/pull/2236) Detect + assembly loading error and encapsulate error instead of failing at app level + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2029](https://github.com/GMOD/jbrowse-components/pull/2029) Polish desktop + builds ([@elliothershberg](https://github.com/elliothershberg)) + - [#2140](https://github.com/GMOD/jbrowse-components/pull/2140) New core + plugin that adds a "bookmarked regions" list widget, new extension points + system ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - - [#2245](https://github.com/GMOD/jbrowse-components/pull/2245) Fix missing regenerator runtime dependency in core ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2202](https://github.com/GMOD/jbrowse-components/pull/2202) Fixed a crash when an incompatible adapter is selected for provided data in 'open track' ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2197](https://github.com/GMOD/jbrowse-components/pull/2197) Fix handle leak for killed worker checker ([@cmdcolin](https://github.com/cmdcolin)) + - [#2245](https://github.com/GMOD/jbrowse-components/pull/2245) Fix missing + regenerator runtime dependency in core + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2202](https://github.com/GMOD/jbrowse-components/pull/2202) Fixed a crash + when an incompatible adapter is selected for provided data in 'open track' + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2197](https://github.com/GMOD/jbrowse-components/pull/2197) Fix handle + leak for killed worker checker ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2208](https://github.com/GMOD/jbrowse-components/pull/2208) Fix issue where collapsed categories were not remembered after toggling a track ([@cmdcolin](https://github.com/cmdcolin)) + - [#2208](https://github.com/GMOD/jbrowse-components/pull/2208) Fix issue + where collapsed categories were not remembered after toggling a track + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2192](https://github.com/GMOD/jbrowse-components/pull/2192) Update Linear Genome View embedding docs ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2192](https://github.com/GMOD/jbrowse-components/pull/2192) Update Linear + Genome View embedding docs + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - `core` - - [#2057](https://github.com/GMOD/jbrowse-components/pull/2057) Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance ([@cmdcolin](https://github.com/cmdcolin)) - - [#2231](https://github.com/GMOD/jbrowse-components/pull/2231) Export offscreenCanvasUtils ([@cmdcolin](https://github.com/cmdcolin)) - - [#2226](https://github.com/GMOD/jbrowse-components/pull/2226) Use superRenderProps and superTrackMenuItems for better simulated inheritance model ([@cmdcolin](https://github.com/cmdcolin)) - - [#1874](https://github.com/GMOD/jbrowse-components/pull/1874) Add aborting to CoreGetFeatures rpcManager call ([@cmdcolin](https://github.com/cmdcolin)) + - [#2057](https://github.com/GMOD/jbrowse-components/pull/2057) Use idMaker + for dataAdapterCache key for faster FromConfigAdapter performance + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2231](https://github.com/GMOD/jbrowse-components/pull/2231) Export + offscreenCanvasUtils ([@cmdcolin](https://github.com/cmdcolin)) + - [#2226](https://github.com/GMOD/jbrowse-components/pull/2226) Use + superRenderProps and superTrackMenuItems for better simulated inheritance + model ([@cmdcolin](https://github.com/cmdcolin)) + - [#1874](https://github.com/GMOD/jbrowse-components/pull/1874) Add aborting + to CoreGetFeatures rpcManager call + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2232](https://github.com/GMOD/jbrowse-components/pull/2232) Remove filtering display type from core ([@cmdcolin](https://github.com/cmdcolin)) - - [#2234](https://github.com/GMOD/jbrowse-components/pull/2234) Add rootModel setError on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#2232](https://github.com/GMOD/jbrowse-components/pull/2232) Remove + filtering display type from core ([@cmdcolin](https://github.com/cmdcolin)) + - [#2234](https://github.com/GMOD/jbrowse-components/pull/2234) Add rootModel + setError on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) @@ -2517,30 +3833,53 @@ Broken releases missing some packages #### :rocket: Enhancement - Other - - [#2127](https://github.com/GMOD/jbrowse-components/pull/2127) Add example dataset for COLO829 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2127](https://github.com/GMOD/jbrowse-components/pull/2127) Add example + dataset for COLO829 ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2141](https://github.com/GMOD/jbrowse-components/pull/2141) Update to @material-ui/core@4.12.2 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2126](https://github.com/GMOD/jbrowse-components/pull/2126) Allow opening plaintext .vcf files from the "Add track" workflow ([@cmdcolin](https://github.com/cmdcolin)) + - [#2141](https://github.com/GMOD/jbrowse-components/pull/2141) Update to + @material-ui/core@4.12.2 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2126](https://github.com/GMOD/jbrowse-components/pull/2126) Allow opening + plaintext .vcf files from the "Add track" workflow + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2159](https://github.com/GMOD/jbrowse-components/pull/2159) Stop local storage quota-exceeded errors preventing the app from starting ([@cmdcolin](https://github.com/cmdcolin)) - - [#2161](https://github.com/GMOD/jbrowse-components/pull/2161) Remove outline from clicking on SVG chord tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2157](https://github.com/GMOD/jbrowse-components/pull/2157) Fix rendering of negative strand alignment modifications/methylation ([@cmdcolin](https://github.com/cmdcolin)) - - [#2131](https://github.com/GMOD/jbrowse-components/pull/2131) Fix mouseovers/click handlers after "force load" button pressed ([@cmdcolin](https://github.com/cmdcolin)) - - [#2128](https://github.com/GMOD/jbrowse-components/pull/2128) Fix using the "Color by modifications" setting on files that need ref renaming ([@cmdcolin](https://github.com/cmdcolin)) - - [#2115](https://github.com/GMOD/jbrowse-components/pull/2115) Fix bug where sometimes plugin could not be removed from UI ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2119](https://github.com/GMOD/jbrowse-components/pull/2119) Fix loading indicator on the reference sequence selector getting stuck ([@cmdcolin](https://github.com/cmdcolin)) + - [#2159](https://github.com/GMOD/jbrowse-components/pull/2159) Stop local + storage quota-exceeded errors preventing the app from starting + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2161](https://github.com/GMOD/jbrowse-components/pull/2161) Remove outline + from clicking on SVG chord tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2157](https://github.com/GMOD/jbrowse-components/pull/2157) Fix rendering + of negative strand alignment modifications/methylation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2131](https://github.com/GMOD/jbrowse-components/pull/2131) Fix + mouseovers/click handlers after "force load" button pressed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2128](https://github.com/GMOD/jbrowse-components/pull/2128) Fix using the + "Color by modifications" setting on files that need ref renaming + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2115](https://github.com/GMOD/jbrowse-components/pull/2115) Fix bug where + sometimes plugin could not be removed from UI + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2119](https://github.com/GMOD/jbrowse-components/pull/2119) Fix loading + indicator on the reference sequence selector getting stuck + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2101](https://github.com/GMOD/jbrowse-components/pull/2101) Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item ([@teresam856](https://github.com/teresam856)) + - [#2101](https://github.com/GMOD/jbrowse-components/pull/2101) Fix behavior + of the end-of-list indicator in refNameAutocomplete to always display as a + disabled item ([@teresam856](https://github.com/teresam856)) #### :house: Internal - Other - - [#2152](https://github.com/GMOD/jbrowse-components/pull/2152) Remove storybook symlink workaround ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2152](https://github.com/GMOD/jbrowse-components/pull/2152) Remove + storybook symlink workaround + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2099](https://github.com/GMOD/jbrowse-components/pull/2099) Use rbush data structure for layout of feature tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2099](https://github.com/GMOD/jbrowse-components/pull/2099) Use rbush data + structure for layout of feature tracks + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -2571,14 +3910,22 @@ Broken releases missing some packages #### :rocket: Enhancement - Other - - [#2100](https://github.com/GMOD/jbrowse-components/pull/2100) Improve descriptions on VCF SVs ([@cmdcolin](https://github.com/cmdcolin)) + - [#2100](https://github.com/GMOD/jbrowse-components/pull/2100) Improve + descriptions on VCF SVs ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2106](https://github.com/GMOD/jbrowse-components/pull/2106) Use more accurate estimator for feature label widths ([@cmdcolin](https://github.com/cmdcolin)) + - [#2106](https://github.com/GMOD/jbrowse-components/pull/2106) Use more + accurate estimator for feature label widths + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#2109](https://github.com/GMOD/jbrowse-components/pull/2109) Make sure to wait for assembly to load before downloading canonical refnames in SV inspector ([@cmdcolin](https://github.com/cmdcolin)) -- [#2111](https://github.com/GMOD/jbrowse-components/pull/2111) Fix "Can't resolve '@jbrowse/plugin-legacy-jbrowse'" in `@jbrowse/react-linear-genome-view` ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2109](https://github.com/GMOD/jbrowse-components/pull/2109) Make sure to + wait for assembly to load before downloading canonical refnames in SV + inspector ([@cmdcolin](https://github.com/cmdcolin)) +- [#2111](https://github.com/GMOD/jbrowse-components/pull/2111) Fix "Can't + resolve '@jbrowse/plugin-legacy-jbrowse'" in + `@jbrowse/react-linear-genome-view` + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 @@ -2624,45 +3971,91 @@ Broken releases missing some packages #### :rocket: Enhancement - `core` - - [#2094](https://github.com/GMOD/jbrowse-components/pull/2094) More usage of typography to improve consistent text styling ([@cmdcolin](https://github.com/cmdcolin)) - - [#2068](https://github.com/GMOD/jbrowse-components/pull/2068) Add non-indexed and plaintext VCF Adapter to variants plugin ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2067](https://github.com/GMOD/jbrowse-components/pull/2067) Better error message if a file location has an empty string ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2064](https://github.com/GMOD/jbrowse-components/pull/2064) Export offscreenCanvasPonyfil from core/util ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2060](https://github.com/GMOD/jbrowse-components/pull/2060) Improve performance with large numbers of reference sequences by using MST volatiles ([@cmdcolin](https://github.com/cmdcolin)) - - [#2050](https://github.com/GMOD/jbrowse-components/pull/2050) Configurable app logo for web ([@elliothershberg](https://github.com/elliothershberg)) + - [#2094](https://github.com/GMOD/jbrowse-components/pull/2094) More usage of + typography to improve consistent text styling + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2068](https://github.com/GMOD/jbrowse-components/pull/2068) Add + non-indexed and plaintext VCF Adapter to variants plugin + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2067](https://github.com/GMOD/jbrowse-components/pull/2067) Better error + message if a file location has an empty string + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2064](https://github.com/GMOD/jbrowse-components/pull/2064) Export + offscreenCanvasPonyfil from core/util + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2060](https://github.com/GMOD/jbrowse-components/pull/2060) Improve + performance with large numbers of reference sequences by using MST volatiles + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2050](https://github.com/GMOD/jbrowse-components/pull/2050) Configurable + app logo for web ([@elliothershberg](https://github.com/elliothershberg)) - Other - - [#2104](https://github.com/GMOD/jbrowse-components/pull/2104) Use ScopedCssBaseline to help style the embedded component ([@cmdcolin](https://github.com/cmdcolin)) - - [#2015](https://github.com/GMOD/jbrowse-components/pull/2015) Deprecate ThemeProvider in `@jbrowse/react-linear-genome-view` ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2104](https://github.com/GMOD/jbrowse-components/pull/2104) Use + ScopedCssBaseline to help style the embedded component + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2015](https://github.com/GMOD/jbrowse-components/pull/2015) Deprecate + ThemeProvider in `@jbrowse/react-linear-genome-view` + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#2097](https://github.com/GMOD/jbrowse-components/pull/2097) Improve speed for laying out features for embedded/mainthreadrpc scenarios ([@cmdcolin](https://github.com/cmdcolin)) - - [#2096](https://github.com/GMOD/jbrowse-components/pull/2096) Fix issue with page reload after editing session title ([@cmdcolin](https://github.com/cmdcolin)) - - [#2074](https://github.com/GMOD/jbrowse-components/pull/2074) Fix support for opening local files in spreadsheet/SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#2061](https://github.com/GMOD/jbrowse-components/pull/2061) Fix issue with using --force error when no track was previously loaded ([@cmdcolin](https://github.com/cmdcolin)) - - [#2024](https://github.com/GMOD/jbrowse-components/pull/2024) Flip drawing of negative strand PAF features in linear synteny and dotplot views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2023](https://github.com/GMOD/jbrowse-components/pull/2023) Fix infinite loop in adding some plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2019](https://github.com/GMOD/jbrowse-components/pull/2019) Fix session import to use blob map for opening local files ([@cmdcolin](https://github.com/cmdcolin)) + - [#2097](https://github.com/GMOD/jbrowse-components/pull/2097) Improve speed + for laying out features for embedded/mainthreadrpc scenarios + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2096](https://github.com/GMOD/jbrowse-components/pull/2096) Fix issue with + page reload after editing session title + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2074](https://github.com/GMOD/jbrowse-components/pull/2074) Fix support + for opening local files in spreadsheet/SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2061](https://github.com/GMOD/jbrowse-components/pull/2061) Fix issue with + using --force error when no track was previously loaded + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2024](https://github.com/GMOD/jbrowse-components/pull/2024) Flip drawing + of negative strand PAF features in linear synteny and dotplot views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2023](https://github.com/GMOD/jbrowse-components/pull/2023) Fix infinite + loop in adding some plugins on desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2019](https://github.com/GMOD/jbrowse-components/pull/2019) Fix session + import to use blob map for opening local files + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2071](https://github.com/GMOD/jbrowse-components/pull/2071) Add indicator to the end of ref name dropdown to suggest user to type the searchbox for more ([@teresam856](https://github.com/teresam856)) - - [#2056](https://github.com/GMOD/jbrowse-components/pull/2056) Fix infinite recursion in FromConfigAdaptor by avoiding mutating the passed in data when using SimpleFeature ([@cmdcolin](https://github.com/cmdcolin)) - - [#2018](https://github.com/GMOD/jbrowse-components/pull/2018) Fix 3'UTR in sequence detail panels when no UTRs are in gff ([@cmdcolin](https://github.com/cmdcolin)) + - [#2071](https://github.com/GMOD/jbrowse-components/pull/2071) Add indicator + to the end of ref name dropdown to suggest user to type the searchbox for + more ([@teresam856](https://github.com/teresam856)) + - [#2056](https://github.com/GMOD/jbrowse-components/pull/2056) Fix infinite + recursion in FromConfigAdaptor by avoiding mutating the passed in data when + using SimpleFeature ([@cmdcolin](https://github.com/cmdcolin)) + - [#2018](https://github.com/GMOD/jbrowse-components/pull/2018) Fix 3'UTR in + sequence detail panels when no UTRs are in gff + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#1967](https://github.com/GMOD/jbrowse-components/pull/1967) Omit configurationSchema snapshot when it matches the default ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2078](https://github.com/GMOD/jbrowse-components/pull/2078) Restore eslint rule for no-unused-vars ([@cmdcolin](https://github.com/cmdcolin)) - - [#2051](https://github.com/GMOD/jbrowse-components/pull/2051) Add missing named exports to shared core modules ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2045](https://github.com/GMOD/jbrowse-components/pull/2045) Add basic architecture for text searching ([@teresam856](https://github.com/teresam856)) + - [#1967](https://github.com/GMOD/jbrowse-components/pull/1967) Omit + configurationSchema snapshot when it matches the default + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2078](https://github.com/GMOD/jbrowse-components/pull/2078) Restore eslint + rule for no-unused-vars ([@cmdcolin](https://github.com/cmdcolin)) + - [#2051](https://github.com/GMOD/jbrowse-components/pull/2051) Add missing + named exports to shared core modules + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2045](https://github.com/GMOD/jbrowse-components/pull/2045) Add basic + architecture for text searching + ([@teresam856](https://github.com/teresam856)) - Other - - [#2070](https://github.com/GMOD/jbrowse-components/pull/2070) Remove service worker from jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - - [#1995](https://github.com/GMOD/jbrowse-components/pull/1995) Pass initialDisplay snapshot via separate param to showTrack ([@cmdcolin](https://github.com/cmdcolin)) + - [#2070](https://github.com/GMOD/jbrowse-components/pull/2070) Remove service + worker from jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) + - [#1995](https://github.com/GMOD/jbrowse-components/pull/1995) Pass + initialDisplay snapshot via separate param to showTrack + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 5 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) @@ -2711,42 +4104,83 @@ Broken releases missing some packages #### :rocket: Enhancement - Other - - [#2001](https://github.com/GMOD/jbrowse-components/pull/2001) Make tracks added using the add track widget a session track if not in adminMode ([@cmdcolin](https://github.com/cmdcolin)) - - [#1980](https://github.com/GMOD/jbrowse-components/pull/1980) Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist ([@cmdcolin](https://github.com/cmdcolin)) - - [#1977](https://github.com/GMOD/jbrowse-components/pull/1977) Upgrade @material-ui/data-grid ([@cmdcolin](https://github.com/cmdcolin)) + - [#2001](https://github.com/GMOD/jbrowse-components/pull/2001) Make tracks + added using the add track widget a session track if not in adminMode + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1980](https://github.com/GMOD/jbrowse-components/pull/1980) Add popup + confirmation dialog for unknown session plugins, and use plugins.json as a + whitelist ([@cmdcolin](https://github.com/cmdcolin)) + - [#1977](https://github.com/GMOD/jbrowse-components/pull/1977) Upgrade + @material-ui/data-grid ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#1982](https://github.com/GMOD/jbrowse-components/pull/1982) Allow manually specifying adapter type if filename does not match expected pattern ([@cmdcolin](https://github.com/cmdcolin)) - - [#1975](https://github.com/GMOD/jbrowse-components/pull/1975) Allow local files on the users computer to be opened as tracks in jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - - [#1865](https://github.com/GMOD/jbrowse-components/pull/1865) Show modified bases using MM and MP/ML tags in BAM/CRAM ([@cmdcolin](https://github.com/cmdcolin)) - - [#1984](https://github.com/GMOD/jbrowse-components/pull/1984) Better feature details when there are short arrays of json supplied as feature data ([@cmdcolin](https://github.com/cmdcolin)) - - [#1931](https://github.com/GMOD/jbrowse-components/pull/1931) Create in app graphical plugin store ([@elliothershberg](https://github.com/elliothershberg)) + - [#1982](https://github.com/GMOD/jbrowse-components/pull/1982) Allow manually + specifying adapter type if filename does not match expected pattern + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1975](https://github.com/GMOD/jbrowse-components/pull/1975) Allow local + files on the users computer to be opened as tracks in jbrowse-web + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1865](https://github.com/GMOD/jbrowse-components/pull/1865) Show modified + bases using MM and MP/ML tags in BAM/CRAM + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1984](https://github.com/GMOD/jbrowse-components/pull/1984) Better feature + details when there are short arrays of json supplied as feature data + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1931](https://github.com/GMOD/jbrowse-components/pull/1931) Create in app + graphical plugin store + ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - - [#1985](https://github.com/GMOD/jbrowse-components/pull/1985) Avoid error calculating UTR on features that have no exon subfeatures ([@cmdcolin](https://github.com/cmdcolin)) - - [#1954](https://github.com/GMOD/jbrowse-components/pull/1954) Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering ([@cmdcolin](https://github.com/cmdcolin)) - - [#1963](https://github.com/GMOD/jbrowse-components/pull/1963) Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#1945](https://github.com/GMOD/jbrowse-components/pull/1945) Fix hic not being able to render due to incorrect lazy loading ([@cmdcolin](https://github.com/cmdcolin)) + - [#1985](https://github.com/GMOD/jbrowse-components/pull/1985) Avoid error + calculating UTR on features that have no exon subfeatures + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1954](https://github.com/GMOD/jbrowse-components/pull/1954) Add more + environments to configSchema create calls to fix ability to use custom jexl + commands with main thread rendering + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1963](https://github.com/GMOD/jbrowse-components/pull/1963) Fix ability to + use DialogComponent (used for svg export, pileup sort, etc) on embedded + components ([@cmdcolin](https://github.com/cmdcolin)) + - [#1945](https://github.com/GMOD/jbrowse-components/pull/1945) Fix hic not + being able to render due to incorrect lazy loading + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1956](https://github.com/GMOD/jbrowse-components/pull/1956) Fix connection behavior ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1966](https://github.com/GMOD/jbrowse-components/pull/1966) Fix ability to use add-track force on symlink tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1951](https://github.com/GMOD/jbrowse-components/pull/1951) Fix breakpoint split view demo configuration on website ([@cmdcolin](https://github.com/cmdcolin)) + - [#1956](https://github.com/GMOD/jbrowse-components/pull/1956) Fix connection + behavior ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1966](https://github.com/GMOD/jbrowse-components/pull/1966) Fix ability to + use add-track force on symlink tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1951](https://github.com/GMOD/jbrowse-components/pull/1951) Fix breakpoint + split view demo configuration on website + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2002](https://github.com/GMOD/jbrowse-components/pull/2002) Add @jbrowse/img to homepage ([@cmdcolin](https://github.com/cmdcolin)) -- [#2007](https://github.com/GMOD/jbrowse-components/pull/2007) Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details ([@cmdcolin](https://github.com/cmdcolin)) -- [#1976](https://github.com/GMOD/jbrowse-components/pull/1976) reorganize the demo page to emphasize the cancer sv demo more ([@rbuels](https://github.com/rbuels)) -- [#1952](https://github.com/GMOD/jbrowse-components/pull/1952) Add demo for 1000 genomes extended trio dataset to website ([@cmdcolin](https://github.com/cmdcolin)) -- [#1862](https://github.com/GMOD/jbrowse-components/pull/1862) Add example for using a build-time included plugin to storybook ([@cmdcolin](https://github.com/cmdcolin)) +- [#2002](https://github.com/GMOD/jbrowse-components/pull/2002) Add @jbrowse/img + to homepage ([@cmdcolin](https://github.com/cmdcolin)) +- [#2007](https://github.com/GMOD/jbrowse-components/pull/2007) Update docs for + modifications/methylation coloring, plugin store, and the sequence panel in + feature details ([@cmdcolin](https://github.com/cmdcolin)) +- [#1976](https://github.com/GMOD/jbrowse-components/pull/1976) reorganize the + demo page to emphasize the cancer sv demo more + ([@rbuels](https://github.com/rbuels)) +- [#1952](https://github.com/GMOD/jbrowse-components/pull/1952) Add demo for + 1000 genomes extended trio dataset to website + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1862](https://github.com/GMOD/jbrowse-components/pull/1862) Add example for + using a build-time included plugin to storybook + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#2003](https://github.com/GMOD/jbrowse-components/pull/2003) Make SNPCoverage independently generate the modifications tag-color mapping ([@cmdcolin](https://github.com/cmdcolin)) + - [#2003](https://github.com/GMOD/jbrowse-components/pull/2003) Make + SNPCoverage independently generate the modifications tag-color mapping + ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `development-tools` - - [#1930](https://github.com/GMOD/jbrowse-components/pull/1930) Upgrade react scripts+react to latest versions ([@cmdcolin](https://github.com/cmdcolin)) + - [#1930](https://github.com/GMOD/jbrowse-components/pull/1930) Upgrade react + scripts+react to latest versions ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 @@ -2798,53 +4232,116 @@ Broken releases missing some packages #### :rocket: Enhancement - `core` - - [#1125](https://github.com/GMOD/jbrowse-components/pull/1125) Export SVG ([@cmdcolin](https://github.com/cmdcolin)) - - [#1867](https://github.com/GMOD/jbrowse-components/pull/1867) Virtualized tree for tracklist to support having thousands of tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1660](https://github.com/GMOD/jbrowse-components/pull/1660) Allow connections to have multiple assemblies ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1864](https://github.com/GMOD/jbrowse-components/pull/1864) Add Material UI's DataGrid to re-exports ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1875](https://github.com/GMOD/jbrowse-components/pull/1875) Make drawer widget titles stay visible when scrolling inside the widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#1877](https://github.com/GMOD/jbrowse-components/pull/1877) Add ability to copy the text produced by the feature details sequence panel to MS Word/Google Docs and preserve styling ([@cmdcolin](https://github.com/cmdcolin)) - - [#1854](https://github.com/GMOD/jbrowse-components/pull/1854) Make "About track" dialog available from tracklist and for non-LGV tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1853](https://github.com/GMOD/jbrowse-components/pull/1853) Add mouseovers in feature details that show field descriptions for VCF fields ([@cmdcolin](https://github.com/cmdcolin)) + - [#1125](https://github.com/GMOD/jbrowse-components/pull/1125) Export SVG + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1867](https://github.com/GMOD/jbrowse-components/pull/1867) Virtualized + tree for tracklist to support having thousands of tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1660](https://github.com/GMOD/jbrowse-components/pull/1660) Allow + connections to have multiple assemblies + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1864](https://github.com/GMOD/jbrowse-components/pull/1864) Add Material + UI's DataGrid to re-exports + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1875](https://github.com/GMOD/jbrowse-components/pull/1875) Make drawer + widget titles stay visible when scrolling inside the widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1877](https://github.com/GMOD/jbrowse-components/pull/1877) Add ability to + copy the text produced by the feature details sequence panel to MS + Word/Google Docs and preserve styling + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1854](https://github.com/GMOD/jbrowse-components/pull/1854) Make "About + track" dialog available from tracklist and for non-LGV tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1853](https://github.com/GMOD/jbrowse-components/pull/1853) Add mouseovers + in feature details that show field descriptions for VCF fields + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1892](https://github.com/GMOD/jbrowse-components/pull/1892) Create new JB2 plugin store ([@elliothershberg](https://github.com/elliothershberg)) - - [#1901](https://github.com/GMOD/jbrowse-components/pull/1901) Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink ([@cmdcolin](https://github.com/cmdcolin)) - - [#1850](https://github.com/GMOD/jbrowse-components/pull/1850) Add true breakend ALT strings to the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete to set-default-session, fix --session ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1861](https://github.com/GMOD/jbrowse-components/pull/1861) Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict ([@cmdcolin](https://github.com/cmdcolin)) + - [#1892](https://github.com/GMOD/jbrowse-components/pull/1892) Create new JB2 + plugin store ([@elliothershberg](https://github.com/elliothershberg)) + - [#1901](https://github.com/GMOD/jbrowse-components/pull/1901) Make using + --out for add-assembly create output directory if it does not exist and fix + outputting to symlink ([@cmdcolin](https://github.com/cmdcolin)) + - [#1850](https://github.com/GMOD/jbrowse-components/pull/1850) Add true + breakend ALT strings to the feature details panel + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete + to set-default-session, fix --session + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1861](https://github.com/GMOD/jbrowse-components/pull/1861) Change + Alignments track "Fade mismatches by quality" setting to a separate config + param and made it less strict ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#1924](https://github.com/GMOD/jbrowse-components/pull/1924) Fix import of BED and navToLocString from spreadsheet views ([@cmdcolin](https://github.com/cmdcolin)) - - [#1918](https://github.com/GMOD/jbrowse-components/pull/1918) Fix issue with some falsy values being hidden in feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1911](https://github.com/GMOD/jbrowse-components/pull/1911) Fix breakpoint split view visualizations for files that need ref renaming (e.g. chr1 vs 1) ([@cmdcolin](https://github.com/cmdcolin)) - - [#1904](https://github.com/GMOD/jbrowse-components/pull/1904) Fix issue with synteny polygons displaying slightly offset ([@cmdcolin](https://github.com/cmdcolin)) - - [#1884](https://github.com/GMOD/jbrowse-components/pull/1884) Fix rIC ponyfill for use on Safari ([@cmdcolin](https://github.com/cmdcolin)) + - [#1924](https://github.com/GMOD/jbrowse-components/pull/1924) Fix import of + BED and navToLocString from spreadsheet views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1918](https://github.com/GMOD/jbrowse-components/pull/1918) Fix issue with + some falsy values being hidden in feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1911](https://github.com/GMOD/jbrowse-components/pull/1911) Fix breakpoint + split view visualizations for files that need ref renaming (e.g. chr1 vs 1) + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1904](https://github.com/GMOD/jbrowse-components/pull/1904) Fix issue with + synteny polygons displaying slightly offset + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1884](https://github.com/GMOD/jbrowse-components/pull/1884) Fix rIC + ponyfill for use on Safari ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1912](https://github.com/GMOD/jbrowse-components/pull/1912) Fix reloading of local sessions when using React.StrictMode ([@cmdcolin](https://github.com/cmdcolin)) - - [#1900](https://github.com/GMOD/jbrowse-components/pull/1900) Make clicking away from autocomplete popup on track container work ([@cmdcolin](https://github.com/cmdcolin)) - - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete to set-default-session, fix --session ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1871](https://github.com/GMOD/jbrowse-components/pull/1871) Fix crash on dotplot/linear synteny import form and when closing linear synteny track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1860](https://github.com/GMOD/jbrowse-components/pull/1860) Fix alignments read filter jexl syntax ([@cmdcolin](https://github.com/cmdcolin)) + - [#1912](https://github.com/GMOD/jbrowse-components/pull/1912) Fix reloading + of local sessions when using React.StrictMode + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1900](https://github.com/GMOD/jbrowse-components/pull/1900) Make clicking + away from autocomplete popup on track container work + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete + to set-default-session, fix --session + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1871](https://github.com/GMOD/jbrowse-components/pull/1871) Fix crash on + dotplot/linear synteny import form and when closing linear synteny track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1860](https://github.com/GMOD/jbrowse-components/pull/1860) Fix alignments + read filter jexl syntax ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1914](https://github.com/GMOD/jbrowse-components/pull/1914) Use MDX to add proper image captions in web and pdf documentation ([@cmdcolin](https://github.com/cmdcolin)) -- [#1855](https://github.com/GMOD/jbrowse-components/pull/1855) Add download page in website header and new super-quick-start guide ([@cmdcolin](https://github.com/cmdcolin)) +- [#1914](https://github.com/GMOD/jbrowse-components/pull/1914) Use MDX to add + proper image captions in web and pdf documentation + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1855](https://github.com/GMOD/jbrowse-components/pull/1855) Add download + page in website header and new super-quick-start guide + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#1932](https://github.com/GMOD/jbrowse-components/pull/1932) Update analytics and share API URLs to refer to more stable locations ([@peterkxie](https://github.com/peterkxie)) - - [#1888](https://github.com/GMOD/jbrowse-components/pull/1888) More lazy loading of react components to reduce bundle size ([@cmdcolin](https://github.com/cmdcolin)) - - [#1790](https://github.com/GMOD/jbrowse-components/pull/1790) Allow MainThreadRpcDriver to skip serialization during RPC, improving main-thread rendering performance ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1932](https://github.com/GMOD/jbrowse-components/pull/1932) Update + analytics and share API URLs to refer to more stable locations + ([@peterkxie](https://github.com/peterkxie)) + - [#1888](https://github.com/GMOD/jbrowse-components/pull/1888) More lazy + loading of react components to reduce bundle size + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1790](https://github.com/GMOD/jbrowse-components/pull/1790) Allow + MainThreadRpcDriver to skip serialization during RPC, improving main-thread + rendering performance + ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - - [#1926](https://github.com/GMOD/jbrowse-components/pull/1926) Update website to link to demos on cloudfront for better compression ([@cmdcolin](https://github.com/cmdcolin)) - - [#1868](https://github.com/GMOD/jbrowse-components/pull/1868) Export XYPlotRenderer and configSchema ([@elliothershberg](https://github.com/elliothershberg)) - - [#1863](https://github.com/GMOD/jbrowse-components/pull/1863) Update @gmod/indexedfasta ([@cmdcolin](https://github.com/cmdcolin)) - - [#1795](https://github.com/GMOD/jbrowse-components/pull/1795) Make LinearAlignmentsDisplay fully configurable in the UI ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1822](https://github.com/GMOD/jbrowse-components/pull/1822) Let React LGV navigate without setting displayedRegion first ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1926](https://github.com/GMOD/jbrowse-components/pull/1926) Update website + to link to demos on cloudfront for better compression + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1868](https://github.com/GMOD/jbrowse-components/pull/1868) Export + XYPlotRenderer and configSchema + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1863](https://github.com/GMOD/jbrowse-components/pull/1863) Update + @gmod/indexedfasta ([@cmdcolin](https://github.com/cmdcolin)) + - [#1795](https://github.com/GMOD/jbrowse-components/pull/1795) Make + LinearAlignmentsDisplay fully configurable in the UI + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1822](https://github.com/GMOD/jbrowse-components/pull/1822) Let React LGV + navigate without setting displayedRegion first + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 4 @@ -2892,44 +4389,87 @@ Broken releases missing some packages #### :rocket: Enhancement - `core` - - [#1846](https://github.com/GMOD/jbrowse-components/pull/1846) Improve copy+paste in the data grids for feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1814](https://github.com/GMOD/jbrowse-components/pull/1814) Add ability to get promoter sequence and intron sequence for genes from the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#1816](https://github.com/GMOD/jbrowse-components/pull/1816) Remove some animation effects ([@cmdcolin](https://github.com/cmdcolin)) - - [#1778](https://github.com/GMOD/jbrowse-components/pull/1778) Adds dropdown to show drawer widget stack ([@teresam856](https://github.com/teresam856)) - - [#1685](https://github.com/GMOD/jbrowse-components/pull/1685) Change callbacks language from JavaScript to Jexl ([@peterkxie](https://github.com/peterkxie)) + - [#1846](https://github.com/GMOD/jbrowse-components/pull/1846) Improve + copy+paste in the data grids for feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1814](https://github.com/GMOD/jbrowse-components/pull/1814) Add ability to + get promoter sequence and intron sequence for genes from the feature details + panel ([@cmdcolin](https://github.com/cmdcolin)) + - [#1816](https://github.com/GMOD/jbrowse-components/pull/1816) Remove some + animation effects ([@cmdcolin](https://github.com/cmdcolin)) + - [#1778](https://github.com/GMOD/jbrowse-components/pull/1778) Adds dropdown + to show drawer widget stack ([@teresam856](https://github.com/teresam856)) + - [#1685](https://github.com/GMOD/jbrowse-components/pull/1685) Change + callbacks language from JavaScript to Jexl + ([@peterkxie](https://github.com/peterkxie)) - Other - - [#1831](https://github.com/GMOD/jbrowse-components/pull/1831) Add dialog for launching breakpoint split view from variant feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1803](https://github.com/GMOD/jbrowse-components/pull/1803) Transcript and gene glyphs can now display implied UTRs, active by default ([@cmdcolin](https://github.com/cmdcolin)) - - [#1808](https://github.com/GMOD/jbrowse-components/pull/1808) Add another heuristic for returning gene features from BigBed ([@cmdcolin](https://github.com/cmdcolin)) - - [#1774](https://github.com/GMOD/jbrowse-components/pull/1774) Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view ([@cmdcolin](https://github.com/cmdcolin)) + - [#1831](https://github.com/GMOD/jbrowse-components/pull/1831) Add dialog for + launching breakpoint split view from variant feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1803](https://github.com/GMOD/jbrowse-components/pull/1803) Transcript and + gene glyphs can now display implied UTRs, active by default + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1808](https://github.com/GMOD/jbrowse-components/pull/1808) Add another + heuristic for returning gene features from BigBed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1774](https://github.com/GMOD/jbrowse-components/pull/1774) Add warning + dialog in LGV before returning to import form to prevent accidentally losing + the current view ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#1811](https://github.com/GMOD/jbrowse-components/pull/1811) Check for existence of window more robustly to allow in SSR or node applications ([@elliothershberg](https://github.com/elliothershberg)) - - [#1793](https://github.com/GMOD/jbrowse-components/pull/1793) Fix dotplot rendering outside it's allowed bounds ([@cmdcolin](https://github.com/cmdcolin)) - - [#1783](https://github.com/GMOD/jbrowse-components/pull/1783) Add hic aborting and fix remoteAbort signal propagation ([@cmdcolin](https://github.com/cmdcolin)) - - [#1723](https://github.com/GMOD/jbrowse-components/pull/1723) A few bugfixes ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1811](https://github.com/GMOD/jbrowse-components/pull/1811) Check for + existence of window more robustly to allow in SSR or node applications + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1793](https://github.com/GMOD/jbrowse-components/pull/1793) Fix dotplot + rendering outside it's allowed bounds + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1783](https://github.com/GMOD/jbrowse-components/pull/1783) Add hic + aborting and fix remoteAbort signal propagation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1723](https://github.com/GMOD/jbrowse-components/pull/1723) A few bugfixes + ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - - [#1815](https://github.com/GMOD/jbrowse-components/pull/1815) Clear tracks when using "Return to import form" ([@cmdcolin](https://github.com/cmdcolin)) - - [#1819](https://github.com/GMOD/jbrowse-components/pull/1819) Standardized sentence casing on drawer widget titles ([@cmdcolin](https://github.com/cmdcolin)) - - [#1796](https://github.com/GMOD/jbrowse-components/pull/1796) Bump generic-filehandle for fixing CORS errors from Chrome cache pollution ([@cmdcolin](https://github.com/cmdcolin)) + - [#1815](https://github.com/GMOD/jbrowse-components/pull/1815) Clear tracks + when using "Return to import form" + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1819](https://github.com/GMOD/jbrowse-components/pull/1819) Standardized + sentence casing on drawer widget titles + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1796](https://github.com/GMOD/jbrowse-components/pull/1796) Bump + generic-filehandle for fixing CORS errors from Chrome cache pollution + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1824](https://github.com/GMOD/jbrowse-components/pull/1824) Add storybook docs page for nextjs usage ([@elliothershberg](https://github.com/elliothershberg)) -- [#1770](https://github.com/GMOD/jbrowse-components/pull/1770) 1469 storybook deploy ([@elliothershberg](https://github.com/elliothershberg)) -- [#1807](https://github.com/GMOD/jbrowse-components/pull/1807) Update developer guide to cover displays, and highlight working external plugins ([@cmdcolin](https://github.com/cmdcolin)) -- [#1779](https://github.com/GMOD/jbrowse-components/pull/1779) Collaborative release announcement editing ([@rbuels](https://github.com/rbuels)) -- [#1791](https://github.com/GMOD/jbrowse-components/pull/1791) Add a couple more demos for our live version with MDX ([@cmdcolin](https://github.com/cmdcolin)) +- [#1824](https://github.com/GMOD/jbrowse-components/pull/1824) Add storybook + docs page for nextjs usage + ([@elliothershberg](https://github.com/elliothershberg)) +- [#1770](https://github.com/GMOD/jbrowse-components/pull/1770) 1469 storybook + deploy ([@elliothershberg](https://github.com/elliothershberg)) +- [#1807](https://github.com/GMOD/jbrowse-components/pull/1807) Update developer + guide to cover displays, and highlight working external plugins + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1779](https://github.com/GMOD/jbrowse-components/pull/1779) Collaborative + release announcement editing ([@rbuels](https://github.com/rbuels)) +- [#1791](https://github.com/GMOD/jbrowse-components/pull/1791) Add a couple + more demos for our live version with MDX + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#1820](https://github.com/GMOD/jbrowse-components/pull/1820) Create v1.1.0.md, draft of release announcements ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1823](https://github.com/GMOD/jbrowse-components/pull/1823) Add note about previewing changelog to CONTRIBUTING.md ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1820](https://github.com/GMOD/jbrowse-components/pull/1820) Create + v1.1.0.md, draft of release announcements + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1823](https://github.com/GMOD/jbrowse-components/pull/1823) Add note about + previewing changelog to CONTRIBUTING.md + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#1834](https://github.com/GMOD/jbrowse-components/pull/1834) Change jbrowse-components monorepo default branch from 'master' to 'main' ([@rbuels](https://github.com/rbuels)) + - [#1834](https://github.com/GMOD/jbrowse-components/pull/1834) Change + jbrowse-components monorepo default branch from 'master' to 'main' + ([@rbuels](https://github.com/rbuels)) #### Committers: 6 @@ -2980,90 +4520,213 @@ Broken releases missing some packages #### :rocket: Enhancement - `core` - - [#1758](https://github.com/GMOD/jbrowse-components/pull/1758) Add ability to get stitched together CDS, protein, and cDNA sequences in feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1721](https://github.com/GMOD/jbrowse-components/pull/1721) Manually adjust feature height and spacing on alignments track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1728](https://github.com/GMOD/jbrowse-components/pull/1728) Add list of loaded plugins to the "About widget" ([@rbuels](https://github.com/rbuels)) - - [#1711](https://github.com/GMOD/jbrowse-components/pull/1711) Add plugin top-level configuration ([@teresam856](https://github.com/teresam856)) - - [#1699](https://github.com/GMOD/jbrowse-components/pull/1699) Add sequence track for both read and reference genome in the "Linear read vs ref" comparison ([@cmdcolin](https://github.com/cmdcolin)) - - [#1701](https://github.com/GMOD/jbrowse-components/pull/1701) Add clickable navigation links to supplementary alignments/paired ends locations and BND/TRA endpoints in detail widgets ([@cmdcolin](https://github.com/cmdcolin)) - - [#1601](https://github.com/GMOD/jbrowse-components/pull/1601) Add ability to color by per-base quality in alignment tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1640](https://github.com/GMOD/jbrowse-components/pull/1640) Move stats calculation to BaseFeatureAdapter ([@cmdcolin](https://github.com/cmdcolin)) - - [#1588](https://github.com/GMOD/jbrowse-components/pull/1588) Add "Get sequence" action to LGV rubber-band ([@teresam856](https://github.com/teresam856)) -- Other - - [#1743](https://github.com/GMOD/jbrowse-components/pull/1743) Add color picker and choice of summary score style for wiggle track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1763](https://github.com/GMOD/jbrowse-components/pull/1763) Add a "CSS reset" to jbrowse-react-linear-genome-view to prevent parent styles from outside the component leaking in ([@cmdcolin](https://github.com/cmdcolin)) - - [#1756](https://github.com/GMOD/jbrowse-components/pull/1756) Split alignments track menu items into "Pileup" and "SNPCoverage" submenus ([@cmdcolin](https://github.com/cmdcolin)) - - [#1742](https://github.com/GMOD/jbrowse-components/pull/1742) Add ability to display crosshatches on the wiggle line/xyplot renderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) - - [#1394](https://github.com/GMOD/jbrowse-components/pull/1394) Add new menu items for show/hide feature labels, set max height, and set compact display mode ([@cmdcolin](https://github.com/cmdcolin)) - - [#1720](https://github.com/GMOD/jbrowse-components/pull/1720) Standardize phred qual scaling between BAM and CRAM and add option to make mismatches render in a lighter color when quality is low ([@cmdcolin](https://github.com/cmdcolin)) - - [#1704](https://github.com/GMOD/jbrowse-components/pull/1704) Add "Show all regions in assembly" to import form and make import form show entire region when refName selected ([@cmdcolin](https://github.com/cmdcolin)) - - [#1687](https://github.com/GMOD/jbrowse-components/pull/1687) Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events ([@cmdcolin](https://github.com/cmdcolin)) - - [#1695](https://github.com/GMOD/jbrowse-components/pull/1695) Improve zoomed-out display of quantitative displays tracks when bicolor pivot is active ([@cmdcolin](https://github.com/cmdcolin)) - - [#1680](https://github.com/GMOD/jbrowse-components/pull/1680) Add on click functionality to quantitative track features ([@teresam856](https://github.com/teresam856)) - - [#1630](https://github.com/GMOD/jbrowse-components/pull/1630) Get column names from BED tabix files and other utils for external jbrowse-plugin-gwas support ([@cmdcolin](https://github.com/cmdcolin)) - - [#1709](https://github.com/GMOD/jbrowse-components/pull/1709) Improve sorting and filtering in variant detail widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#1688](https://github.com/GMOD/jbrowse-components/pull/1688) Bold insertion indicator for large insertions on pileup track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1669](https://github.com/GMOD/jbrowse-components/pull/1669) Allow plain json encoding of the session in the URL ([@cmdcolin](https://github.com/cmdcolin)) - - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable locstring navigation from LGV import form ([@teresam856](https://github.com/teresam856)) - - [#1655](https://github.com/GMOD/jbrowse-components/pull/1655) Add GFF3Tabix and BEDTabix inference to JB1 connection ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1643](https://github.com/GMOD/jbrowse-components/pull/1643) Add an offset that allows all wiggle y-scalebar labels to be visible ([@cmdcolin](https://github.com/cmdcolin)) - - [#1632](https://github.com/GMOD/jbrowse-components/pull/1632) Displays warnings when receiving a session with custom callbacks ([@peterkxie](https://github.com/peterkxie)) - - [#1615](https://github.com/GMOD/jbrowse-components/pull/1615) Increase pileup maxHeight ([@cmdcolin](https://github.com/cmdcolin)) - - [#1624](https://github.com/GMOD/jbrowse-components/pull/1624) GCContent adapter ([@cmdcolin](https://github.com/cmdcolin)) - - [#1614](https://github.com/GMOD/jbrowse-components/pull/1614) Add insertion and clip indicators to SNPCoverage views (part of Alignments tracks) ([@cmdcolin](https://github.com/cmdcolin)) - - [#1610](https://github.com/GMOD/jbrowse-components/pull/1610) Display error message from dynamodb session sharing error ([@cmdcolin](https://github.com/cmdcolin)) + - [#1758](https://github.com/GMOD/jbrowse-components/pull/1758) Add ability to + get stitched together CDS, protein, and cDNA sequences in feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1721](https://github.com/GMOD/jbrowse-components/pull/1721) Manually + adjust feature height and spacing on alignments track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1728](https://github.com/GMOD/jbrowse-components/pull/1728) Add list of + loaded plugins to the "About widget" ([@rbuels](https://github.com/rbuels)) + - [#1711](https://github.com/GMOD/jbrowse-components/pull/1711) Add plugin + top-level configuration ([@teresam856](https://github.com/teresam856)) + - [#1699](https://github.com/GMOD/jbrowse-components/pull/1699) Add sequence + track for both read and reference genome in the "Linear read vs ref" + comparison ([@cmdcolin](https://github.com/cmdcolin)) + - [#1701](https://github.com/GMOD/jbrowse-components/pull/1701) Add clickable + navigation links to supplementary alignments/paired ends locations and + BND/TRA endpoints in detail widgets + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1601](https://github.com/GMOD/jbrowse-components/pull/1601) Add ability to + color by per-base quality in alignment tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1640](https://github.com/GMOD/jbrowse-components/pull/1640) Move stats + calculation to BaseFeatureAdapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#1588](https://github.com/GMOD/jbrowse-components/pull/1588) Add "Get + sequence" action to LGV rubber-band + ([@teresam856](https://github.com/teresam856)) +- Other + - [#1743](https://github.com/GMOD/jbrowse-components/pull/1743) Add color + picker and choice of summary score style for wiggle track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1763](https://github.com/GMOD/jbrowse-components/pull/1763) Add a "CSS + reset" to jbrowse-react-linear-genome-view to prevent parent styles from + outside the component leaking in ([@cmdcolin](https://github.com/cmdcolin)) + - [#1756](https://github.com/GMOD/jbrowse-components/pull/1756) Split + alignments track menu items into "Pileup" and "SNPCoverage" submenus + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1742](https://github.com/GMOD/jbrowse-components/pull/1742) Add ability to + display crosshatches on the wiggle line/xyplot renderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI + add-track --load inPlace to put exact contents into the config, add better + CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) + - [#1394](https://github.com/GMOD/jbrowse-components/pull/1394) Add new menu + items for show/hide feature labels, set max height, and set compact display + mode ([@cmdcolin](https://github.com/cmdcolin)) + - [#1720](https://github.com/GMOD/jbrowse-components/pull/1720) Standardize + phred qual scaling between BAM and CRAM and add option to make mismatches + render in a lighter color when quality is low + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1704](https://github.com/GMOD/jbrowse-components/pull/1704) Add "Show all + regions in assembly" to import form and make import form show entire region + when refName selected ([@cmdcolin](https://github.com/cmdcolin)) + - [#1687](https://github.com/GMOD/jbrowse-components/pull/1687) Threshold for + indicators on SNPCoverage + inverted bargraph of interbase counts for + sub-threshold events ([@cmdcolin](https://github.com/cmdcolin)) + - [#1695](https://github.com/GMOD/jbrowse-components/pull/1695) Improve + zoomed-out display of quantitative displays tracks when bicolor pivot is + active ([@cmdcolin](https://github.com/cmdcolin)) + - [#1680](https://github.com/GMOD/jbrowse-components/pull/1680) Add on click + functionality to quantitative track features + ([@teresam856](https://github.com/teresam856)) + - [#1630](https://github.com/GMOD/jbrowse-components/pull/1630) Get column + names from BED tabix files and other utils for external jbrowse-plugin-gwas + support ([@cmdcolin](https://github.com/cmdcolin)) + - [#1709](https://github.com/GMOD/jbrowse-components/pull/1709) Improve + sorting and filtering in variant detail widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1688](https://github.com/GMOD/jbrowse-components/pull/1688) Bold insertion + indicator for large insertions on pileup track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1669](https://github.com/GMOD/jbrowse-components/pull/1669) Allow plain + json encoding of the session in the URL + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable + locstring navigation from LGV import form + ([@teresam856](https://github.com/teresam856)) + - [#1655](https://github.com/GMOD/jbrowse-components/pull/1655) Add GFF3Tabix + and BEDTabix inference to JB1 connection + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1643](https://github.com/GMOD/jbrowse-components/pull/1643) Add an offset + that allows all wiggle y-scalebar labels to be visible + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1632](https://github.com/GMOD/jbrowse-components/pull/1632) Displays + warnings when receiving a session with custom callbacks + ([@peterkxie](https://github.com/peterkxie)) + - [#1615](https://github.com/GMOD/jbrowse-components/pull/1615) Increase + pileup maxHeight ([@cmdcolin](https://github.com/cmdcolin)) + - [#1624](https://github.com/GMOD/jbrowse-components/pull/1624) GCContent + adapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#1614](https://github.com/GMOD/jbrowse-components/pull/1614) Add insertion + and clip indicators to SNPCoverage views (part of Alignments tracks) + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1610](https://github.com/GMOD/jbrowse-components/pull/1610) Display error + message from dynamodb session sharing error + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#1777](https://github.com/GMOD/jbrowse-components/pull/1777) Quick fix for block error ([@cmdcolin](https://github.com/cmdcolin)) - - [#1748](https://github.com/GMOD/jbrowse-components/pull/1748) External plugins load after confirming config warning ([@peterkxie](https://github.com/peterkxie)) - - [#1750](https://github.com/GMOD/jbrowse-components/pull/1750) Fix pileup sorting when using string tag ([@cmdcolin](https://github.com/cmdcolin)) - - [#1747](https://github.com/GMOD/jbrowse-components/pull/1747) Fix the position of the popup menu after rubberband select when there is a margin on the component e.g. in embedded ([@cmdcolin](https://github.com/cmdcolin)) - - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) - - [#1731](https://github.com/GMOD/jbrowse-components/pull/1731) Fix alignment track ability to remember the height of the SNPCoverage subtrack on refresh ([@cmdcolin](https://github.com/cmdcolin)) - - [#1719](https://github.com/GMOD/jbrowse-components/pull/1719) Fix for navigation past end of chromosome ([@cmdcolin](https://github.com/cmdcolin)) - - [#1698](https://github.com/GMOD/jbrowse-components/pull/1698) Fix rendering read vs ref comparisons with CIGAR strings that use = sign matches ([@cmdcolin](https://github.com/cmdcolin)) - - [#1697](https://github.com/GMOD/jbrowse-components/pull/1697) Fix softclipping configuration setting causing bases to be missed ([@cmdcolin](https://github.com/cmdcolin)) - - [#1689](https://github.com/GMOD/jbrowse-components/pull/1689) Disable copy/delete menu items for reference sequence track ([@teresam856](https://github.com/teresam856)) - - [#1682](https://github.com/GMOD/jbrowse-components/pull/1682) Fix parsing of BED and BEDPE files with comment header for spreadsheet view ([@cmdcolin](https://github.com/cmdcolin)) - - [#1679](https://github.com/GMOD/jbrowse-components/pull/1679) Fix issue with using launching the add track widget on views that are not displaying any regions ([@teresam856](https://github.com/teresam856)) - - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable locstring navigation from LGV import form ([@teresam856](https://github.com/teresam856)) - - [#1626](https://github.com/GMOD/jbrowse-components/pull/1626) Bug Fix: specify assembly in locstring ([@teresam856](https://github.com/teresam856)) - - [#1619](https://github.com/GMOD/jbrowse-components/pull/1619) Fix overview scale polygon not appearing properly in some cases ([@cmdcolin](https://github.com/cmdcolin)) -- `core` - - [#1714](https://github.com/GMOD/jbrowse-components/pull/1714) Fix ability to add a PAF on initial dotplot view creation ([@cmdcolin](https://github.com/cmdcolin)) - - [#1657](https://github.com/GMOD/jbrowse-components/pull/1657) Fix for track using assembly alias not displaying ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1620](https://github.com/GMOD/jbrowse-components/pull/1620) Add error reporting on a worker failure ([@cmdcolin](https://github.com/cmdcolin)) + - [#1777](https://github.com/GMOD/jbrowse-components/pull/1777) Quick fix for + block error ([@cmdcolin](https://github.com/cmdcolin)) + - [#1748](https://github.com/GMOD/jbrowse-components/pull/1748) External + plugins load after confirming config warning + ([@peterkxie](https://github.com/peterkxie)) + - [#1750](https://github.com/GMOD/jbrowse-components/pull/1750) Fix pileup + sorting when using string tag ([@cmdcolin](https://github.com/cmdcolin)) + - [#1747](https://github.com/GMOD/jbrowse-components/pull/1747) Fix the + position of the popup menu after rubberband select when there is a margin on + the component e.g. in embedded ([@cmdcolin](https://github.com/cmdcolin)) + - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI + add-track --load inPlace to put exact contents into the config, add better + CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) + - [#1731](https://github.com/GMOD/jbrowse-components/pull/1731) Fix alignment + track ability to remember the height of the SNPCoverage subtrack on refresh + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1719](https://github.com/GMOD/jbrowse-components/pull/1719) Fix for + navigation past end of chromosome ([@cmdcolin](https://github.com/cmdcolin)) + - [#1698](https://github.com/GMOD/jbrowse-components/pull/1698) Fix rendering + read vs ref comparisons with CIGAR strings that use = sign matches + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1697](https://github.com/GMOD/jbrowse-components/pull/1697) Fix + softclipping configuration setting causing bases to be missed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1689](https://github.com/GMOD/jbrowse-components/pull/1689) Disable + copy/delete menu items for reference sequence track + ([@teresam856](https://github.com/teresam856)) + - [#1682](https://github.com/GMOD/jbrowse-components/pull/1682) Fix parsing of + BED and BEDPE files with comment header for spreadsheet view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1679](https://github.com/GMOD/jbrowse-components/pull/1679) Fix issue with + using launching the add track widget on views that are not displaying any + regions ([@teresam856](https://github.com/teresam856)) + - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable + locstring navigation from LGV import form + ([@teresam856](https://github.com/teresam856)) + - [#1626](https://github.com/GMOD/jbrowse-components/pull/1626) Bug Fix: + specify assembly in locstring ([@teresam856](https://github.com/teresam856)) + - [#1619](https://github.com/GMOD/jbrowse-components/pull/1619) Fix overview + scale polygon not appearing properly in some cases + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#1714](https://github.com/GMOD/jbrowse-components/pull/1714) Fix ability to + add a PAF on initial dotplot view creation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1657](https://github.com/GMOD/jbrowse-components/pull/1657) Fix for track + using assembly alias not displaying + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1620](https://github.com/GMOD/jbrowse-components/pull/1620) Add error + reporting on a worker failure ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1725](https://github.com/GMOD/jbrowse-components/pull/1725) JBrowseR release ([@elliothershberg](https://github.com/elliothershberg)) -- [#1677](https://github.com/GMOD/jbrowse-components/pull/1677) Config guide updates ([@elliothershberg](https://github.com/elliothershberg)) -- [#1665](https://github.com/GMOD/jbrowse-components/pull/1665) Add Nextstrain COVID storybook ([@elliothershberg](https://github.com/elliothershberg)) -- [#1670](https://github.com/GMOD/jbrowse-components/pull/1670) typo in developer guide docs ([@teresam856](https://github.com/teresam856)) -- [#1592](https://github.com/GMOD/jbrowse-components/pull/1592) Website copy edits ([@rbuels](https://github.com/rbuels)) -- [#1646](https://github.com/GMOD/jbrowse-components/pull/1646) Fix "See code" link in CLI docs ([@garrettjstevens](https://github.com/garrettjstevens)) -- [#1618](https://github.com/GMOD/jbrowse-components/pull/1618) Add whole-genome view and color/sort alignments tutorials to user guide ([@cmdcolin](https://github.com/cmdcolin)) +- [#1725](https://github.com/GMOD/jbrowse-components/pull/1725) JBrowseR release + ([@elliothershberg](https://github.com/elliothershberg)) +- [#1677](https://github.com/GMOD/jbrowse-components/pull/1677) Config guide + updates ([@elliothershberg](https://github.com/elliothershberg)) +- [#1665](https://github.com/GMOD/jbrowse-components/pull/1665) Add Nextstrain + COVID storybook ([@elliothershberg](https://github.com/elliothershberg)) +- [#1670](https://github.com/GMOD/jbrowse-components/pull/1670) typo in + developer guide docs ([@teresam856](https://github.com/teresam856)) +- [#1592](https://github.com/GMOD/jbrowse-components/pull/1592) Website copy + edits ([@rbuels](https://github.com/rbuels)) +- [#1646](https://github.com/GMOD/jbrowse-components/pull/1646) Fix "See code" + link in CLI docs ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#1618](https://github.com/GMOD/jbrowse-components/pull/1618) Add whole-genome + view and color/sort alignments tutorials to user guide + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#1666](https://github.com/GMOD/jbrowse-components/pull/1666) Move "mouseover" config from BaseLinearDisplay to LinearBasicDisplay display ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1751](https://github.com/GMOD/jbrowse-components/pull/1751) Make the variant display derive from the feature display ([@cmdcolin](https://github.com/cmdcolin)) - - [#1716](https://github.com/GMOD/jbrowse-components/pull/1716) Stringify labels before adding to rendering to avoid undefineds on label.length ([@cmdcolin](https://github.com/cmdcolin)) - - [#1713](https://github.com/GMOD/jbrowse-components/pull/1713) Add console.error log in block setError ([@cmdcolin](https://github.com/cmdcolin)) - - [#1663](https://github.com/GMOD/jbrowse-components/pull/1663) Make LGV "initialized" not depend on displayedRegions ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1672](https://github.com/GMOD/jbrowse-components/pull/1672) Fix import forms crashing if there are no assemblies ([@cmdcolin](https://github.com/cmdcolin)) - - [#1644](https://github.com/GMOD/jbrowse-components/pull/1644) Bump electron from 9.3.1 to 9.4.0 ([@dependabot[bot]](https://github.com/apps/dependabot)) - - [#1641](https://github.com/GMOD/jbrowse-components/pull/1641) Remove codecov pr annotations ([@cmdcolin](https://github.com/cmdcolin)) - - [#1609](https://github.com/GMOD/jbrowse-components/pull/1609) Add extra checks for release script ([@peterkxie](https://github.com/peterkxie)) + - [#1666](https://github.com/GMOD/jbrowse-components/pull/1666) Move + "mouseover" config from BaseLinearDisplay to LinearBasicDisplay display + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1751](https://github.com/GMOD/jbrowse-components/pull/1751) Make the + variant display derive from the feature display + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1716](https://github.com/GMOD/jbrowse-components/pull/1716) Stringify + labels before adding to rendering to avoid undefineds on label.length + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1713](https://github.com/GMOD/jbrowse-components/pull/1713) Add + console.error log in block setError + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1663](https://github.com/GMOD/jbrowse-components/pull/1663) Make LGV + "initialized" not depend on displayedRegions + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1672](https://github.com/GMOD/jbrowse-components/pull/1672) Fix import + forms crashing if there are no assemblies + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1644](https://github.com/GMOD/jbrowse-components/pull/1644) Bump electron + from 9.3.1 to 9.4.0 ([@dependabot[bot]](https://github.com/apps/dependabot)) + - [#1641](https://github.com/GMOD/jbrowse-components/pull/1641) Remove codecov + pr annotations ([@cmdcolin](https://github.com/cmdcolin)) + - [#1609](https://github.com/GMOD/jbrowse-components/pull/1609) Add extra + checks for release script ([@peterkxie](https://github.com/peterkxie)) - `core` - - [#1762](https://github.com/GMOD/jbrowse-components/pull/1762) Add requestidlecallback ponyfill in @jbrowse/core/util ([@cmdcolin](https://github.com/cmdcolin)) - - [#1629](https://github.com/GMOD/jbrowse-components/pull/1629) Add RegionsAdapter/SequenceAdapter, reorganize base adapters ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1625](https://github.com/GMOD/jbrowse-components/pull/1625) Make renderArgs consistent and don't duplicate data ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1414](https://github.com/GMOD/jbrowse-components/pull/1414) Typescriptify and MST'ify the add track workflow ([@cmdcolin](https://github.com/cmdcolin)) + - [#1762](https://github.com/GMOD/jbrowse-components/pull/1762) Add + requestidlecallback ponyfill in @jbrowse/core/util + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1629](https://github.com/GMOD/jbrowse-components/pull/1629) Add + RegionsAdapter/SequenceAdapter, reorganize base adapters + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1625](https://github.com/GMOD/jbrowse-components/pull/1625) Make + renderArgs consistent and don't duplicate data + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1414](https://github.com/GMOD/jbrowse-components/pull/1414) Typescriptify + and MST'ify the add track workflow + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 7 @@ -3112,61 +4775,143 @@ Broken releases missing some packages #### :rocket: Enhancement - Other - - [#1560](https://github.com/GMOD/jbrowse-components/pull/1560) Provide a dialog to add extra genomic context for linear read vs. ref visualization ([@elliothershberg](https://github.com/elliothershberg)) - - [#1604](https://github.com/GMOD/jbrowse-components/pull/1604) Add ability to filter for read name to the alignments filter dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#1599](https://github.com/GMOD/jbrowse-components/pull/1599) Replace 'show all regions' with 'show all regions in assembly' ([@cmdcolin](https://github.com/cmdcolin)) - - [#1595](https://github.com/GMOD/jbrowse-components/pull/1595) Admin server GUI enhancements ([@elliothershberg](https://github.com/elliothershberg)) - - [#1584](https://github.com/GMOD/jbrowse-components/pull/1584) Restructure demo page and release cancer demo ([@elliothershberg](https://github.com/elliothershberg)) - - [#1579](https://github.com/GMOD/jbrowse-components/pull/1579) Create --branch and --nightly flags for `jbrowse create` and `jbrowse upgrade` commands ([@cmdcolin](https://github.com/cmdcolin)) - - [#1575](https://github.com/GMOD/jbrowse-components/pull/1575) Improve mobx-state-tree type validation errors ([@cmdcolin](https://github.com/cmdcolin)) - - [#1574](https://github.com/GMOD/jbrowse-components/pull/1574) Make softclip indicator black if no seq available ([@cmdcolin](https://github.com/cmdcolin)) - - [#1554](https://github.com/GMOD/jbrowse-components/pull/1554) Coloring options with simple color for tag ([@peterkxie](https://github.com/peterkxie)) - - [#1565](https://github.com/GMOD/jbrowse-components/pull/1565) Rename jbrowse cli add-track --type to --trackType ([@cmdcolin](https://github.com/cmdcolin)) - - [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) - - [#1533](https://github.com/GMOD/jbrowse-components/pull/1533) Display file headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix package versions ([@cmdcolin](https://github.com/cmdcolin)) - - [#1541](https://github.com/GMOD/jbrowse-components/pull/1541) Add more info about adding a PAF file to the synteny import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#1509](https://github.com/GMOD/jbrowse-components/pull/1509) Combine Search and Dropdown component on LGV ([@teresam856](https://github.com/teresam856)) - - [#1530](https://github.com/GMOD/jbrowse-components/pull/1530) Add spreadsheet filter support for derived columns ([@elliothershberg](https://github.com/elliothershberg)) - - [#1483](https://github.com/GMOD/jbrowse-components/pull/1483) Add session export to and import from file ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1519](https://github.com/GMOD/jbrowse-components/pull/1519) Add autoSql to the bigBed "About this track" dialog ([@cmdcolin](https://github.com/cmdcolin)) -- `core` - - [#1531](https://github.com/GMOD/jbrowse-components/pull/1531) Add track menu options for autoscale, log scale, histogram fill, setting min/max score, and zoom level/resolution for wiggle/snpcoverage tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1473](https://github.com/GMOD/jbrowse-components/pull/1473) Color, filter, and sort options for the alignments ([@cmdcolin](https://github.com/cmdcolin)) - - [#1576](https://github.com/GMOD/jbrowse-components/pull/1576) Add location string to tooltip for wiggle and SNPCoverage tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1529](https://github.com/GMOD/jbrowse-components/pull/1529) Display subfeatures in feature details widget ([@cmdcolin](https://github.com/cmdcolin)) + - [#1560](https://github.com/GMOD/jbrowse-components/pull/1560) Provide a + dialog to add extra genomic context for linear read vs. ref visualization + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1604](https://github.com/GMOD/jbrowse-components/pull/1604) Add ability to + filter for read name to the alignments filter dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1599](https://github.com/GMOD/jbrowse-components/pull/1599) Replace 'show + all regions' with 'show all regions in assembly' + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1595](https://github.com/GMOD/jbrowse-components/pull/1595) Admin server + GUI enhancements ([@elliothershberg](https://github.com/elliothershberg)) + - [#1584](https://github.com/GMOD/jbrowse-components/pull/1584) Restructure + demo page and release cancer demo + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1579](https://github.com/GMOD/jbrowse-components/pull/1579) Create + --branch and --nightly flags for `jbrowse create` and `jbrowse upgrade` + commands ([@cmdcolin](https://github.com/cmdcolin)) + - [#1575](https://github.com/GMOD/jbrowse-components/pull/1575) Improve + mobx-state-tree type validation errors + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1574](https://github.com/GMOD/jbrowse-components/pull/1574) Make softclip + indicator black if no seq available + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1554](https://github.com/GMOD/jbrowse-components/pull/1554) Coloring + options with simple color for tag + ([@peterkxie](https://github.com/peterkxie)) + - [#1565](https://github.com/GMOD/jbrowse-components/pull/1565) Rename jbrowse + cli add-track --type to --trackType + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for + sequence track, variant track, launching synteny from dotplot, and add UCSC + plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) + - [#1533](https://github.com/GMOD/jbrowse-components/pull/1533) Display file + headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix + package versions ([@cmdcolin](https://github.com/cmdcolin)) + - [#1541](https://github.com/GMOD/jbrowse-components/pull/1541) Add more info + about adding a PAF file to the synteny import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1509](https://github.com/GMOD/jbrowse-components/pull/1509) Combine Search + and Dropdown component on LGV ([@teresam856](https://github.com/teresam856)) + - [#1530](https://github.com/GMOD/jbrowse-components/pull/1530) Add + spreadsheet filter support for derived columns + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1483](https://github.com/GMOD/jbrowse-components/pull/1483) Add session + export to and import from file + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1519](https://github.com/GMOD/jbrowse-components/pull/1519) Add autoSql to + the bigBed "About this track" dialog + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#1531](https://github.com/GMOD/jbrowse-components/pull/1531) Add track menu + options for autoscale, log scale, histogram fill, setting min/max score, and + zoom level/resolution for wiggle/snpcoverage tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1473](https://github.com/GMOD/jbrowse-components/pull/1473) Color, filter, + and sort options for the alignments + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1576](https://github.com/GMOD/jbrowse-components/pull/1576) Add location + string to tooltip for wiggle and SNPCoverage tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1529](https://github.com/GMOD/jbrowse-components/pull/1529) Display + subfeatures in feature details widget + ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `development-tools` - - [#1578](https://github.com/GMOD/jbrowse-components/pull/1578) Update build system for external plugins ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1578](https://github.com/GMOD/jbrowse-components/pull/1578) Update build + system for external plugins + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#1608](https://github.com/GMOD/jbrowse-components/pull/1608) Take into account offsetX of the rubberband on scalebar zooming ([@cmdcolin](https://github.com/cmdcolin)) - - [#1597](https://github.com/GMOD/jbrowse-components/pull/1597) Fix crash when there are undefined references in the state tree e.g. when a track is deleted but still referred to by a session ([@peterkxie](https://github.com/peterkxie)) - - [#1598](https://github.com/GMOD/jbrowse-components/pull/1598) Disable 'copy to clipboard' while share url being generated ([@peterkxie](https://github.com/peterkxie)) - - [#1589](https://github.com/GMOD/jbrowse-components/pull/1589) Fix the display of trackhub registry results ([@cmdcolin](https://github.com/cmdcolin)) - - [#1573](https://github.com/GMOD/jbrowse-components/pull/1573) Update hic-straw to fix error for hic files with many scaffolds ([@cmdcolin](https://github.com/cmdcolin)) - - [#1563](https://github.com/GMOD/jbrowse-components/pull/1563) Remove softclip and hardclip from being counted as SNPs in the SNPCoverage ([@cmdcolin](https://github.com/cmdcolin)) - - [#1559](https://github.com/GMOD/jbrowse-components/pull/1559) Avoid errors from breakpoint split view related to getBoundingClientRect on null track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1540](https://github.com/GMOD/jbrowse-components/pull/1540) Fix memory leak when side scrolling LGV blocks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1534](https://github.com/GMOD/jbrowse-components/pull/1534) Fix breakpoint split view showing too many connections for paired end ends ([@cmdcolin](https://github.com/cmdcolin)) - - [#1524](https://github.com/GMOD/jbrowse-components/pull/1524) Move loading flag for spreadsheet import wizard to volatile to avoid it persisting across refresh ([@cmdcolin](https://github.com/cmdcolin)) - - [#1521](https://github.com/GMOD/jbrowse-components/pull/1521) Add missing dep to react-linear-genome-view ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1608](https://github.com/GMOD/jbrowse-components/pull/1608) Take into + account offsetX of the rubberband on scalebar zooming + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1597](https://github.com/GMOD/jbrowse-components/pull/1597) Fix crash when + there are undefined references in the state tree e.g. when a track is + deleted but still referred to by a session + ([@peterkxie](https://github.com/peterkxie)) + - [#1598](https://github.com/GMOD/jbrowse-components/pull/1598) Disable 'copy + to clipboard' while share url being generated + ([@peterkxie](https://github.com/peterkxie)) + - [#1589](https://github.com/GMOD/jbrowse-components/pull/1589) Fix the + display of trackhub registry results + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1573](https://github.com/GMOD/jbrowse-components/pull/1573) Update + hic-straw to fix error for hic files with many scaffolds + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1563](https://github.com/GMOD/jbrowse-components/pull/1563) Remove + softclip and hardclip from being counted as SNPs in the SNPCoverage + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1559](https://github.com/GMOD/jbrowse-components/pull/1559) Avoid errors + from breakpoint split view related to getBoundingClientRect on null track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1540](https://github.com/GMOD/jbrowse-components/pull/1540) Fix memory + leak when side scrolling LGV blocks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1534](https://github.com/GMOD/jbrowse-components/pull/1534) Fix breakpoint + split view showing too many connections for paired end ends + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1524](https://github.com/GMOD/jbrowse-components/pull/1524) Move loading + flag for spreadsheet import wizard to volatile to avoid it persisting across + refresh ([@cmdcolin](https://github.com/cmdcolin)) + - [#1521](https://github.com/GMOD/jbrowse-components/pull/1521) Add missing + dep to react-linear-genome-view + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#1587](https://github.com/GMOD/jbrowse-components/pull/1587) Fix positioning of scalebar tooltips, overview scalebar plotting, and refName label positioning when displaying many regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#1547](https://github.com/GMOD/jbrowse-components/pull/1547) Fix analytics crashing when using plugins ([@cmdcolin](https://github.com/cmdcolin)) + - [#1587](https://github.com/GMOD/jbrowse-components/pull/1587) Fix + positioning of scalebar tooltips, overview scalebar plotting, and refName + label positioning when displaying many regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1547](https://github.com/GMOD/jbrowse-components/pull/1547) Fix analytics + crashing when using plugins ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1594](https://github.com/GMOD/jbrowse-components/pull/1594) Add GFF3 example to quickstart ([@cmdcolin](https://github.com/cmdcolin)) -- [#1581](https://github.com/GMOD/jbrowse-components/pull/1581) Add some features that are missing from jbrowse 2 to the feature comparison table ([@cmdcolin](https://github.com/cmdcolin)) -- [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) -- [#1537](https://github.com/GMOD/jbrowse-components/pull/1537) Add CONTRIBUTING.md with tips for getting started with codebase ([@cmdcolin](https://github.com/cmdcolin)) +- [#1594](https://github.com/GMOD/jbrowse-components/pull/1594) Add GFF3 example + to quickstart ([@cmdcolin](https://github.com/cmdcolin)) +- [#1581](https://github.com/GMOD/jbrowse-components/pull/1581) Add some + features that are missing from jbrowse 2 to the feature comparison table + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for + sequence track, variant track, launching synteny from dotplot, and add UCSC + plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) +- [#1537](https://github.com/GMOD/jbrowse-components/pull/1537) Add + CONTRIBUTING.md with tips for getting started with codebase + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#1606](https://github.com/GMOD/jbrowse-components/pull/1606) Upgrade @testing-library/react and improve test reliability ([@cmdcolin](https://github.com/cmdcolin)) -- [#1555](https://github.com/GMOD/jbrowse-components/pull/1555) Remove the TextDecoder/TextEncoder polyfill ([@cmdcolin](https://github.com/cmdcolin)) -- [#1522](https://github.com/GMOD/jbrowse-components/pull/1522) Update oclif and remove now unnecessary file copy ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#1606](https://github.com/GMOD/jbrowse-components/pull/1606) Upgrade + @testing-library/react and improve test reliability + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1555](https://github.com/GMOD/jbrowse-components/pull/1555) Remove the + TextDecoder/TextEncoder polyfill ([@cmdcolin](https://github.com/cmdcolin)) +- [#1522](https://github.com/GMOD/jbrowse-components/pull/1522) Update oclif and + remove now unnecessary file copy + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 6 @@ -3221,19 +4966,33 @@ Broken releases missing some packages #### :rocket: Enhancement - `core` - - [#1513](https://github.com/GMOD/jbrowse-components/pull/1513) Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX ([@elliothershberg](https://github.com/elliothershberg)) + - [#1513](https://github.com/GMOD/jbrowse-components/pull/1513) Add a custom + scrollbar that overrides the auto-hiding behavior of scrollbars on OSX + ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - Other - - [#1514](https://github.com/GMOD/jbrowse-components/pull/1514) react-linear-genome-view bug fixes ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1517](https://github.com/GMOD/jbrowse-components/pull/1517) Fix the use of filtering display on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#1512](https://github.com/GMOD/jbrowse-components/pull/1512) Fix setting maxDisplayedBpPerPx for pileup display, helps prevent too large an area from being rendered ([@cmdcolin](https://github.com/cmdcolin)) - - [#1442](https://github.com/GMOD/jbrowse-components/pull/1442) Change track selector togglebutton to normal button ([@cmdcolin](https://github.com/cmdcolin)) - - [#1506](https://github.com/GMOD/jbrowse-components/pull/1506) Fix horizontally flipped translation frames position ([@cmdcolin](https://github.com/cmdcolin)) - - [#1501](https://github.com/GMOD/jbrowse-components/pull/1501) Fix CLI to allow jbrowse create to download newer monorepo tag format ([@cmdcolin](https://github.com/cmdcolin)) + - [#1514](https://github.com/GMOD/jbrowse-components/pull/1514) + react-linear-genome-view bug fixes + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1517](https://github.com/GMOD/jbrowse-components/pull/1517) Fix the use of + filtering display on desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#1512](https://github.com/GMOD/jbrowse-components/pull/1512) Fix setting + maxDisplayedBpPerPx for pileup display, helps prevent too large an area from + being rendered ([@cmdcolin](https://github.com/cmdcolin)) + - [#1442](https://github.com/GMOD/jbrowse-components/pull/1442) Change track + selector togglebutton to normal button + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1506](https://github.com/GMOD/jbrowse-components/pull/1506) Fix + horizontally flipped translation frames position + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1501](https://github.com/GMOD/jbrowse-components/pull/1501) Fix CLI to + allow jbrowse create to download newer monorepo tag format + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#1505](https://github.com/GMOD/jbrowse-components/pull/1505) Fix loading of local files in jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#1505](https://github.com/GMOD/jbrowse-components/pull/1505) Fix loading of + local files in jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 @@ -3286,51 +5045,107 @@ Broken releases missing some packages #### :rocket: Enhancement - Other - - [#1462](https://github.com/GMOD/jbrowse-components/pull/1462) Allow importing gzip and bgzip files in the spreadsheet and SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support for more bigBed subtypes and fallback for unsupported types ([@peterkxie](https://github.com/peterkxie)) - - [#1455](https://github.com/GMOD/jbrowse-components/pull/1455) Add the ability to use connection across refreshes in jbrowse-web using session connections ([@peterkxie](https://github.com/peterkxie)) - - [#1439](https://github.com/GMOD/jbrowse-components/pull/1439) 1381 improve assembly add form ([@elliothershberg](https://github.com/elliothershberg)) - - [#1433](https://github.com/GMOD/jbrowse-components/pull/1433) Make add track warning a bit more lenient ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1420](https://github.com/GMOD/jbrowse-components/pull/1420) Add the assembly manager feature to jbrowse-desktop ([@elliothershberg](https://github.com/elliothershberg)) + - [#1462](https://github.com/GMOD/jbrowse-components/pull/1462) Allow + importing gzip and bgzip files in the spreadsheet and SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support + for more bigBed subtypes and fallback for unsupported types + ([@peterkxie](https://github.com/peterkxie)) + - [#1455](https://github.com/GMOD/jbrowse-components/pull/1455) Add the + ability to use connection across refreshes in jbrowse-web using session + connections ([@peterkxie](https://github.com/peterkxie)) + - [#1439](https://github.com/GMOD/jbrowse-components/pull/1439) 1381 improve + assembly add form ([@elliothershberg](https://github.com/elliothershberg)) + - [#1433](https://github.com/GMOD/jbrowse-components/pull/1433) Make add track + warning a bit more lenient + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1420](https://github.com/GMOD/jbrowse-components/pull/1420) Add the + assembly manager feature to jbrowse-desktop + ([@elliothershberg](https://github.com/elliothershberg)) - `core` - - [#1458](https://github.com/GMOD/jbrowse-components/pull/1458) Add three frame translation to the sequence track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1453](https://github.com/GMOD/jbrowse-components/pull/1453) Change "Factory reset" to "Reset session" in jbrowse-web ([@teresam856](https://github.com/teresam856)) - - [#1441](https://github.com/GMOD/jbrowse-components/pull/1441) New icon for the track selector ([@cmdcolin](https://github.com/cmdcolin)) - - [#1438](https://github.com/GMOD/jbrowse-components/pull/1438) Improve assembly loading time by moving to main thread ([@cmdcolin](https://github.com/cmdcolin)) - - [#1434](https://github.com/GMOD/jbrowse-components/pull/1434) Create separate config schema for ReferenceSequenceTrack ([@elliothershberg](https://github.com/elliothershberg)) + - [#1458](https://github.com/GMOD/jbrowse-components/pull/1458) Add three + frame translation to the sequence track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1453](https://github.com/GMOD/jbrowse-components/pull/1453) Change + "Factory reset" to "Reset session" in jbrowse-web + ([@teresam856](https://github.com/teresam856)) + - [#1441](https://github.com/GMOD/jbrowse-components/pull/1441) New icon for + the track selector ([@cmdcolin](https://github.com/cmdcolin)) + - [#1438](https://github.com/GMOD/jbrowse-components/pull/1438) Improve + assembly loading time by moving to main thread + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1434](https://github.com/GMOD/jbrowse-components/pull/1434) Create + separate config schema for ReferenceSequenceTrack + ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - - [#1491](https://github.com/GMOD/jbrowse-components/pull/1491) Fix ability to add a PAF synteny track with add-track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1470](https://github.com/GMOD/jbrowse-components/pull/1470) Avoid rendering the literal string 'null' in the feature details ([@cmdcolin](https://github.com/cmdcolin)) + - [#1491](https://github.com/GMOD/jbrowse-components/pull/1491) Fix ability to + add a PAF synteny track with add-track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1470](https://github.com/GMOD/jbrowse-components/pull/1470) Avoid + rendering the literal string 'null' in the feature details + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1489](https://github.com/GMOD/jbrowse-components/pull/1489) Fix long read vs ref CIGAR rendering for horizontally flipped synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support for more bigBed subtypes and fallback for unsupported types ([@peterkxie](https://github.com/peterkxie)) - - [#1472](https://github.com/GMOD/jbrowse-components/pull/1472) Wait on assemblies that are being tracked by the assemblyManager only ([@cmdcolin](https://github.com/cmdcolin)) - - [#1466](https://github.com/GMOD/jbrowse-components/pull/1466) Avoid rendering the display and renderer settings in the about this track dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#1461](https://github.com/GMOD/jbrowse-components/pull/1461) Fix usage of jbrowse-cli on node 10.9 related to fs.promises ([@cmdcolin](https://github.com/cmdcolin)) - - [#1452](https://github.com/GMOD/jbrowse-components/pull/1452) Bug: search box disappears from LGV header on smaller widths ([@teresam856](https://github.com/teresam856)) - - [#1432](https://github.com/GMOD/jbrowse-components/pull/1432) Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web ([@teresam856](https://github.com/teresam856)) - - [#1431](https://github.com/GMOD/jbrowse-components/pull/1431) Fix connection tracks not showing up in track selector ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1428](https://github.com/GMOD/jbrowse-components/pull/1428) Fix the listVersions behavior of the jbrowse-cli returning duplicate entries ([@cmdcolin](https://github.com/cmdcolin)) - - [#1422](https://github.com/GMOD/jbrowse-components/pull/1422) Fix crash from empty ALT field in VCF ([@cmdcolin](https://github.com/cmdcolin)) - - [#1413](https://github.com/GMOD/jbrowse-components/pull/1413) Fix ability to add CRAM tracks using the web based add-track GUI ([@cmdcolin](https://github.com/cmdcolin)) + - [#1489](https://github.com/GMOD/jbrowse-components/pull/1489) Fix long read + vs ref CIGAR rendering for horizontally flipped synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support + for more bigBed subtypes and fallback for unsupported types + ([@peterkxie](https://github.com/peterkxie)) + - [#1472](https://github.com/GMOD/jbrowse-components/pull/1472) Wait on + assemblies that are being tracked by the assemblyManager only + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1466](https://github.com/GMOD/jbrowse-components/pull/1466) Avoid + rendering the display and renderer settings in the about this track dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1461](https://github.com/GMOD/jbrowse-components/pull/1461) Fix usage of + jbrowse-cli on node 10.9 related to fs.promises + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1452](https://github.com/GMOD/jbrowse-components/pull/1452) Bug: search + box disappears from LGV header on smaller widths + ([@teresam856](https://github.com/teresam856)) + - [#1432](https://github.com/GMOD/jbrowse-components/pull/1432) Make global + variables window.JBrowseSession and window.JBrowseRootModel available in + jbrowse-web ([@teresam856](https://github.com/teresam856)) + - [#1431](https://github.com/GMOD/jbrowse-components/pull/1431) Fix connection + tracks not showing up in track selector + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1428](https://github.com/GMOD/jbrowse-components/pull/1428) Fix the + listVersions behavior of the jbrowse-cli returning duplicate entries + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1422](https://github.com/GMOD/jbrowse-components/pull/1422) Fix crash from + empty ALT field in VCF ([@cmdcolin](https://github.com/cmdcolin)) + - [#1413](https://github.com/GMOD/jbrowse-components/pull/1413) Fix ability to + add CRAM tracks using the web based add-track GUI + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1435](https://github.com/GMOD/jbrowse-components/pull/1435) Updates to quickstart guides ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#1435](https://github.com/GMOD/jbrowse-components/pull/1435) Updates to + quickstart guides ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - Other - - [#1437](https://github.com/GMOD/jbrowse-components/pull/1437) Use lerna-changelog for changelog generation ([@cmdcolin](https://github.com/cmdcolin)) - - [#1465](https://github.com/GMOD/jbrowse-components/pull/1465) Establish minimum node version of 10.4 for using jbrowse-cli tools ([@cmdcolin](https://github.com/cmdcolin)) - - [#1454](https://github.com/GMOD/jbrowse-components/pull/1454) Fix GH workflow build ([@elliothershberg](https://github.com/elliothershberg)) - - [#1448](https://github.com/GMOD/jbrowse-components/pull/1448) Move building and testing from Travis to GitHub Workflow ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1450](https://github.com/GMOD/jbrowse-components/pull/1450) Fix website build ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1437](https://github.com/GMOD/jbrowse-components/pull/1437) Use + lerna-changelog for changelog generation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1465](https://github.com/GMOD/jbrowse-components/pull/1465) Establish + minimum node version of 10.4 for using jbrowse-cli tools + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1454](https://github.com/GMOD/jbrowse-components/pull/1454) Fix GH + workflow build ([@elliothershberg](https://github.com/elliothershberg)) + - [#1448](https://github.com/GMOD/jbrowse-components/pull/1448) Move building + and testing from Travis to GitHub Workflow + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1450](https://github.com/GMOD/jbrowse-components/pull/1450) Fix website + build ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#1468](https://github.com/GMOD/jbrowse-components/pull/1468) Have assembly manager get plugin manager from factory function args ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1468](https://github.com/GMOD/jbrowse-components/pull/1468) Have assembly + manager get plugin manager from factory function args + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 5 diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 50ec11bef9..84bc472f3d 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -5,9 +5,9 @@ In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body -size, disability, ethnicity, sex characteristics, gender identity and expression, -level of experience, education, socio-economic status, nationality, personal -appearance, race, religion, or sexual identity and orientation. +size, disability, ethnicity, sex characteristics, gender identity and +expression, level of experience, education, socio-economic status, nationality, +personal appearance, race, religion, or sexual identity and orientation. ## Our Standards @@ -37,11 +37,11 @@ Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. -Project maintainers have the right and responsibility to remove, edit, or -reject comments, commits, code, wiki edits, issues, and other contributions -that are not aligned to this Code of Conduct, or to ban temporarily or -permanently any contributor for other behaviors that they deem inappropriate, -threatening, offensive, or harmful. +Project maintainers have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, or to ban temporarily or permanently any +contributor for other behaviors that they deem inappropriate, threatening, +offensive, or harmful. ## Scope @@ -55,11 +55,12 @@ a project may be further defined and clarified by project maintainers. ## Enforcement Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported by contacting the project team at jbrowse-conduct@lists.berkeley.edu. All -complaints will be reviewed and investigated and will result in a response that -is deemed necessary and appropriate to the circumstances. The project team is -obligated to maintain confidentiality with regard to the reporter of an incident. -Further details of specific enforcement policies may be posted separately. +reported by contacting the project team at jbrowse-conduct@lists.berkeley.edu. +All complaints will be reviewed and investigated and will result in a response +that is deemed necessary and appropriate to the circumstances. The project team +is obligated to maintain confidentiality with regard to the reporter of an +incident. Further details of specific enforcement policies may be posted +separately. Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other @@ -67,8 +68,9 @@ members of the project's leadership. ## Attribution -This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, -available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 1.4, available at +https://www.contributor-covenant.org/version/1/4/code-of-conduct.html [homepage]: https://www.contributor-covenant.org diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 904f554648..87279238f3 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -41,8 +41,8 @@ yarn yarn start ``` -You can edit the markdown by hand. The documentation is built into a website -and a PDF using latex here http://jbrowse.org/jb2/jbrowse2.pdf +You can edit the markdown by hand. The documentation is built into a website and +a PDF using latex here http://jbrowse.org/jb2/jbrowse2.pdf ### Adding images to the docs @@ -55,8 +55,8 @@ line in the markdown Your caption of the image here ``` -This creates a caption of the image properly in the PDF, and just shows the -text below the image on the website +This creates a caption of the image properly in the PDF, and just shows the text +below the image on the website ## Developers @@ -78,21 +78,19 @@ script: need to generate an access token. - Make sure you have a GitHub access token with public_repo scope. To generate - one, go to https://github.com/settings/tokens, click "Generate new token," - add a note describing what you want the token to be for, select the - "public_repo" checkbox (under "repo"), and then click "Generate token." Make - sure to save this token in a safe place to use for future releases as you - won't be able to see it again. If you do lose your token, delete/revoke the - token you lost and generate a new one. + one, go to https://github.com/settings/tokens, click "Generate new token," add + a note describing what you want the token to be for, select the "public_repo" + checkbox (under "repo"), and then click "Generate token." Make sure to save + this token in a safe place to use for future releases as you won't be able to + see it again. If you do lose your token, delete/revoke the token you lost and + generate a new one. - Decide if the release should have a major, minor, or patch level version increase. All packages that are published will get the same version number. Run the script like this: -``` -scripts/release.sh myGitHubAuthToken versionIncreaseLevel -``` +`scripts/release.sh myGitHubAuthToken versionIncreaseLevel` If you don't provide `versionIncreaseLevel`, it will default to "patch". @@ -104,9 +102,9 @@ those to the release as well. Once the draft release has been created (you can look for it [here](https://github.com/GMOD/jbrowse-components/releases)), go to the release and click "Edit," then add a description to the release. Usually you can copy -the content of the blog post that was generated (it will be named something -like `website/blog/${DATE}-${RELEASE_TAG}-release.md`), removing the -"Downloads" section. +the content of the blog post that was generated (it will be named something like +`website/blog/${DATE}-${RELEASE_TAG}-release.md`), removing the "Downloads" +section. Note that it is very helpful to run the release from a computer with a stable and fast internet connection. One option for this is to run it from a AWS @@ -126,8 +124,8 @@ uploaded, the workflows will refuse to add them to the published release since it looks for draft releases) Finally, run the update_demos.sh script from within the demos folder of the -monorepo after the packages have been published. This will update the `demos` -to use the latest version, and then publish them to our S3 bucket e.g. at +monorepo after the packages have been published. This will update the `demos` to +use the latest version, and then publish them to our S3 bucket e.g. at https://jbrowse.org/demos/lgv ## Monorepo code organization @@ -179,10 +177,8 @@ This package provides the "alignments" related features including - BamAdapter - our BAM parser that wraps @gmod/bam NPM module - CramAdapter - our CRAM parser that wraps the @gmod/cram NPM module -- PileupTrack type - draws alignments as boxes in a "pileup" style view -- SNPCoverageTrack - draws calculated coverage with mismatches drawn over the coverage -- AlignmentsTrack - a "supertrack" which contains a PileupTrack and - SNPCoverageTrack "subtracks" +- AlignmentsTrack - a "supertrack" which contains a PileupDisplay and + SNPCoverageDisplay "subtracks" - AlignmentsFeatureWidget for alignments features #### plugins/variants/ @@ -192,8 +188,8 @@ Provides variant features including - VCF tabix parser - VCF non-tabix parser - VariantFeatureWidget -- VariantTrack that is basically just a normal track, but has logic to popup - the VariantFeatureWidget on feature click +- VariantTrack that is basically just a normal track, but has logic to popup the + VariantFeatureWidget on feature click #### plugins/hic @@ -231,8 +227,8 @@ General usage of this involves referencing the SvgFeatureRenderer #### plugins/spreadsheet-view -This provides a spreadsheet-in-the-browser that can be used as a data backend -to power other views +This provides a spreadsheet-in-the-browser that can be used as a data backend to +power other views #### plugins/circular-view @@ -278,8 +274,22 @@ jbrowse text-index -a hg19 --tracks ncbi_gff_hg19 --out config_demo.json --force ## Notes about monorepo setup -Our setup for the monorepo takes notes from the material-ui repository. Some particular notes include +Our setup for the monorepo takes notes from the material-ui repository. Some +particular notes include -1. The use of the "flat" packages/core package, where you can import from nested subpaths like '@jbrowse/core/util' +1. The use of the "flat" packages/core package, where you can import from nested + subpaths like '@jbrowse/core/util' 2. The use of tsconfig.build.json to generate types in the final release 3. The use of referring to the src directory at development time + +## Notes about yarn + +Using `yarn upgrade` or `yarn upgrade-interactive --latest` can produce errors +with the latest version of yarn. This is commonly cited around the web, but +using npx to one-off run an older version of yarn can fix this issues + +Example: + +``` +npx yarn@1.19.1 upgrade-interactive --latest +``` diff --git a/README.md b/README.md index e8d8c31bd6..7e08e22963 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build Status](https://img.shields.io/github/workflow/status/GMOD/jbrowse-components/Push/main?logo=github&style=for-the-badge)](https://github.com/GMOD/jbrowse-components/actions?query=branch%3Amain+workflow%3APush+) +[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/jbrowse-components/push.yml?branch=main&logo=github&style=for-the-badge)](https://github.com/GMOD/jbrowse-components/actions) [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/jbrowse-components/main.svg?logo=codecov&style=for-the-badge)](https://codecov.io/gh/GMOD/jbrowse-components/branch/main) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg?style=for-the-badge&logo=data:image/svg+xml;base64,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)](CODE_OF_CONDUCT.md) @@ -61,15 +61,19 @@ cd products/jbrowse-web yarn start ``` -For jbrowse-desktop +For jbrowse-desktop, launch two tabs ```sh +# starts webpack dev server cd products/jbrowse-desktop yarn start + +# starts electron window +cd products/jbrowse-desktop +yarn electron ``` -For running like jbrowse-react-linear-genome-view you can use -storybook +For running e.g. jbrowse-react-linear-genome-view you can use storybook ```sh cd products/jbrowse-react-linear-genome-view diff --git a/component_tests/cgv/README.md b/component_tests/cgv/README.md index bed3ed0f57..6e7caaf96b 100644 --- a/component_tests/cgv/README.md +++ b/component_tests/cgv/README.md @@ -1,6 +1,7 @@ # Demo of `@jbrowse/react-linear-genome-view` -This module uses "packed" builds of the repo, and runs an e2e test using cypress. +This module uses "packed" builds of the repo, and runs an e2e test using +cypress. It is most similar to a test that a user would get from installing the module from NPM. Note that these `packed` builds can be heavily cached by the yarn diff --git a/component_tests/cgv/package.json b/component_tests/cgv/package.json index 50db873c45..323149f1d6 100644 --- a/component_tests/cgv/package.json +++ b/component_tests/cgv/package.json @@ -1,5 +1,5 @@ { - "name": "jbrowse-react-circular-genome-view-demo", + "name": "jbrowse-react-circular-genome-view-demo-integration", "version": "0.1.0", "private": true, "dependencies": { @@ -27,10 +27,12 @@ "resolutions": { "@jbrowse/core": "file:./packed/jbrowse-core.tgz", "@jbrowse/plugin-alignments": "file:./packed/jbrowse-plugin-alignments.tgz", + "@jbrowse/plugin-authentication": "file:./packed/jbrowse-plugin-authentication.tgz", "@jbrowse/plugin-bed": "file:./packed/jbrowse-plugin-bed.tgz", "@jbrowse/plugin-circular-view": "file:./packed/jbrowse-plugin-circular-view.tgz", "@jbrowse/plugin-config": "file:./packed/jbrowse-plugin-config.tgz", "@jbrowse/plugin-data-management": "file:./packed/jbrowse-plugin-data-management.tgz", + "@jbrowse/plugin-gccontent": "file:./packed/jbrowse-plugin-gccontent.tgz", "@jbrowse/plugin-gff3": "file:./packed/jbrowse-plugin-gff3.tgz", "@jbrowse/plugin-linear-genome-view": "file:./packed/jbrowse-plugin-linear-genome-view.tgz", "@jbrowse/plugin-sequence": "file:./packed/jbrowse-plugin-sequence.tgz", diff --git a/component_tests/lgv/README.md b/component_tests/lgv/README.md index bed3ed0f57..6e7caaf96b 100644 --- a/component_tests/lgv/README.md +++ b/component_tests/lgv/README.md @@ -1,6 +1,7 @@ # Demo of `@jbrowse/react-linear-genome-view` -This module uses "packed" builds of the repo, and runs an e2e test using cypress. +This module uses "packed" builds of the repo, and runs an e2e test using +cypress. It is most similar to a test that a user would get from installing the module from NPM. Note that these `packed` builds can be heavily cached by the yarn diff --git a/component_tests/lgv/cypress/integration/basic.spec.ts b/component_tests/lgv/cypress/integration/basic.spec.ts index 460c79d69f..376075d1e6 100644 --- a/component_tests/lgv/cypress/integration/basic.spec.ts +++ b/component_tests/lgv/cypress/integration/basic.spec.ts @@ -1,5 +1,11 @@ describe('JBrowse embedded view', () => { it('page loads', () => { + Cypress.on( + // from https://github.com/cypress-io/cypress/issues/8418 + 'uncaught:exception', + // @ts-ignore thinks we are es5 and don't have includes, may be able to update + err => !err.message.includes('ResizeObserver loop limit exceeded'), + ) cy.visit('/') cy.contains('JBrowse 2 React Linear Genome View Demo') }) @@ -8,7 +14,7 @@ describe('JBrowse embedded view', () => { // eslint-disable-next-line testing-library/await-async-query,testing-library/prefer-screen-queries cy.findByTestId('Blockset-pileup', { timeout: 30000 }).findByTestId( - 'prerendered_canvas_{GRCh38}10:29,838,637..29,838,705-0_done', + 'prerendered_canvas_{GRCh38}10:29838637..29838705-0_done', { timeout: 30000 }, ) }) diff --git a/component_tests/lgv/package.json b/component_tests/lgv/package.json index 68325b3030..2ab049f467 100644 --- a/component_tests/lgv/package.json +++ b/component_tests/lgv/package.json @@ -1,5 +1,5 @@ { - "name": "jbrowse-react-linear-genome-view-demo", + "name": "jbrowse-react-linear-genome-view-demo-integration", "version": "0.1.0", "private": true, "dependencies": { @@ -12,8 +12,8 @@ "@testing-library/user-event": "^13.5.0", "@types/jest": "^27.4.1", "@types/node": "^16.11.26", - "@types/react": "^17.0.44", - "@types/react-dom": "^17.0.15", + "@types/react": "^18.0.0", + "@types/react-dom": "^18.0.0", "cypress": "^9.2.1", "node-polyfill-webpack-plugin": "^1.1.4", "react": "^17.0.0", @@ -27,10 +27,12 @@ "resolutions": { "@jbrowse/core": "file:./packed/jbrowse-core.tgz", "@jbrowse/plugin-alignments": "file:./packed/jbrowse-plugin-alignments.tgz", + "@jbrowse/plugin-authentication": "file:./packed/jbrowse-plugin-authentication.tgz", "@jbrowse/plugin-bed": "file:./packed/jbrowse-plugin-bed.tgz", "@jbrowse/plugin-circular-view": "file:./packed/jbrowse-plugin-circular-view.tgz", "@jbrowse/plugin-config": "file:./packed/jbrowse-plugin-config.tgz", "@jbrowse/plugin-data-management": "file:./packed/jbrowse-plugin-data-management.tgz", + "@jbrowse/plugin-gccontent": "file:./packed/jbrowse-plugin-gccontent.tgz", "@jbrowse/plugin-gff3": "file:./packed/jbrowse-plugin-gff3.tgz", "@jbrowse/plugin-linear-genome-view": "file:./packed/jbrowse-plugin-linear-genome-view.tgz", "@jbrowse/plugin-sequence": "file:./packed/jbrowse-plugin-sequence.tgz", diff --git a/component_tests/lgv/tsconfig.json b/component_tests/lgv/tsconfig.json index 9d379a3c4a..42c57d41a1 100644 --- a/component_tests/lgv/tsconfig.json +++ b/component_tests/lgv/tsconfig.json @@ -1,6 +1,6 @@ { "compilerOptions": { - "target": "es5", + "target": "es2018", "lib": ["dom", "dom.iterable", "esnext"], "allowJs": true, "skipLibCheck": true, diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/App.css b/demos/jbrowse-react-circular-genome-view-cra5/src/App.css deleted file mode 100644 index 74b5e05345..0000000000 --- a/demos/jbrowse-react-circular-genome-view-cra5/src/App.css +++ /dev/null @@ -1,38 +0,0 @@ -.App { - text-align: center; -} - -.App-logo { - height: 40vmin; - pointer-events: none; -} - -@media (prefers-reduced-motion: no-preference) { - .App-logo { - animation: App-logo-spin infinite 20s linear; - } -} - -.App-header { - background-color: #282c34; - min-height: 100vh; - display: flex; - flex-direction: column; - align-items: center; - justify-content: center; - font-size: calc(10px + 2vmin); - color: white; -} - -.App-link { - color: #61dafb; -} - -@keyframes App-logo-spin { - from { - transform: rotate(0deg); - } - to { - transform: rotate(360deg); - } -} diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/App.test.tsx b/demos/jbrowse-react-circular-genome-view-cra5/src/App.test.tsx deleted file mode 100644 index 3a7a8cc56f..0000000000 --- a/demos/jbrowse-react-circular-genome-view-cra5/src/App.test.tsx +++ /dev/null @@ -1,9 +0,0 @@ -import React from 'react' -import { render, screen } from '@testing-library/react' -import App from './App' - -test('renders learn react link', () => { - render() - const linkElement = screen.getByText(/learn react/i) - expect(linkElement).toBeInTheDocument() -}) diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/logo.svg b/demos/jbrowse-react-circular-genome-view-cra5/src/logo.svg deleted file mode 100644 index 9dfc1c058c..0000000000 --- a/demos/jbrowse-react-circular-genome-view-cra5/src/logo.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/setupTests.ts b/demos/jbrowse-react-circular-genome-view-cra5/src/setupTests.ts deleted file mode 100644 index 52aaef1d24..0000000000 --- a/demos/jbrowse-react-circular-genome-view-cra5/src/setupTests.ts +++ /dev/null @@ -1,5 +0,0 @@ -// jest-dom adds custom jest matchers for asserting on DOM nodes. -// allows you to do things like: -// expect(element).toHaveTextContent(/react/i) -// learn more: https://github.com/testing-library/jest-dom -import '@testing-library/jest-dom' diff --git a/demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js b/demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js deleted file mode 100644 index 7e6de068b4..0000000000 --- a/demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js +++ /dev/null @@ -1,52 +0,0 @@ -/* global JBrowseReactCircularGenomeView React, ReactDOM */ -import assembly from './assembly.js' -import tracks from './tracks.js' - -const { createViewState, JBrowseCircularGenomeView } = - JBrowseReactCircularGenomeView -const { createElement } = React -const { render } = ReactDOM - -const defaultSession = { - name: 'My session', - view: { - id: 'circularView', - type: 'CircularView', - bpPerPx: 5000000, - tracks: [ - { - id: 'uPdLKHik1', - type: 'VariantTrack', - configuration: 'pacbio_sv_vcf', - displays: [ - { - id: 'v9QVAR3oaB', - type: 'ChordVariantDisplay', - configuration: 'pacbio_sv_vcf-ChordVariantDisplay', - }, - ], - }, - ], - }, -} - -const updates = document.getElementById('update') -const state = new createViewState({ - assembly, - tracks, - defaultSession, - onChange: patch => { - updates.innerHTML += JSON.stringify(patch) + '\n' - }, -}) - -const textArea = document.getElementById('viewstate') -document.getElementById('showviewstate').addEventListener('click', () => { - textArea.innerHTML = JSON.stringify(state.session.view, undefined, 2) -}) - -const domContainer = document.getElementById('jbrowse_circular_genome_view') -render( - createElement(JBrowseCircularGenomeView, { viewState: state }), - domContainer, -) diff --git a/demos/jbrowse-react-circular-genome-view/src/App.test.tsx b/demos/jbrowse-react-circular-genome-view/src/App.test.tsx deleted file mode 100644 index 3a7a8cc56f..0000000000 --- a/demos/jbrowse-react-circular-genome-view/src/App.test.tsx +++ /dev/null @@ -1,9 +0,0 @@ -import React from 'react' -import { render, screen } from '@testing-library/react' -import App from './App' - -test('renders learn react link', () => { - render() - const linkElement = screen.getByText(/learn react/i) - expect(linkElement).toBeInTheDocument() -}) diff --git a/demos/jbrowse-react-circular-genome-view/src/setupTests.ts b/demos/jbrowse-react-circular-genome-view/src/setupTests.ts deleted file mode 100644 index 52aaef1d24..0000000000 --- a/demos/jbrowse-react-circular-genome-view/src/setupTests.ts +++ /dev/null @@ -1,5 +0,0 @@ -// jest-dom adds custom jest matchers for asserting on DOM nodes. -// allows you to do things like: -// expect(element).toHaveTextContent(/react/i) -// learn more: https://github.com/testing-library/jest-dom -import '@testing-library/jest-dom' diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/App.css b/demos/jbrowse-react-linear-genome-view-cra5/src/App.css deleted file mode 100644 index 74b5e05345..0000000000 --- a/demos/jbrowse-react-linear-genome-view-cra5/src/App.css +++ /dev/null @@ -1,38 +0,0 @@ -.App { - text-align: center; -} - -.App-logo { - height: 40vmin; - pointer-events: none; -} - -@media (prefers-reduced-motion: no-preference) { - .App-logo { - animation: App-logo-spin infinite 20s linear; - } -} - -.App-header { - background-color: #282c34; - min-height: 100vh; - display: flex; - flex-direction: column; - align-items: center; - justify-content: center; - font-size: calc(10px + 2vmin); - color: white; -} - -.App-link { - color: #61dafb; -} - -@keyframes App-logo-spin { - from { - transform: rotate(0deg); - } - to { - transform: rotate(360deg); - } -} diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/App.test.tsx b/demos/jbrowse-react-linear-genome-view-cra5/src/App.test.tsx deleted file mode 100644 index 3a7a8cc56f..0000000000 --- a/demos/jbrowse-react-linear-genome-view-cra5/src/App.test.tsx +++ /dev/null @@ -1,9 +0,0 @@ -import React from 'react' -import { render, screen } from '@testing-library/react' -import App from './App' - -test('renders learn react link', () => { - render() - const linkElement = screen.getByText(/learn react/i) - expect(linkElement).toBeInTheDocument() -}) diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/logo.svg b/demos/jbrowse-react-linear-genome-view-cra5/src/logo.svg deleted file mode 100644 index 9dfc1c058c..0000000000 --- a/demos/jbrowse-react-linear-genome-view-cra5/src/logo.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/setupTests.ts b/demos/jbrowse-react-linear-genome-view-cra5/src/setupTests.ts deleted file mode 100644 index 52aaef1d24..0000000000 --- a/demos/jbrowse-react-linear-genome-view-cra5/src/setupTests.ts +++ /dev/null @@ -1,5 +0,0 @@ -// jest-dom adds custom jest matchers for asserting on DOM nodes. -// allows you to do things like: -// expect(element).toHaveTextContent(/react/i) -// learn more: https://github.com/testing-library/jest-dom -import '@testing-library/jest-dom' diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/yarn.lock b/demos/jbrowse-react-linear-genome-view-nextjs/yarn.lock deleted file mode 100644 index f884af0d1b..0000000000 --- a/demos/jbrowse-react-linear-genome-view-nextjs/yarn.lock +++ /dev/null @@ -1,1709 +0,0 @@ -# THIS IS AN AUTOGENERATED FILE. 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name: 'GRCh38', - sequence: { - type: 'ReferenceSequenceTrack', - trackId: 'GRCh38-ReferenceSequenceTrack', - adapter: { - type: 'BgzipFastaAdapter', - fastaLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz', - locationType: 'UriLocation', - }, - faiLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai', - locationType: 'UriLocation', - }, - gziLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi', - locationType: 'UriLocation', - }, - }, - }, - aliases: ['hg38'], - refNameAliases: { - adapter: { - type: 'RefNameAliasAdapter', - location: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt', - locationType: 'UriLocation', - }, - }, - }, -} diff --git a/demos/jbrowse-react-linear-genome-view-vanillajs/genomeView.js b/demos/jbrowse-react-linear-genome-view-vanillajs/genomeView.js deleted file mode 100644 index cb5646bed6..0000000000 --- a/demos/jbrowse-react-linear-genome-view-vanillajs/genomeView.js +++ /dev/null @@ -1,96 +0,0 @@ -/* global JBrowseReactLinearGenomeView React, ReactDOM */ -import assembly from './assembly.js' -import tracks from './tracks.js' - -const { createViewState, JBrowseLinearGenomeView } = - JBrowseReactLinearGenomeView - -const updates = document.getElementById('update') - -const defaultSession = { - name: 'this session', - view: { - id: 'linearGenomeView', - type: 'LinearGenomeView', - tracks: [ - { - id: '7PWx6ki1_', - type: 'ReferenceSequenceTrack', - configuration: 'GRCh38-ReferenceSequenceTrack', - displays: [ - { - id: 'pa_7lx6FDh', - type: 'LinearReferenceSequenceDisplay', - height: 210, - configuration: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - }, - ], - }, - { - id: 'KHwe41KXk', - type: 'AlignmentsTrack', - configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', - displays: [ - { - id: '_-kwYVczT8', - type: 'LinearAlignmentsDisplay', - PileupDisplay: { - id: '1HTk32IDZJ', - type: 'LinearPileupDisplay', - height: 100, - configuration: { - type: 'LinearPileupDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_pileup_xyz', - }, - }, - SNPCoverageDisplay: { - id: 'ZBXRXmuDrc', - type: 'LinearSNPCoverageDisplay', - height: 45, - configuration: { - type: 'LinearSNPCoverageDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', - }, - }, - configuration: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', - height: 250, - }, - ], - }, - ], - }, -} -const state = new createViewState({ - assembly, - tracks, - location: '1:100,987,269..100,987,368', - defaultSession, - onChange: patch => { - updates.innerHTML += JSON.stringify(patch) + '\n' - }, -}) - -function navTo(event) { - state.session.view.navToLocString(event.target.dataset.location) -} -const buttons = document.getElementsByTagName('button') -for (const button of buttons) { - if (button.dataset.type === 'gene_button') { - button.addEventListener('click', navTo) - } -} - -const textArea = document.getElementById('viewstate') -document.getElementById('showviewstate').addEventListener('click', () => { - textArea.innerHTML = JSON.stringify(state.session.view, undefined, 2) -}) - -const domContainer = document.getElementById('jbrowse_linear_genome_view') -ReactDOM.render( - React.createElement(JBrowseLinearGenomeView, { viewState: state }), - domContainer, -) diff --git a/demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js b/demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js deleted file mode 100644 index bf72d97944..0000000000 --- a/demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js +++ /dev/null @@ -1,82 +0,0 @@ -export default [ - { - type: 'BasicTrack', - trackId: - 'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff', - name: 'NCBI RefSeq Genes', - category: ['Genes'], - assemblyNames: ['GRCh38'], - adapter: { - type: 'Gff3TabixAdapter', - gffGzLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz', - locationType: 'UriLocation', - }, - index: { - location: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.tbi', - locationType: 'UriLocation', - }, - indexType: 'TBI', - }, - }, - renderer: { - type: 'SvgFeatureRenderer', - }, - }, - { - type: 'AlignmentsTrack', - trackId: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', - name: 'NA12878 Exome', - category: ['1000 Genomes', 'Alignments'], - assemblyNames: ['GRCh38'], - adapter: { - type: 'CramAdapter', - cramLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram', - locationType: 'UriLocation', - }, - craiLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai', - locationType: 'UriLocation', - }, - sequenceAdapter: { - type: 'BgzipFastaAdapter', - fastaLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz', - locationType: 'UriLocation', - }, - faiLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai', - locationType: 'UriLocation', - }, - gziLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi', - locationType: 'UriLocation', - }, - }, - }, - }, - { - type: 'VariantTrack', - trackId: - 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', - name: '1000 Genomes Variant Calls', - category: ['1000 Genomes', 'Variants'], - assemblyNames: ['GRCh38'], - adapter: { - type: 'VcfTabixAdapter', - vcfGzLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz', - locationType: 'UriLocation', - }, - index: { - location: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz.tbi', - locationType: 'UriLocation', - }, - indexType: 'TBI', - }, - }, - }, -] diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/App.css b/demos/jbrowse-react-linear-genome-view-vite/src/App.css deleted file mode 100644 index 8da3fde63d..0000000000 --- a/demos/jbrowse-react-linear-genome-view-vite/src/App.css +++ /dev/null @@ -1,42 +0,0 @@ -.App { - text-align: center; -} - -.App-logo { - height: 40vmin; - pointer-events: none; -} - -@media (prefers-reduced-motion: no-preference) { - .App-logo { - animation: App-logo-spin infinite 20s linear; - } -} - -.App-header { - background-color: #282c34; - min-height: 100vh; - display: flex; - flex-direction: column; - align-items: center; - justify-content: center; - font-size: calc(10px + 2vmin); - color: white; -} - -.App-link { - color: #61dafb; -} - -@keyframes App-logo-spin { - from { - transform: rotate(0deg); - } - to { - transform: rotate(360deg); - } -} - -button { - font-size: calc(10px + 2vmin); -} diff --git a/demos/jbrowse-react-linear-genome-view/src/App.test.tsx b/demos/jbrowse-react-linear-genome-view/src/App.test.tsx deleted file mode 100644 index 3a7a8cc56f..0000000000 --- a/demos/jbrowse-react-linear-genome-view/src/App.test.tsx +++ /dev/null @@ -1,9 +0,0 @@ -import React from 'react' -import { render, screen } from '@testing-library/react' -import App from './App' - -test('renders learn react link', () => { - render() - const linkElement = screen.getByText(/learn react/i) - expect(linkElement).toBeInTheDocument() -}) diff --git a/demos/jbrowse-react-linear-genome-view/src/setupTests.ts b/demos/jbrowse-react-linear-genome-view/src/setupTests.ts deleted file mode 100644 index 52aaef1d24..0000000000 --- a/demos/jbrowse-react-linear-genome-view/src/setupTests.ts +++ /dev/null @@ -1,5 +0,0 @@ -// jest-dom adds custom jest matchers for asserting on DOM nodes. -// allows you to do things like: -// expect(element).toHaveTextContent(/react/i) -// learn more: https://github.com/testing-library/jest-dom -import '@testing-library/jest-dom' diff --git a/docs/README.md b/docs/README.md index a257df2aa7..f892acf727 100644 --- a/docs/README.md +++ b/docs/README.md @@ -34,7 +34,8 @@ and */ ``` -it is not able to document a single variable, so in some places, a dummy function is put below the `#config/#stateModel` comments +it is not able to document a single variable, so in some places, a dummy +function is put below the `#config/#stateModel` comments ``` function x(){} diff --git a/docs/generateConfigDocs.ts b/docs/generateConfigDocs.ts index 40a2f191ef..58e441c032 100644 --- a/docs/generateConfigDocs.ts +++ b/docs/generateConfigDocs.ts @@ -38,8 +38,9 @@ async function generateConfigDocs(files: string[]) { }) } +// eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { - generateConfigDocs(await getAllFiles()) + await generateConfigDocs(await getAllFiles()) Object.values(contents).forEach(({ config, slots, id, derives }) => { if (config) { @@ -96,7 +97,7 @@ ${idstr} ${slotstr} ${derivesstr} - + `, ) } diff --git a/docs/generateStateModelDocs.ts b/docs/generateStateModelDocs.ts index 18de7619e4..52876908a6 100644 --- a/docs/generateStateModelDocs.ts +++ b/docs/generateStateModelDocs.ts @@ -43,6 +43,7 @@ function generateStateModelDocs(files: string[]) { }) } +// eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { generateStateModelDocs(await getAllFiles()) @@ -146,7 +147,7 @@ ${getterstr} ${methodstr} ${actionstr} - + `, ) } diff --git a/embedded_demos/README.md b/embedded_demos/README.md new file mode 100644 index 0000000000..985858d858 --- /dev/null +++ b/embedded_demos/README.md @@ -0,0 +1,22 @@ +# JBrowse 2 embedded demos + +## Linear genome view demo + +This demo shows a variety of tracks on hg38 + +The text searching index created by running `jbrowse text-index` on the specific +gene track file. This uses the --fileId to say what the trackId is of the file +we are indexing with --file + +```bash +## create index +jbrowse text-index --file https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz --fileId genes + +## upload to aws +aws s3 sync trix s3://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix --delete + +``` + +## Circular genome view demo + +This demo shows translocations SVs diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/assembly.ts b/embedded_demos/base/circular/assembly.ts similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/src/assembly.ts rename to embedded_demos/base/circular/assembly.ts diff --git a/embedded_demos/base/circular/defaultSession.ts b/embedded_demos/base/circular/defaultSession.ts new file mode 100644 index 0000000000..582c6b2e64 --- /dev/null +++ b/embedded_demos/base/circular/defaultSession.ts @@ -0,0 +1,22 @@ +export default { + name: 'My session', + view: { + id: 'circularView', + type: 'CircularView', + bpPerPx: 5000000, + tracks: [ + { + id: 'uPdLKHik1', + type: 'VariantTrack', + configuration: 'pacbio_sv_vcf', + displays: [ + { + id: 'v9QVAR3oaB', + type: 'ChordVariantDisplay', + configuration: 'pacbio_sv_vcf-ChordVariantDisplay', + }, + ], + }, + ], + }, +} diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/tracks.ts b/embedded_demos/base/circular/tracks.ts similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/src/tracks.ts rename to embedded_demos/base/circular/tracks.ts diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts b/embedded_demos/base/linear/assembly.ts similarity index 75% rename from demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts rename to embedded_demos/base/linear/assembly.ts index 5c26ea9164..af9f6755d9 100644 --- a/demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts +++ b/embedded_demos/base/linear/assembly.ts @@ -16,16 +16,6 @@ const assembly = { uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', }, }, - displays: [ - { - type: 'LinearReferenceSequenceDisplay', - displayId: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - renderer: { - type: 'DivSequenceRenderer', - }, - }, - ], }, refNameAliases: { adapter: { diff --git a/embedded_demos/base/linear/defaultSession.ts b/embedded_demos/base/linear/defaultSession.ts new file mode 100644 index 0000000000..d9e0281ccc --- /dev/null +++ b/embedded_demos/base/linear/defaultSession.ts @@ -0,0 +1,130 @@ +export default { + name: 'this session', + margin: 0, + view: { + id: 'linearGenomeView', + minimized: false, + type: 'LinearGenomeView', + offsetPx: 191980240, + bpPerPx: 0.1554251851851852, + displayedRegions: [ + { + refName: '10', + start: 0, + end: 133797422, + reversed: false, + assemblyName: 'GRCh38', + }, + ], + tracks: [ + { + id: '4aZAiE-A3', + type: 'ReferenceSequenceTrack', + configuration: 'GRCh38-ReferenceSequenceTrack', + minimized: false, + displays: [ + { + id: 'AD3gqvG0_6', + type: 'LinearReferenceSequenceDisplay', + height: 180, + configuration: + 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', + showForward: true, + showReverse: true, + showTranslation: true, + }, + ], + }, + { + id: 'T6uhrtY40O', + type: 'AlignmentsTrack', + configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + minimized: false, + displays: [ + { + id: 'FinKswChSr', + type: 'LinearAlignmentsDisplay', + PileupDisplay: { + id: 'YAAaF494z', + type: 'LinearPileupDisplay', + height: 134, + configuration: { + type: 'LinearPileupDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz', + }, + showSoftClipping: false, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + SNPCoverageDisplay: { + id: 'VTQ_VGbAVJ', + type: 'LinearSNPCoverageDisplay', + height: 45, + configuration: { + type: 'LinearSNPCoverageDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', + }, + selectedRendering: '', + resolution: 1, + constraints: {}, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + snpCovHeight: 45, + configuration: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', + height: 179, + lowerPanelType: 'LinearPileupDisplay', + }, + ], + }, + { + id: 'EUnTnpVI6', + type: 'QuantitativeTrack', + configuration: 'hg38.100way.phyloP100way', + minimized: false, + displays: [ + { + id: 'mrlawr9Wtg', + type: 'LinearWiggleDisplay', + height: 100, + configuration: 'hg38.100way.phyloP100way-LinearWiggleDisplay', + selectedRendering: '', + resolution: 1, + constraints: {}, + }, + ], + }, + { + id: 'Cbnwl72EX', + type: 'VariantTrack', + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + minimized: false, + displays: [ + { + id: 'dvXz01Wf6w', + type: 'LinearVariantDisplay', + height: 100, + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay', + }, + ], + }, + ], + hideHeader: false, + hideHeaderOverview: false, + hideNoTracksActive: false, + trackSelectorType: 'hierarchical', + trackLabels: 'overlapping', + showCenterLine: false, + showCytobandsSetting: true, + showGridlines: true, + }, +} diff --git a/demos/jbrowse-react-linear-genome-view/src/tracks.ts b/embedded_demos/base/linear/tracks.ts similarity index 79% rename from demos/jbrowse-react-linear-genome-view/src/tracks.ts rename to embedded_demos/base/linear/tracks.ts index fb3435d769..fb6422b271 100644 --- a/demos/jbrowse-react-linear-genome-view/src/tracks.ts +++ b/embedded_demos/base/linear/tracks.ts @@ -1,8 +1,7 @@ const tracks = [ { - type: 'BasicTrack', - trackId: - 'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff', + type: 'FeatureTrack', + trackId: 'genes', name: 'NCBI RefSeq Genes', assemblyNames: ['GRCh38'], category: ['Genes'], @@ -17,6 +16,36 @@ const tracks = [ }, }, }, + textSearching: { + textSearchAdapter: { + type: 'TrixTextSearchAdapter', + textSearchAdapterId: 'gff3tabix_genes-index', + ixFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix', + }, + ixxFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx', + }, + metaFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json', + }, + assemblyNames: ['GRCh38'], + }, + }, + }, + { + type: 'FeatureTrack', + trackId: 'repeats_hg38', + name: 'Repeats', + assemblyNames: ['hg38'], + category: ['Annotation'], + adapter: { + type: 'BigBedAdapter', + bigBedLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb', + locationType: 'UriLocation', + }, + }, }, { type: 'AlignmentsTrack', @@ -46,21 +75,6 @@ const tracks = [ }, }, }, - - { - type: 'FeatureTrack', - trackId: 'repeats_hg38', - name: 'Repeats', - assemblyNames: ['hg38'], - category: ['Annotation'], - adapter: { - type: 'BigBedAdapter', - bigBedLocation: { - uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb', - locationType: 'UriLocation', - }, - }, - }, { type: 'VariantTrack', trackId: diff --git a/embedded_demos/build_demos.sh b/embedded_demos/build_demos.sh new file mode 100755 index 0000000000..d53c804f0b --- /dev/null +++ b/embedded_demos/build_demos.sh @@ -0,0 +1,2 @@ +#!/bin/bash +for i in jbrowse*; do cd $i; yarn; yarn build; cd -; done; diff --git a/embedded_demos/copy_files.sh b/embedded_demos/copy_files.sh new file mode 100755 index 0000000000..1544ed1fbe --- /dev/null +++ b/embedded_demos/copy_files.sh @@ -0,0 +1,30 @@ +#!/bin/bash +## linear +cp base/linear/assembly.ts jbrowse-react-linear-genome-view/src/ +cp base/linear/assembly.ts jbrowse-react-linear-genome-view-cra5/src/ +cp base/linear/assembly.ts jbrowse-react-linear-genome-view-vite/src/ +cp base/linear/assembly.ts jbrowse-react-linear-genome-view-nextjs/utils/ +cp base/linear/assembly.ts jbrowse-react-linear-genome-view-vanillajs/assembly.js +cp base/linear/tracks.ts jbrowse-react-linear-genome-view/src/ +cp base/linear/tracks.ts jbrowse-react-linear-genome-view-cra5/src/ +cp base/linear/tracks.ts jbrowse-react-linear-genome-view-vite/src/ +cp base/linear/tracks.ts jbrowse-react-linear-genome-view-nextjs/utils/ +cp base/linear/tracks.ts jbrowse-react-linear-genome-view-vanillajs/tracks.js +cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view/src/ +cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-cra5/src/ +cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-vite/src/ +cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-nextjs/utils/ +cp base/linear/defaultSession.ts jbrowse-react-linear-genome-view-vanillajs/defaultSession.js + + + +## circular +cp base/circular/assembly.ts jbrowse-react-circular-genome-view/src/ +cp base/circular/assembly.ts jbrowse-react-circular-genome-view-cra5/src/ +cp base/circular/assembly.ts jbrowse-react-circular-genome-view-vanillajs/assembly.js +cp base/circular/tracks.ts jbrowse-react-circular-genome-view/src/ +cp base/circular/tracks.ts jbrowse-react-circular-genome-view-cra5/src/ +cp base/circular/tracks.ts jbrowse-react-circular-genome-view-vanillajs/tracks.js +cp base/circular/defaultSession.ts jbrowse-react-circular-genome-view/src/ +cp base/circular/defaultSession.ts jbrowse-react-circular-genome-view-cra5/src/ +cp base/circular/defaultSession.ts jbrowse-react-circular-genome-view-vanillajs/defaultSession.js diff --git a/demos/deploy_demos.sh b/embedded_demos/deploy_demos.sh similarity index 100% rename from demos/deploy_demos.sh rename to embedded_demos/deploy_demos.sh diff --git a/demos/jbrowse-react-circular-genome-view-cra5/.gitignore b/embedded_demos/jbrowse-react-circular-genome-view-cra5/.gitignore similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/.gitignore rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/.gitignore diff --git a/demos/jbrowse-react-circular-genome-view-cra5/README.md b/embedded_demos/jbrowse-react-circular-genome-view-cra5/README.md similarity index 63% rename from demos/jbrowse-react-circular-genome-view-cra5/README.md rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/README.md index 2a1ba95801..4e9f2e7a90 100644 --- a/demos/jbrowse-react-circular-genome-view-cra5/README.md +++ b/embedded_demos/jbrowse-react-circular-genome-view-cra5/README.md @@ -1,14 +1,17 @@ # jbrowse-react-circular-genome-view-cra5 -This is a demo of using the circular genome view with create-react-app v5 (which uses webpack 5) +This is a demo of using the circular genome view with create-react-app v5 (which +uses webpack 5) -It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill, etc) +It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill, +etc) # Demo of `@jbrowse/react-circular-genome-view` with CRA 5 See this app running at https://jbrowse.org/demos/cgv-cra5/. -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-cra5 +Download this directory from the monorepo using +https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-circular-genome-view-cra5 ## Usage diff --git a/demos/jbrowse-react-circular-genome-view-cra5/craco.config.js b/embedded_demos/jbrowse-react-circular-genome-view-cra5/craco.config.js similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/craco.config.js rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/craco.config.js diff --git a/demos/jbrowse-react-circular-genome-view-cra5/package.json b/embedded_demos/jbrowse-react-circular-genome-view-cra5/package.json similarity index 91% rename from demos/jbrowse-react-circular-genome-view-cra5/package.json rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/package.json index 70aa9fe224..c1740ec5d9 100644 --- a/demos/jbrowse-react-circular-genome-view-cra5/package.json +++ b/embedded_demos/jbrowse-react-circular-genome-view-cra5/package.json @@ -1,12 +1,13 @@ { "name": "jbrowse-react-circular-genome-view-cra5", "version": "0.1.0", + "license": "MIT", "private": true, "dependencies": { "@craco/craco": "^6.4.3", "@fontsource/roboto": "^4.5.5", - "@jbrowse/plugin-linear-genome-view": "^2.0.0", - "@jbrowse/react-circular-genome-view": "^2.0.0", + "@jbrowse/plugin-linear-genome-view": "^2.2.0", + "@jbrowse/react-circular-genome-view": "^2.2.0", "@testing-library/jest-dom": "^5.16.4", "@testing-library/react": "^12.1.4", "@testing-library/user-event": "^13.5.0", diff --git a/demos/jbrowse-react-circular-genome-view-cra5/public/favicon.ico b/embedded_demos/jbrowse-react-circular-genome-view-cra5/public/favicon.ico similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/public/favicon.ico rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/public/favicon.ico diff --git a/demos/jbrowse-react-circular-genome-view-cra5/public/index.html b/embedded_demos/jbrowse-react-circular-genome-view-cra5/public/index.html similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/public/index.html rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/public/index.html diff --git a/demos/jbrowse-react-circular-genome-view-cra5/public/logo192.png b/embedded_demos/jbrowse-react-circular-genome-view-cra5/public/logo192.png similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/public/logo192.png rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/public/logo192.png diff --git a/demos/jbrowse-react-circular-genome-view-cra5/public/logo512.png b/embedded_demos/jbrowse-react-circular-genome-view-cra5/public/logo512.png similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/public/logo512.png rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/public/logo512.png diff --git a/demos/jbrowse-react-circular-genome-view-cra5/public/manifest.json b/embedded_demos/jbrowse-react-circular-genome-view-cra5/public/manifest.json similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/public/manifest.json rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/public/manifest.json diff --git a/demos/jbrowse-react-circular-genome-view-cra5/public/robots.txt b/embedded_demos/jbrowse-react-circular-genome-view-cra5/public/robots.txt similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/public/robots.txt rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/public/robots.txt diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx similarity index 80% rename from demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx index 6f8239812f..44bebed5cb 100644 --- a/demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx +++ b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/App.tsx @@ -7,33 +7,12 @@ import { import assembly from './assembly' import tracks from './tracks' +import defaultSession from './defaultSession' -const defaultSession = { - name: 'My session', - view: { - id: 'circularView', - type: 'CircularView', - bpPerPx: 5000000, - tracks: [ - { - id: 'uPdLKHik1', - type: 'VariantTrack', - configuration: 'pacbio_sv_vcf', - displays: [ - { - id: 'v9QVAR3oaB', - type: 'ChordVariantDisplay', - configuration: 'pacbio_sv_vcf-ChordVariantDisplay', - }, - ], - }, - ], - }, -} +type ViewModel = ReturnType function View() { - const [viewState, setViewState] = - useState>() + const [viewState, setViewState] = useState() const [patches, setPatches] = useState('') const [stateSnapshot, setStateSnapshot] = useState('') @@ -63,11 +42,11 @@ function View() {

The code for this app is available at{' '} - https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view-cra5 + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view-cra5 .

diff --git a/demos/jbrowse-react-circular-genome-view/src/assembly.ts b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/assembly.ts similarity index 100% rename from demos/jbrowse-react-circular-genome-view/src/assembly.ts rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/src/assembly.ts diff --git a/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/defaultSession.ts b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/defaultSession.ts new file mode 100644 index 0000000000..582c6b2e64 --- /dev/null +++ b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/defaultSession.ts @@ -0,0 +1,22 @@ +export default { + name: 'My session', + view: { + id: 'circularView', + type: 'CircularView', + bpPerPx: 5000000, + tracks: [ + { + id: 'uPdLKHik1', + type: 'VariantTrack', + configuration: 'pacbio_sv_vcf', + displays: [ + { + id: 'v9QVAR3oaB', + type: 'ChordVariantDisplay', + configuration: 'pacbio_sv_vcf-ChordVariantDisplay', + }, + ], + }, + ], + }, +} diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/index.css b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/index.css similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/src/index.css rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/src/index.css diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/index.tsx b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/index.tsx similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/src/index.tsx rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/src/index.tsx diff --git a/demos/jbrowse-react-circular-genome-view-cra5/src/react-app-env.d.ts b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/react-app-env.d.ts similarity index 100% rename from demos/jbrowse-react-circular-genome-view-cra5/src/react-app-env.d.ts rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/src/react-app-env.d.ts diff --git a/demos/jbrowse-react-circular-genome-view/src/tracks.ts b/embedded_demos/jbrowse-react-circular-genome-view-cra5/src/tracks.ts similarity index 100% rename from demos/jbrowse-react-circular-genome-view/src/tracks.ts rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/src/tracks.ts diff --git a/demos/jbrowse-react-circular-genome-view-cra5/tsconfig.json b/embedded_demos/jbrowse-react-circular-genome-view-cra5/tsconfig.json similarity index 95% rename from demos/jbrowse-react-circular-genome-view-cra5/tsconfig.json rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/tsconfig.json index 9d379a3c4a..42c57d41a1 100644 --- a/demos/jbrowse-react-circular-genome-view-cra5/tsconfig.json +++ b/embedded_demos/jbrowse-react-circular-genome-view-cra5/tsconfig.json @@ -1,6 +1,6 @@ { "compilerOptions": { - "target": "es5", + "target": "es2018", "lib": ["dom", "dom.iterable", "esnext"], "allowJs": true, "skipLibCheck": true, diff --git a/demos/jbrowse-react-circular-genome-view-cra5/yarn.lock b/embedded_demos/jbrowse-react-circular-genome-view-cra5/yarn.lock similarity index 88% rename from demos/jbrowse-react-circular-genome-view-cra5/yarn.lock rename to embedded_demos/jbrowse-react-circular-genome-view-cra5/yarn.lock index 31cb08e604..6419ad3352 100644 --- a/demos/jbrowse-react-circular-genome-view-cra5/yarn.lock +++ b/embedded_demos/jbrowse-react-circular-genome-view-cra5/yarn.lock @@ -31,26 +31,26 @@ dependencies: "@babel/highlight" "^7.18.6" -"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.19.3", "@babel/compat-data@^7.19.4": - version "7.19.4" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.19.4.tgz#95c86de137bf0317f3a570e1b6e996b427299747" - integrity sha512-CHIGpJcUQ5lU9KrPHTjBMhVwQG6CQjxfg36fGXl3qk/Gik1WwWachaXFuo0uCWJT/mStOKtcbFJCaVLihC1CMw== +"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.20.0", "@babel/compat-data@^7.20.1": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.20.5.tgz#86f172690b093373a933223b4745deeb6049e733" + integrity sha512-KZXo2t10+/jxmkhNXc7pZTqRvSOIvVv/+lJwHS+B2rErwOyjuVRh60yVpb7liQ1U5t7lLJ1bz+t8tSypUZdm0g== "@babel/core@^7.1.0", "@babel/core@^7.11.1", "@babel/core@^7.12.3", "@babel/core@^7.16.0", "@babel/core@^7.7.2", "@babel/core@^7.8.0": - 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version "7.19.5" - resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.19.5.tgz#da3f4b301c8086717eee9cab14da91b1fa5dcca7" - integrity sha512-DxbNz9Lz4aMZ99qPpO1raTbcrI1ZeYh+9NR9qhfkQIbFtVEqotHojEBxHzmxhVONkGt6VyrqVQcgpefMy9pqcg== +"@babel/generator@^7.20.5", "@babel/generator@^7.7.2": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.20.5.tgz#cb25abee3178adf58d6814b68517c62bdbfdda95" + integrity sha512-jl7JY2Ykn9S0yj4DQP82sYvPU+T3g0HFcWTqDLqiuA9tGRNIj9VfbtXGAYTTkyNEnQk1jkMGOdYka8aG/lulCA== dependencies: - "@babel/types" "^7.19.4" + "@babel/types" "^7.20.5" "@jridgewell/gen-mapping" "^0.3.2" jsesc "^2.5.1" @@ -90,36 +90,36 @@ "@babel/helper-explode-assignable-expression" "^7.18.6" "@babel/types" "^7.18.9" -"@babel/helper-compilation-targets@^7.17.7", "@babel/helper-compilation-targets@^7.18.9", "@babel/helper-compilation-targets@^7.19.0", "@babel/helper-compilation-targets@^7.19.3": - version "7.19.3" - resolved "https://registry.yarnpkg.com/@babel/helper-compilation-targets/-/helper-compilation-targets-7.19.3.tgz#a10a04588125675d7c7ae299af86fa1b2ee038ca" - 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version "3.25.5" - resolved "https://registry.yarnpkg.com/core-js/-/core-js-3.25.5.tgz#e86f651a2ca8a0237a5f064c2fe56cef89646e27" - integrity sha512-nbm6eZSjm+ZuBQxCUPQKQCoUEfFOXjUZ8dTTyikyKaWrTYmAVbykQfwsKE5dBK88u3QCkCrzsx/PPlKfhsvgpw== + version "3.26.1" + resolved "https://registry.yarnpkg.com/core-js/-/core-js-3.26.1.tgz#7a9816dabd9ee846c1c0fe0e8fcad68f3709134e" + integrity sha512-21491RRQVzUn0GGM9Z1Jrpr6PNPxPi+Za8OM9q4tksTSnlbXXGKK1nXNg/QvwFYettXvSX6zWKCtHHfjN4puyA== core-util-is@~1.0.0: version "1.0.3" @@ -3991,9 +4005,9 @@ cosmiconfig@^6.0.0: yaml "^1.7.2" cosmiconfig@^7, cosmiconfig@^7.0.0, cosmiconfig@^7.0.1: - version "7.0.1" - resolved "https://registry.yarnpkg.com/cosmiconfig/-/cosmiconfig-7.0.1.tgz#714d756522cace867867ccb4474c5d01bbae5d6d" - integrity sha512-a1YWNUV2HwGimB7dU2s1wUMurNKjpx60HxBB6xUM8Re+2s1g1IIfJvFR0/iCF+XHdE0GMTKTuLR32UQff4TEyQ== + version "7.1.0" + resolved "https://registry.yarnpkg.com/cosmiconfig/-/cosmiconfig-7.1.0.tgz#1443b9afa596b670082ea46cbd8f6a62b84635f6" + integrity sha512-AdmX6xUzdNASswsFtmwSt7Vj8po9IuqXm0UXz7QKPuEUmPB4XyjGfaAr2PSuELMwkRMVH1EpIkX5bTZGRB3eCA== dependencies: "@types/parse-json" "^4.0.0" import-fresh "^3.2.1" @@ -4075,7 +4089,7 @@ css-blank-pseudo@^3.0.3: dependencies: postcss-selector-parser "^6.0.9" -css-declaration-sorter@^6.3.0: +css-declaration-sorter@^6.3.1: version "6.3.1" resolved "https://registry.yarnpkg.com/css-declaration-sorter/-/css-declaration-sorter-6.3.1.tgz#be5e1d71b7a992433fb1c542c7a1b835e45682ec" integrity sha512-fBffmak0bPAnyqc/HO8C3n2sHrp9wcqQz6ES9koRF2/mLOVAx9zIQ3Y7R29sYCteTPqMCwns4WYQoCX91Xl3+w== @@ -4088,18 +4102,18 @@ css-has-pseudo@^3.0.4: postcss-selector-parser "^6.0.9" css-loader@^6.5.1: - version "6.7.1" - resolved "https://registry.yarnpkg.com/css-loader/-/css-loader-6.7.1.tgz#e98106f154f6e1baf3fc3bc455cb9981c1d5fd2e" - integrity sha512-yB5CNFa14MbPJcomwNh3wLThtkZgcNyI2bNMRt8iE5Z8Vwl7f8vQXFAzn2HDOJvtDq2NTZBUGMSUNNyrv3/+cw== + version "6.7.3" + resolved "https://registry.yarnpkg.com/css-loader/-/css-loader-6.7.3.tgz#1e8799f3ccc5874fdd55461af51137fcc5befbcd" + integrity sha512-qhOH1KlBMnZP8FzRO6YCH9UHXQhVMcEGLyNdb7Hv2cpcmJbW0YrddO+tG1ab5nT41KpHIYGsbeHqxB9xPu1pKQ== dependencies: icss-utils "^5.1.0" - postcss "^8.4.7" + postcss "^8.4.19" postcss-modules-extract-imports "^3.0.0" postcss-modules-local-by-default "^4.0.0" postcss-modules-scope "^3.0.0" postcss-modules-values "^4.0.0" postcss-value-parser "^4.2.0" - semver "^7.3.5" + semver "^7.3.8" css-minimizer-webpack-plugin@^3.2.0: version "3.4.1" @@ -4175,35 +4189,35 @@ css.escape@^1.5.1: resolved "https://registry.yarnpkg.com/css.escape/-/css.escape-1.5.1.tgz#42e27d4fa04ae32f931a4b4d4191fa9cddee97cb" integrity sha512-YUifsXXuknHlUsmlgyY0PKzgPOr7/FjCePfHNt0jxm83wHZi44VDMQ7/fGNkjY3/jV1MC+1CmZbaHzugyeRtpg== -cssdb@^7.0.1: - 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css-declaration-sorter "^6.3.0" + css-declaration-sorter "^6.3.1" cssnano-utils "^3.1.0" postcss-calc "^8.2.3" postcss-colormin "^5.3.0" - postcss-convert-values "^5.1.2" + postcss-convert-values "^5.1.3" postcss-discard-comments "^5.1.2" postcss-discard-duplicates "^5.1.0" postcss-discard-empty "^5.1.1" postcss-discard-overridden "^5.1.0" - postcss-merge-longhand "^5.1.6" - postcss-merge-rules "^5.1.2" + postcss-merge-longhand "^5.1.7" + postcss-merge-rules "^5.1.3" postcss-minify-font-values "^5.1.0" postcss-minify-gradients "^5.1.1" - postcss-minify-params "^5.1.3" + postcss-minify-params "^5.1.4" postcss-minify-selectors "^5.2.1" postcss-normalize-charset "^5.1.0" postcss-normalize-display-values "^5.1.0" @@ -4211,11 +4225,11 @@ cssnano-preset-default@^5.2.12: postcss-normalize-repeat-style "^5.1.1" postcss-normalize-string "^5.1.0" postcss-normalize-timing-functions "^5.1.0" - postcss-normalize-unicode "^5.1.0" + postcss-normalize-unicode "^5.1.1" postcss-normalize-url "^5.1.0" postcss-normalize-whitespace "^5.1.1" postcss-ordered-values "^5.1.3" - postcss-reduce-initial "^5.1.0" + postcss-reduce-initial "^5.1.1" postcss-reduce-transforms "^5.1.0" postcss-svgo "^5.1.0" postcss-unique-selectors "^5.1.1" @@ -4226,11 +4240,11 @@ cssnano-utils@^3.1.0: integrity sha512-JQNR19/YZhz4psLX/rQ9M83e3z2Wf/HdJbryzte4a3NSuafyp9w/I4U+hx5C2S9g41qlstH7DEWnZaaj83OuEA== cssnano@^5.0.6: - version "5.1.13" - resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-5.1.13.tgz#83d0926e72955332dc4802a7070296e6258efc0a" - integrity sha512-S2SL2ekdEz6w6a2epXn4CmMKU4K3KpcyXLKfAYc9UQQqJRkD/2eLUG0vJ3Db/9OvO5GuAdgXw3pFbR6abqghDQ== + version "5.1.14" + resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-5.1.14.tgz#07b0af6da73641276fe5a6d45757702ebae2eb05" + integrity sha512-Oou7ihiTocbKqi0J1bB+TRJIQX5RMR3JghA8hcWSw9mjBLQ5Y3RWqEDoYG3sRNlAbCIXpqMoZGbq5KDR3vdzgw== dependencies: - cssnano-preset-default "^5.2.12" + cssnano-preset-default "^5.2.13" lilconfig "^2.0.3" yaml "^1.10.2" @@ -4358,15 +4372,36 @@ debug@^3.2.7: ms "^2.1.1" decimal.js@^10.2.1: - version "10.4.2" - 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version "5.10.0" - resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.10.0.tgz#0dc579c3bb2a1032e357ac45b8f3a6f3ad4fb1e6" - integrity sha512-T0yTFjdpldGY8PmuXXR0PyQ1ufZpEGiHVrp7zHKB7jdR4qlmZHhONVM5AQOAWXuF/w3dnHbEQVrNptJgt7F+cQ== + version "5.12.0" + resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.12.0.tgz#300e1c90228f5b570c4d35babf263f6da7155634" + integrity sha512-QHTXI/sZQmko1cbDoNAa3mJ5qhWUUNAq3vR0/YiD379fWQrcfuoX1+HW2S0MTt7XmoPLapdaDKUtelUSPic7hQ== dependencies: graceful-fs "^4.2.4" tapable "^2.2.0" @@ -4722,10 +4757,10 @@ error-stack-parser@^2.0.6: dependencies: stackframe "^1.3.4" -es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19.2, es-abstract@^1.19.5, es-abstract@^1.20.0, es-abstract@^1.20.1: - version "1.20.4" - resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.4.tgz#1d103f9f8d78d4cf0713edcd6d0ed1a46eed5861" - integrity sha512-0UtvRN79eMe2L+UNEF1BwRe364sj/DXhQ/k5FmivgoSdpM90b8Jc0mDzKMGo7QS0BVbOP/bTwBKNnDc9rNzaPA== +es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.20.4: + version "1.20.5" + resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.5.tgz#e6dc99177be37cacda5988e692c3fa8b218e95d2" + integrity sha512-7h8MM2EQhsCA7pU/Nv78qOXFpD8Rhqd12gYiSJVkrH9+e8VuA8JlPJK/hQjjlLv6pJvx/z1iRFKzYb0XT/RuAQ== dependencies: call-bind "^1.0.2" es-to-primitive "^1.2.1" @@ -4733,6 +4768,7 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 function.prototype.name "^1.1.5" get-intrinsic "^1.1.3" get-symbol-description "^1.0.0" + gopd "^1.0.1" has "^1.0.3" has-property-descriptors "^1.0.0" has-symbols "^1.0.3" @@ -4748,8 +4784,8 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 object.assign "^4.1.4" regexp.prototype.flags "^1.4.3" safe-regex-test "^1.0.0" - string.prototype.trimend "^1.0.5" - string.prototype.trimstart "^1.0.5" + string.prototype.trimend "^1.0.6" + string.prototype.trimstart "^1.0.6" unbox-primitive "^1.0.2" es-array-method-boxes-properly@^1.0.0: @@ -4757,6 +4793,20 @@ es-array-method-boxes-properly@^1.0.0: resolved "https://registry.yarnpkg.com/es-array-method-boxes-properly/-/es-array-method-boxes-properly-1.0.0.tgz#873f3e84418de4ee19c5be752990b2e44718d09e" integrity sha512-wd6JXUmyHmt8T5a2xreUwKcGPq6f1f+WwIJkijUqiGcJz1qqnZgP6XIK+QyIWU5lT7imeNxUll48bziG+TSYcA== +es-get-iterator@^1.1.2: + version "1.1.2" + resolved "https://registry.yarnpkg.com/es-get-iterator/-/es-get-iterator-1.1.2.tgz#9234c54aba713486d7ebde0220864af5e2b283f7" + integrity sha512-+DTO8GYwbMCwbywjimwZMHp8AuYXOS2JZFWoi2AlPOS3ebnII9w/NLpNZtA7A0YLaVDw+O7KFCeoIV7OPvM7hQ== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.0" + has-symbols "^1.0.1" + is-arguments "^1.1.0" + is-map "^2.0.2" + is-set "^2.0.2" + is-string "^1.0.5" + isarray "^2.0.5" + es-module-lexer@^0.9.0: version "0.9.3" resolved "https://registry.yarnpkg.com/es-module-lexer/-/es-module-lexer-0.9.3.tgz#6f13db00cc38417137daf74366f535c8eb438f19" @@ -4783,7 +4833,7 @@ es6-object-assign@^1.1.0: resolved "https://registry.yarnpkg.com/es6-object-assign/-/es6-object-assign-1.1.0.tgz#c2c3582656247c39ea107cb1e6652b6f9f24523c" integrity sha512-MEl9uirslVwqQU369iHNWZXsI8yaZYGg/D65aOgZkeyFJwHYSxilf7rQzXKI7DdDuBPrBXbfk3sl9hJhmd5AUw== -es6-promisify@^6.0.1, es6-promisify@^6.1.1: +es6-promisify@^6.1.1: version "6.1.1" resolved "https://registry.yarnpkg.com/es6-promisify/-/es6-promisify-6.1.1.tgz#46837651b7b06bf6fff893d03f29393668d01621" integrity sha512-HBL8I3mIki5C1Cc9QjKUenHtnG0A5/xA8Q/AllRcfiwl2CZFXGK7ddBiCoRwAix4i2KxcQfjtIVcrVbB3vbmwg== @@ -4924,29 +4974,30 @@ eslint-plugin-react-hooks@^4.3.0: integrity sha512-oFc7Itz9Qxh2x4gNHStv3BqJq54ExXmfC+a1NjAta66IAN87Wu0R/QArgIS9qKzX3dXKPI9H5crl9QchNMY9+g== eslint-plugin-react@^7.27.1: - version "7.31.10" - resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.10.tgz#6782c2c7fe91c09e715d536067644bbb9491419a" - integrity sha512-e4N/nc6AAlg4UKW/mXeYWd3R++qUano5/o+t+wnWxIf+bLsOaH3a4q74kX3nDjYym3VBN4HyO9nEn1GcAqgQOA== + version "7.31.11" + resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.11.tgz#011521d2b16dcf95795df688a4770b4eaab364c8" + integrity sha512-TTvq5JsT5v56wPa9OYHzsrOlHzKZKjV+aLgS+55NJP/cuzdiQPC7PfYoUjMoxlffKtvijpk7vA/jmuqRb9nohw== dependencies: - array-includes "^3.1.5" - array.prototype.flatmap "^1.3.0" + array-includes "^3.1.6" + array.prototype.flatmap "^1.3.1" + array.prototype.tosorted "^1.1.1" doctrine "^2.1.0" estraverse "^5.3.0" jsx-ast-utils "^2.4.1 || ^3.0.0" minimatch "^3.1.2" - object.entries "^1.1.5" - object.fromentries "^2.0.5" - object.hasown "^1.1.1" - object.values "^1.1.5" + object.entries "^1.1.6" + object.fromentries "^2.0.6" + object.hasown "^1.1.2" + object.values "^1.1.6" prop-types "^15.8.1" resolve "^2.0.0-next.3" semver "^6.3.0" - string.prototype.matchall "^4.0.7" + string.prototype.matchall "^4.0.8" eslint-plugin-testing-library@^5.0.1: - version "5.8.0" - resolved "https://registry.yarnpkg.com/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.8.0.tgz#0faed7695ba76c0021fde3aeda9b90748995d2f2" - integrity sha512-QzOKgu4x8WmNq4LdbHb8lz5nBR+KX5kSg5VvIdr/5f1BvHx2IoO1B/tgDa5pD/ng2LsiQ0/HIH6gsUuxpbcrkQ== + version "5.9.1" + resolved "https://registry.yarnpkg.com/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.9.1.tgz#12e4bd34c48683ee98af4df2e3318ec9f51dcf8a" + integrity sha512-6BQp3tmb79jLLasPHJmy8DnxREe+2Pgf7L+7o09TSWPfdqqtQfRZmZNetr5mOs3yqZk/MRNxpN3RUpJe0wB4LQ== dependencies: "@typescript-eslint/utils" "^5.13.0" @@ -4995,13 +5046,14 @@ eslint-webpack-plugin@^3.1.1: schema-utils "^4.0.0" eslint@^8.3.0: - version "8.25.0" - resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.25.0.tgz#00eb962f50962165d0c4ee3327708315eaa8058b" - integrity sha512-DVlJOZ4Pn50zcKW5bYH7GQK/9MsoQG2d5eDH0ebEkE8PbgzTTmtt/VTH9GGJ4BfeZCpBLqFfvsjX35UacUL83A== + version "8.30.0" + resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.30.0.tgz#83a506125d089eef7c5b5910eeea824273a33f50" + integrity sha512-MGADB39QqYuzEGov+F/qb18r4i7DohCDOfatHaxI2iGlPuC65bwG2gxgO+7DkyL38dRFaRH7RaRAgU6JKL9rMQ== dependencies: - 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integrity sha512-YpkpUnK8od0o1hmeSc7UUs/eB/vIPWJYjKck2QKIzAf71Vm1AAQ3EbuZB3g2JIy+pg+ERD0vqI79KyZiB2e2Nw== + version "1.14.0" + resolved "https://registry.yarnpkg.com/fastq/-/fastq-1.14.0.tgz#107f69d7295b11e0fccc264e1fc6389f623731ce" + integrity sha512-eR2D+V9/ExcbF9ls441yIuN6TI2ED1Y2ZcA5BmMtJsOkWOFRJQ0Jt0g1UwqXJJVAb+V+umH5Dfr8oh4EVP7VVg== dependencies: reusify "^1.0.4" @@ -5451,9 +5503,9 @@ functions-have-names@^1.2.2: integrity sha512-xckBUXyTIqT97tq2x2AMb+g163b5JFysYk0x4qxNFwbfQkmNZoiRHb6sPzI9/QV33WeuvVYBUIiD4NzNIyqaRQ== generic-filehandle@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.0.0.tgz#10d5ddc4adf105de616224dba58370f3dcc3877c" - integrity sha512-THrFJ1fq7wjwMmSN7sdp0JnQKZDVE7aooVwHTWREKHrCGVJGKKiD5BSaboNHiFU84RIzJ+oBOqQsN//ISWj1ZQ== + version "3.0.1" + resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.0.1.tgz#9bea8ad8f572bb07c16097df6fccc05a87ec77ff" + integrity sha512-E0eVkls2Ni7fUQ47VxYJN45/ow821pITHcgyaMZXBUt1czZUionT6HSqE0t+bcAozt5MYeJCxVxIrlTxoASXuQ== dependencies: es6-promisify "^6.1.1" @@ -5506,7 +5558,7 @@ glob-parent@^5.1.2, glob-parent@~5.1.2: dependencies: is-glob "^4.0.1" -glob-parent@^6.0.1, glob-parent@^6.0.2: +glob-parent@^6.0.2: version "6.0.2" resolved "https://registry.yarnpkg.com/glob-parent/-/glob-parent-6.0.2.tgz#6d237d99083950c79290f24c7642a3de9a28f9e3" integrity sha512-XxwI8EOhVQgWp6iDL+3b0r86f4d6AX6zSU55HfB4ydCEuXLXc5FcYeOu+nnGftS4TEju/11rt4KJPTMgbfmv4A== @@ -5551,10 +5603,10 @@ globals@^11.1.0: resolved "https://registry.yarnpkg.com/globals/-/globals-11.12.0.tgz#ab8795338868a0babd8525758018c2a7eb95c42e" integrity sha512-WOBp/EEGUiIsJSp7wcv/y6MO+lV9UoncWqxuFfm8eBwzWNgyfBd6Gz+IeKQ9jCmyhoH99g15M3T+QaVHFjizVA== -globals@^13.15.0: - version "13.17.0" - resolved "https://registry.yarnpkg.com/globals/-/globals-13.17.0.tgz#902eb1e680a41da93945adbdcb5a9f361ba69bd4" - integrity sha512-1C+6nQRb1GwGMKm2dH/E7enFAMxGTmGI7/dEdhy/DNelv85w9B72t3uc5frtMNXIbzrarJJ/lTCjcaZwbLJmyw== +globals@^13.19.0: + version "13.19.0" + resolved "https://registry.yarnpkg.com/globals/-/globals-13.19.0.tgz#7a42de8e6ad4f7242fbcca27ea5b23aca367b5c8" + integrity sha512-dkQ957uSRWHw7CFXLUtUHQI3g3aWApYhfNR2O6jn/907riyTYKVBmxYVROkBcY614FSSeSJh7Xm7SrUWCxvJMQ== dependencies: type-fest "^0.20.2" @@ -5570,6 +5622,13 @@ globby@^11.0.4, globby@^11.1.0: merge2 "^1.4.1" slash "^3.0.0" +gopd@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/gopd/-/gopd-1.0.1.tgz#29ff76de69dac7489b7c0918a5788e56477c332c" + integrity sha512-d65bNlIadxvpb/A2abVdlqKqV563juRnZ1Wtk6s1sIR8uNsXR70xqIzVqxVf1eTqDunwT2MkczEeaezCKTZhwA== + dependencies: + get-intrinsic "^1.1.3" + graceful-fs@^4.1.2, graceful-fs@^4.1.6, graceful-fs@^4.2.0, graceful-fs@^4.2.4, graceful-fs@^4.2.6, graceful-fs@^4.2.9: version "4.2.10" resolved "https://registry.yarnpkg.com/graceful-fs/-/graceful-fs-4.2.10.tgz#147d3a006da4ca3ce14728c7aefc287c367d7a6c" @@ -5851,9 +5910,9 @@ icss-utils@^5.0.0, icss-utils@^5.1.0: integrity sha512-soFhflCVWLfRNOPU3iv5Z9VUdT44xFRbzjLsEzSr5AQmgqPMTHdU3PMT1Cf1ssx8fLNJDA1juftYl+PUcv3MqA== idb@^7.0.1: - version "7.1.0" - resolved "https://registry.yarnpkg.com/idb/-/idb-7.1.0.tgz#2cc886be57738419e57f9aab58f647e5e2160270" - integrity sha512-Wsk07aAxDsntgYJY4h0knZJuTxM73eQ4reRAO+Z1liOh8eMCJ/MoDS8fCui1vGT9mnjtl1sOu3I2i/W1swPYZg== + version "7.1.1" + resolved "https://registry.yarnpkg.com/idb/-/idb-7.1.1.tgz#d910ded866d32c7ced9befc5bfdf36f572ced72b" + integrity sha512-gchesWBzyvGHRO9W8tzUWFDycow5gwjvFKfyV9FF32Y7F50yZMp7mP+T2mJIWFx49zicqyC4uefHM17o6xKIVQ== identity-obj-proxy@^3.0.0: version "3.0.0" @@ -5868,14 +5927,14 @@ ieee754@^1.2.1: integrity sha512-dcyqhDvX1C46lXZcVqCpK+FtMRQVdIMN6/Df5js2zouUsqG7I6sFxitIC+7KYK29KdXOLHdu9zL4sFnoVQnqaA== ignore@^5.2.0: - version "5.2.0" - resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.2.0.tgz#6d3bac8fa7fe0d45d9f9be7bac2fc279577e345a" - integrity sha512-CmxgYGiEPCLhfLnpPp1MoRmifwEIOgjcHXxOBjv7mY96c+eWScsOP9c112ZyLdWHi0FxHjI+4uVhKYp/gcdRmQ== + version "5.2.4" + resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.2.4.tgz#a291c0c6178ff1b960befe47fcdec301674a6324" + integrity sha512-MAb38BcSbH0eHNBxn7ql2NH/kX33OkB3lZ1BNdh7ENeRChHTYsTvWrMubiIAMNS2llXEEgZ1MUOBtXChP3kaFQ== immer@^9.0.7: - version "9.0.15" - resolved "https://registry.yarnpkg.com/immer/-/immer-9.0.15.tgz#0b9169e5b1d22137aba7d43f8a81a495dd1b62dc" - integrity sha512-2eB/sswms9AEUSkOm4SbV5Y7Vmt/bKRwByd52jfLkW4OLYeaTP3EEiJ9agqU0O/tq6Dk62Zfj+TJSqfm1rLVGQ== + version "9.0.16" + resolved "https://registry.yarnpkg.com/immer/-/immer-9.0.16.tgz#8e7caab80118c2b54b37ad43e05758cdefad0198" + integrity sha512-qenGE7CstVm1NrHQbMh8YaSzTZTFNP3zPqr3YU0S0UY441j4bJTg4A2Hh5KAhwgaiU6ZZ1Ar6y/2f4TblnMReQ== import-fresh@^3.0.0, import-fresh@^3.1.0, import-fresh@^3.2.1: version "3.3.0" @@ -5927,11 +5986,11 @@ ini@^1.3.5: integrity sha512-JV/yugV2uzW5iMRSiZAyDtQd+nxtUnjeLt0acNdw98kKLrvuRVyB80tsREOE7yvGVgalhZ6RNXCmEHkUKBKxew== internal-slot@^1.0.3: - version "1.0.3" - resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.3.tgz#7347e307deeea2faac2ac6205d4bc7d34967f59c" - integrity sha512-O0DB1JC/sPyZl7cIo78n5dR7eUSwwpYPiXRhTzNxZVAMUuB8vlnRFyLxdrVToks6XPLVnFfbzaVd5WLjhgg+vA== + version "1.0.4" + resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.4.tgz#8551e7baf74a7a6ba5f749cfb16aa60722f0d6f3" + integrity sha512-tA8URYccNzMo94s5MQZgH8NB/XTa6HsOo0MLfXTKKEnHVVdegzaQoFZ7Jp44bdvLvY2waT5dc+j5ICEswhi7UQ== dependencies: - get-intrinsic "^1.1.0" + get-intrinsic "^1.1.3" has "^1.0.3" side-channel "^1.0.4" @@ -5950,7 +6009,7 @@ ipaddr.js@^2.0.1: resolved "https://registry.yarnpkg.com/ipaddr.js/-/ipaddr.js-2.0.1.tgz#eca256a7a877e917aeb368b0a7497ddf42ef81c0" integrity sha512-1qTgH9NG+IIJ4yfKs2e6Pp1bZg8wbDbKHT21HrLIeYBTRLgMYKnMTPAuI3Lcs61nfx5h1xlXnbJtH1kX5/d/ng== -is-arguments@^1.0.4: +is-arguments@^1.0.4, is-arguments@^1.1.0, is-arguments@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== @@ -6002,7 +6061,7 @@ is-core-module@^2.8.1, is-core-module@^2.9.0: dependencies: has "^1.0.3" -is-date-object@^1.0.1: +is-date-object@^1.0.1, is-date-object@^1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/is-date-object/-/is-date-object-1.0.5.tgz#0841d5536e724c25597bf6ea62e1bd38298df31f" integrity sha512-9YQaSxsAiSwcvS33MBk3wTCVnWK+HhF8VZR2jRxehM16QcVOdHqPn4VPHmRK4lSr38n9JriurInLcP90xsYNfQ== @@ -6043,6 +6102,11 @@ is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: dependencies: is-extglob "^2.1.1" +is-map@^2.0.1, is-map@^2.0.2: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-map/-/is-map-2.0.2.tgz#00922db8c9bf73e81b7a335827bc2a43f2b91127" + integrity sha512-cOZFQQozTha1f4MxLFzlgKYPTyj26picdZTx82hbc/Xf4K/tZOOXSCkMvU4pKioRXGDLJRn0GM7Upe7kR721yg== + is-module@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-module/-/is-module-1.0.0.tgz#3258fb69f78c14d5b815d664336b4cffb6441591" @@ -6083,6 +6147,11 @@ is-object@^1.0.1: resolved "https://registry.yarnpkg.com/is-object/-/is-object-1.0.2.tgz#a56552e1c665c9e950b4a025461da87e72f86fcf" integrity sha512-2rRIahhZr2UWb45fIOuvZGpFtz0TyOZLf32KxBbSoUCeZR495zCKlWUKKUByk3geS2eAs7ZAABt0Y/Rx0GiQGA== +is-path-inside@^3.0.3: + version "3.0.3" + resolved "https://registry.yarnpkg.com/is-path-inside/-/is-path-inside-3.0.3.tgz#d231362e53a07ff2b0e0ea7fed049161ffd16283" + integrity sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ== + is-plain-obj@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/is-plain-obj/-/is-plain-obj-3.0.0.tgz#af6f2ea14ac5a646183a5bbdb5baabbc156ad9d7" @@ -6111,6 +6180,11 @@ is-root@^2.1.0: resolved "https://registry.yarnpkg.com/is-root/-/is-root-2.1.0.tgz#809e18129cf1129644302a4f8544035d51984a9c" integrity sha512-AGOriNp96vNBd3HtU+RzFEc75FfR5ymiYv8E553I71SCeXBiMsVDUtdio1OEFvrPyLIQ9tVR5RxXIFe5PUFjMg== +is-set@^2.0.1, is-set@^2.0.2: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-set/-/is-set-2.0.2.tgz#90755fa4c2562dc1c5d4024760d6119b94ca18ec" + integrity sha512-+2cnTEZeY5z/iXGbLhPrOAaK/Mau5k5eXq9j14CpRTftq0pAJu2MwVRSZhyZWBzx3o6X795Lz6Bpb6R0GKf37g== + is-shared-array-buffer@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-shared-array-buffer/-/is-shared-array-buffer-1.0.2.tgz#8f259c573b60b6a32d4058a1a07430c0a7344c79" @@ -6137,15 +6211,15 @@ is-symbol@^1.0.2, is-symbol@^1.0.3: dependencies: has-symbols "^1.0.2" -is-typed-array@^1.1.3, is-typed-array@^1.1.9: - version "1.1.9" - resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.9.tgz#246d77d2871e7d9f5aeb1d54b9f52c71329ece67" - integrity sha512-kfrlnTTn8pZkfpJMUgYD7YZ3qzeJgWUn8XfVYBARc4wnmNOmLbmuuaAs3q5fvB0UJOn6yHAKaGTPM7d6ezoD/A== +is-typed-array@^1.1.10, is-typed-array@^1.1.3: + version "1.1.10" + resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.10.tgz#36a5b5cb4189b575d1a3e4b08536bfb485801e3f" + integrity sha512-PJqgEHiWZvMpaFZ3uTc8kHPM4+4ADTlDniuQL7cU/UDA0Ql7F70yGfHph3cLNe+c9toaigv+DFzTJKhc2CtO6A== dependencies: available-typed-arrays "^1.0.5" call-bind "^1.0.2" - es-abstract "^1.20.0" for-each "^0.3.3" + gopd "^1.0.1" has-tostringtag "^1.0.0" is-typedarray@^1.0.0: @@ -6153,6 +6227,11 @@ is-typedarray@^1.0.0: resolved "https://registry.yarnpkg.com/is-typedarray/-/is-typedarray-1.0.0.tgz#e479c80858df0c1b11ddda6940f96011fcda4a9a" integrity sha512-cyA56iCMHAh5CdzjJIa4aohJyeO1YbwLi3Jc35MmRU6poroFjIGZzUzupGiRPOjgHg9TLu43xbpwXk523fMxKA== +is-weakmap@^2.0.1: + version "2.0.1" + resolved "https://registry.yarnpkg.com/is-weakmap/-/is-weakmap-2.0.1.tgz#5008b59bdc43b698201d18f62b37b2ca243e8cf2" + integrity sha512-NSBR4kH5oVj1Uwvv970ruUkCV7O1mzgVFO4/rev2cLRda9Tm9HrL70ZPut4rOHgY0FNrUu9BCbXA2sdQ+x0chA== + is-weakref@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-weakref/-/is-weakref-1.0.2.tgz#9529f383a9338205e89765e0392efc2f100f06f2" @@ -6160,6 +6239,14 @@ is-weakref@^1.0.2: dependencies: call-bind "^1.0.2" +is-weakset@^2.0.1: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-weakset/-/is-weakset-2.0.2.tgz#4569d67a747a1ce5a994dfd4ef6dcea76e7c0a1d" + integrity sha512-t2yVvttHkQktwnNNmBQ98AhENLdPUTDTE21uPqAQ0ARwQfGeQKRVS0NNurH7bTf7RrvcVn1OOge45CnBeHCSmg== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.1" + is-wsl@^2.2.0: version "2.2.0" resolved "https://registry.yarnpkg.com/is-wsl/-/is-wsl-2.2.0.tgz#74a4c76e77ca9fd3f932f290c17ea326cd157271" @@ -6167,6 +6254,11 @@ is-wsl@^2.2.0: dependencies: is-docker "^2.0.0" +isarray@^2.0.5: + version "2.0.5" + resolved "https://registry.yarnpkg.com/isarray/-/isarray-2.0.5.tgz#8af1e4c1221244cc62459faf38940d4e644a5723" + integrity sha512-xHjhDr3cNBK0BzdUJSPXZntQUx/mwMS5Rw4A7lPJ90XGAO6ISP/ePDNuo0vhqOZU+UD5JoodwCAAoZQd3FeAKw== + isarray@~1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/isarray/-/isarray-1.0.0.tgz#bb935d48582cba168c06834957a54a3e07124f11" @@ -6321,15 +6413,15 @@ jest-diff@^27.5.1: jest-get-type "^27.5.1" pretty-format "^27.5.1" -jest-diff@^29.2.1: - version "29.2.1" - resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-29.2.1.tgz#027e42f5a18b693fb2e88f81b0ccab533c08faee" - integrity sha512-gfh/SMNlQmP3MOUgdzxPOd4XETDJifADpT937fN1iUGz+9DgOu2eUPHH25JDkLVcLwwqxv3GzVyK4VBUr9fjfA== +jest-diff@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-29.3.1.tgz#d8215b72fed8f1e647aed2cae6c752a89e757527" + integrity sha512-vU8vyiO7568tmin2lA3r2DP8oRvzhvRcD4DjpXc6uGveQodyk7CKLhQlCSiwgx3g0pFaE88/KLZ0yaTWMc4Uiw== dependencies: chalk "^4.0.0" - diff-sequences "^29.2.0" + diff-sequences "^29.3.1" jest-get-type "^29.2.0" - pretty-format "^29.2.1" + pretty-format "^29.3.1" jest-docblock@^27.5.1: version "27.5.1" @@ -6445,15 +6537,15 @@ jest-matcher-utils@^27.0.0, jest-matcher-utils@^27.5.1: jest-get-type "^27.5.1" pretty-format "^27.5.1" -jest-matcher-utils@^29.2.1: - version "29.2.1" - resolved "https://registry.yarnpkg.com/jest-matcher-utils/-/jest-matcher-utils-29.2.1.tgz#2bf876c5f891b33786aadf5d65d5da5970744122" - 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version "1.1.5" - resolved "https://registry.yarnpkg.com/object.entries/-/object.entries-1.1.5.tgz#e1acdd17c4de2cd96d5a08487cfb9db84d881861" - integrity sha512-TyxmjUoZggd4OrrU1W66FMDG6CuqJxsFvymeyXI51+vQLN67zYfZseptRge703kKQdo4uccgAKebXFcRCzk4+g== +object.entries@^1.1.6: + version "1.1.6" + resolved "https://registry.yarnpkg.com/object.entries/-/object.entries-1.1.6.tgz#9737d0e5b8291edd340a3e3264bb8a3b00d5fa23" + integrity sha512-leTPzo4Zvg3pmbQ3rDK69Rl8GQvIqMWubrkxONG9/ojtFE2rD9fjMKfSI5BxW3osRH1m6VdzmqK8oAY9aT4x5w== dependencies: call-bind "^1.0.2" - define-properties "^1.1.3" - es-abstract "^1.19.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" -object.fromentries@^2.0.5: - version "2.0.5" - resolved "https://registry.yarnpkg.com/object.fromentries/-/object.fromentries-2.0.5.tgz#7b37b205109c21e741e605727fe8b0ad5fa08251" - integrity sha512-CAyG5mWQRRiBU57Re4FKoTBjXfDoNwdFVH2Y1tS9PqCsfUTymAohOkEMSG3aRNKmv4lV3O7p1et7c187q6bynw== +object.fromentries@^2.0.6: + version "2.0.6" + resolved "https://registry.yarnpkg.com/object.fromentries/-/object.fromentries-2.0.6.tgz#cdb04da08c539cffa912dcd368b886e0904bfa73" + integrity sha512-VciD13dswC4j1Xt5394WR4MzmAQmlgN72phd/riNp9vtD7tp4QQWJ0R4wvclXcafgcYK8veHRed2W6XeGBvcfg== dependencies: call-bind "^1.0.2" - define-properties "^1.1.3" - es-abstract "^1.19.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" object.getownpropertydescriptors@^2.1.0: - version "2.1.4" - resolved "https://registry.yarnpkg.com/object.getownpropertydescriptors/-/object.getownpropertydescriptors-2.1.4.tgz#7965e6437a57278b587383831a9b829455a4bc37" - integrity sha512-sccv3L/pMModT6dJAYF3fzGMVcb38ysQ0tEE6ixv2yXJDtEIPph268OlAdJj5/qZMZDq2g/jqvwppt36uS/uQQ== + version "2.1.5" + resolved "https://registry.yarnpkg.com/object.getownpropertydescriptors/-/object.getownpropertydescriptors-2.1.5.tgz#db5a9002489b64eef903df81d6623c07e5b4b4d3" + integrity sha512-yDNzckpM6ntyQiGTik1fKV1DcVDRS+w8bvpWNCBanvH5LfRX9O8WTHqQzG4RZwRAM4I0oU7TV11Lj5v0g20ibw== dependencies: - array.prototype.reduce "^1.0.4" + array.prototype.reduce "^1.0.5" call-bind "^1.0.2" define-properties "^1.1.4" - es-abstract "^1.20.1" + es-abstract "^1.20.4" -object.hasown@^1.1.1: - version "1.1.1" - resolved "https://registry.yarnpkg.com/object.hasown/-/object.hasown-1.1.1.tgz#ad1eecc60d03f49460600430d97f23882cf592a3" - integrity sha512-LYLe4tivNQzq4JdaWW6WO3HMZZJWzkkH8fnI6EebWl0VZth2wL2Lovm74ep2/gZzlaTdV62JZHEqHQ2yVn8Q/A== +object.hasown@^1.1.2: + version "1.1.2" + resolved "https://registry.yarnpkg.com/object.hasown/-/object.hasown-1.1.2.tgz#f919e21fad4eb38a57bc6345b3afd496515c3f92" + integrity sha512-B5UIT3J1W+WuWIU55h0mjlwaqxiE5vYENJXIXZ4VFe05pNYrkKuK0U/6aFcb0pKywYJh7IhfoqUfKVmrJJHZHw== dependencies: define-properties "^1.1.4" - es-abstract "^1.19.5" + es-abstract "^1.20.4" -object.values@^1.1.0, object.values@^1.1.5: - version "1.1.5" - resolved "https://registry.yarnpkg.com/object.values/-/object.values-1.1.5.tgz#959f63e3ce9ef108720333082131e4a459b716ac" - integrity sha512-QUZRW0ilQ3PnPpbNtgdNV1PDbEqLIiSFB3l+EnGtBQ/8SUTLj1PZwtQHABZtLgwpJZTSZhuGLOGk57Drx2IvYg== +object.values@^1.1.0, object.values@^1.1.5, object.values@^1.1.6: + version "1.1.6" + resolved "https://registry.yarnpkg.com/object.values/-/object.values-1.1.6.tgz#4abbaa71eba47d63589d402856f908243eea9b1d" + integrity sha512-FVVTkD1vENCsAcwNs9k6jea2uHC/X0+JcjG8YA60FN5CMaJmG95wT9jek/xX9nornqGRrBkKtzuAu2wuHpKqvw== dependencies: call-bind "^1.0.2" - define-properties "^1.1.3" - es-abstract "^1.19.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" obuf@^1.0.0, obuf@^1.1.2: version "1.1.2" @@ -7659,9 +7754,9 @@ pako@^1.0.11, pako@~1.0.5: integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw== pako@^2.0.0: - version "2.0.4" - resolved "https://registry.yarnpkg.com/pako/-/pako-2.0.4.tgz#6cebc4bbb0b6c73b0d5b8d7e8476e2b2fbea576d" - integrity sha512-v8tweI900AUkZN6heMU/4Uy4cXRc2AYNRggVmTR+dEncawDJgCdLMximOVA2p4qO57WMynangsfGRb5WD6L1Bg== + version "2.1.0" + resolved "https://registry.yarnpkg.com/pako/-/pako-2.1.0.tgz#266cc37f98c7d883545d11335c00fbd4062c9a86" + integrity sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug== param-case@^3.0.4: version "3.0.4" @@ -7875,12 +7970,12 @@ postcss-colormin@^5.3.0: colord "^2.9.1" postcss-value-parser "^4.2.0" -postcss-convert-values@^5.1.2: - version "5.1.2" - resolved "https://registry.yarnpkg.com/postcss-convert-values/-/postcss-convert-values-5.1.2.tgz#31586df4e184c2e8890e8b34a0b9355313f503ab" - integrity sha512-c6Hzc4GAv95B7suy4udszX9Zy4ETyMCgFPUDtWjdFTKH1SE9eFY/jEpHSwTH1QPuwxHpWslhckUQWbNRM4ho5g== +postcss-convert-values@^5.1.3: + version "5.1.3" + resolved "https://registry.yarnpkg.com/postcss-convert-values/-/postcss-convert-values-5.1.3.tgz#04998bb9ba6b65aa31035d669a6af342c5f9d393" + integrity sha512-82pC1xkJZtcJEfiLw6UXnXVXScgtBrjlO5CBmuDQc+dlb88ZYheFsjTn40+zBVi3DkfF7iezO0nJUPLcJK3pvA== dependencies: - browserslist "^4.20.3" + browserslist "^4.21.4" postcss-value-parser "^4.2.0" postcss-custom-media@^8.0.2: @@ -7890,10 +7985,10 @@ postcss-custom-media@^8.0.2: dependencies: postcss-value-parser "^4.2.0" -postcss-custom-properties@^12.1.9: - version "12.1.9" - resolved "https://registry.yarnpkg.com/postcss-custom-properties/-/postcss-custom-properties-12.1.9.tgz#0883429a7ef99f1ba239d1fea29ce84906daa8bd" - integrity sha512-/E7PRvK8DAVljBbeWrcEQJPG72jaImxF3vvCNFwv9cC8CzigVoNIpeyfnJzphnN3Fd8/auBf5wvkw6W9MfmTyg== +postcss-custom-properties@^12.1.10: + version "12.1.11" + resolved "https://registry.yarnpkg.com/postcss-custom-properties/-/postcss-custom-properties-12.1.11.tgz#d14bb9b3989ac4d40aaa0e110b43be67ac7845cf" + integrity sha512-0IDJYhgU8xDv1KY6+VgUwuQkVtmYzRwu+dMjnmdMafXYv86SWqfxkc7qdDvWS38vsjaEtv8e0vGOUQrAiMBLpQ== dependencies: postcss-value-parser "^4.2.0" @@ -8038,20 +8133,20 @@ postcss-media-minmax@^5.0.0: resolved "https://registry.yarnpkg.com/postcss-media-minmax/-/postcss-media-minmax-5.0.0.tgz#7140bddec173e2d6d657edbd8554a55794e2a5b5" integrity sha512-yDUvFf9QdFZTuCUg0g0uNSHVlJ5X1lSzDZjPSFaiCWvjgsvu8vEVxtahPrLMinIDEEGnx6cBe6iqdx5YWz08wQ== -postcss-merge-longhand@^5.1.6: - version "5.1.6" - resolved "https://registry.yarnpkg.com/postcss-merge-longhand/-/postcss-merge-longhand-5.1.6.tgz#f378a8a7e55766b7b644f48e5d8c789ed7ed51ce" - integrity sha512-6C/UGF/3T5OE2CEbOuX7iNO63dnvqhGZeUnKkDeifebY0XqkkvrctYSZurpNE902LDf2yKwwPFgotnfSoPhQiw== +postcss-merge-longhand@^5.1.7: + version "5.1.7" + resolved "https://registry.yarnpkg.com/postcss-merge-longhand/-/postcss-merge-longhand-5.1.7.tgz#24a1bdf402d9ef0e70f568f39bdc0344d568fb16" + integrity sha512-YCI9gZB+PLNskrK0BB3/2OzPnGhPkBEwmwhfYk1ilBHYVAZB7/tkTHFBAnCrvBBOmeYyMYw3DMjT55SyxMBzjQ== dependencies: postcss-value-parser "^4.2.0" - stylehacks "^5.1.0" + stylehacks "^5.1.1" -postcss-merge-rules@^5.1.2: - version "5.1.2" - resolved "https://registry.yarnpkg.com/postcss-merge-rules/-/postcss-merge-rules-5.1.2.tgz#7049a14d4211045412116d79b751def4484473a5" - integrity sha512-zKMUlnw+zYCWoPN6yhPjtcEdlJaMUZ0WyVcxTAmw3lkkN/NDMRkOkiuctQEoWAOvH7twaxUUdvBWl0d4+hifRQ== +postcss-merge-rules@^5.1.3: + version "5.1.3" + resolved "https://registry.yarnpkg.com/postcss-merge-rules/-/postcss-merge-rules-5.1.3.tgz#8f97679e67cc8d08677a6519afca41edf2220894" + integrity sha512-LbLd7uFC00vpOuMvyZop8+vvhnfRGpp2S+IMQKeuOZZapPRY4SMq5ErjQeHbHsjCUgJkRNrlU+LmxsKIqPKQlA== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" caniuse-api "^3.0.0" cssnano-utils "^3.1.0" postcss-selector-parser "^6.0.5" @@ -8072,12 +8167,12 @@ postcss-minify-gradients@^5.1.1: cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" -postcss-minify-params@^5.1.3: - version "5.1.3" - resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.3.tgz#ac41a6465be2db735099bbd1798d85079a6dc1f9" - integrity sha512-bkzpWcjykkqIujNL+EVEPOlLYi/eZ050oImVtHU7b4lFS82jPnsCb44gvC6pxaNt38Els3jWYDHTjHKf0koTgg== +postcss-minify-params@^5.1.4: + version "5.1.4" + resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.4.tgz#c06a6c787128b3208b38c9364cfc40c8aa5d7352" + integrity sha512-+mePA3MgdmVmv6g+30rn57USjOGSAyuxUmkfiWpzalZ8aiBkdPYjXWtHuwJGm1v5Ojy0Z0LaSYhHaLJQB0P8Jw== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" @@ -8171,12 +8266,12 @@ postcss-normalize-timing-functions@^5.1.0: dependencies: postcss-value-parser "^4.2.0" -postcss-normalize-unicode@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/postcss-normalize-unicode/-/postcss-normalize-unicode-5.1.0.tgz#3d23aede35e160089a285e27bf715de11dc9db75" - integrity sha512-J6M3MizAAZ2dOdSjy2caayJLQT8E8K9XjLce8AUQMwOrCvjCHv24aLC/Lps1R1ylOfol5VIDMaM/Lo9NGlk1SQ== +postcss-normalize-unicode@^5.1.1: + version "5.1.1" + resolved "https://registry.yarnpkg.com/postcss-normalize-unicode/-/postcss-normalize-unicode-5.1.1.tgz#f67297fca3fea7f17e0d2caa40769afc487aa030" + integrity sha512-qnCL5jzkNUmKVhZoENp1mJiGNPcsJCs1aaRmURmeJGES23Z/ajaln+EPTD+rBeNkSryI+2WTdW+lwcVdOikrpA== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" postcss-value-parser "^4.2.0" postcss-normalize-url@^5.1.0: @@ -8204,9 +8299,9 @@ postcss-normalize@^10.0.1: sanitize.css "*" postcss-opacity-percentage@^1.1.2: - version "1.1.2" - resolved "https://registry.yarnpkg.com/postcss-opacity-percentage/-/postcss-opacity-percentage-1.1.2.tgz#bd698bb3670a0a27f6d657cc16744b3ebf3b1145" - integrity sha512-lyUfF7miG+yewZ8EAk9XUBIlrHyUE6fijnesuz+Mj5zrIHIEw6KcIZSOk/elVMqzLvREmXB83Zi/5QpNRYd47w== + version "1.1.3" + resolved "https://registry.yarnpkg.com/postcss-opacity-percentage/-/postcss-opacity-percentage-1.1.3.tgz#5b89b35551a556e20c5d23eb5260fbfcf5245da6" + integrity sha512-An6Ba4pHBiDtyVpSLymUUERMo2cU7s+Obz6BTrS+gxkbnSBNKSuD0AVUc+CpBMrpVPKKfoVz0WQCX+Tnst0i4A== postcss-ordered-values@^5.1.3: version "5.1.3" @@ -8236,11 +8331,11 @@ postcss-place@^7.0.5: postcss-value-parser "^4.2.0" postcss-preset-env@^7.0.1: - version "7.8.2" - resolved "https://registry.yarnpkg.com/postcss-preset-env/-/postcss-preset-env-7.8.2.tgz#4c834d5cbd2e29df2abf59118947c456922b79ba" - integrity sha512-rSMUEaOCnovKnwc5LvBDHUDzpGP+nrUeWZGWt9M72fBvckCi45JmnJigUr4QG4zZeOHmOCNCZnd2LKDvP++ZuQ== + version "7.8.3" + resolved "https://registry.yarnpkg.com/postcss-preset-env/-/postcss-preset-env-7.8.3.tgz#2a50f5e612c3149cc7af75634e202a5b2ad4f1e2" + integrity sha512-T1LgRm5uEVFSEF83vHZJV2z19lHg4yJuZ6gXZZkqVsqv63nlr6zabMH3l4Pc01FQCyfWVrh2GaUeCVy9Po+Aag== dependencies: - "@csstools/postcss-cascade-layers" "^1.1.0" + "@csstools/postcss-cascade-layers" "^1.1.1" "@csstools/postcss-color-function" "^1.1.1" "@csstools/postcss-font-format-keywords" "^1.0.1" "@csstools/postcss-hwb-function" "^1.0.2" @@ -8254,19 +8349,19 @@ postcss-preset-env@^7.0.1: "@csstools/postcss-text-decoration-shorthand" "^1.0.0" "@csstools/postcss-trigonometric-functions" "^1.0.2" "@csstools/postcss-unset-value" "^1.0.2" - autoprefixer "^10.4.11" - browserslist "^4.21.3" + autoprefixer "^10.4.13" + browserslist "^4.21.4" css-blank-pseudo "^3.0.3" css-has-pseudo "^3.0.4" css-prefers-color-scheme "^6.0.3" - cssdb "^7.0.1" + cssdb "^7.1.0" postcss-attribute-case-insensitive "^5.0.2" postcss-clamp "^4.1.0" postcss-color-functional-notation "^4.2.4" postcss-color-hex-alpha "^8.0.4" postcss-color-rebeccapurple "^7.1.1" postcss-custom-media "^8.0.2" - postcss-custom-properties "^12.1.9" + postcss-custom-properties "^12.1.10" postcss-custom-selectors "^6.0.3" postcss-dir-pseudo-class "^6.0.5" postcss-double-position-gradients "^3.1.2" @@ -8297,12 +8392,12 @@ postcss-pseudo-class-any-link@^7.1.6: dependencies: postcss-selector-parser "^6.0.10" -postcss-reduce-initial@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/postcss-reduce-initial/-/postcss-reduce-initial-5.1.0.tgz#fc31659ea6e85c492fb2a7b545370c215822c5d6" - integrity sha512-5OgTUviz0aeH6MtBjHfbr57tml13PuedK/Ecg8szzd4XRMbYxH4572JFG067z+FqBIf6Zp/d+0581glkvvWMFw== +postcss-reduce-initial@^5.1.1: + version "5.1.1" + resolved "https://registry.yarnpkg.com/postcss-reduce-initial/-/postcss-reduce-initial-5.1.1.tgz#c18b7dfb88aee24b1f8e4936541c29adbd35224e" + integrity sha512-//jeDqWcHPuXGZLoolFrUXBDyuEGbr9S2rMo19bkTIjBQ4PqkaO+oI8wua5BOUxpfi97i3PCoInsiFIEBfkm9w== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" caniuse-api "^3.0.0" postcss-reduce-transforms@^5.1.0: @@ -8325,9 +8420,9 @@ postcss-selector-not@^6.0.1: postcss-selector-parser "^6.0.10" postcss-selector-parser@^6.0.10, postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4, postcss-selector-parser@^6.0.5, postcss-selector-parser@^6.0.9: - version "6.0.10" - resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-6.0.10.tgz#79b61e2c0d1bfc2602d549e11d0876256f8df88d" - integrity sha512-IQ7TZdoaqbT+LCpShg46jnZVlhWD2w6iQYAcYXfHARZ7X1t/UGhhceQDs5X0cGqKvYlHNOuv7Oa1xmb0oQuA3w== + version "6.0.11" + resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-6.0.11.tgz#2e41dc39b7ad74046e1615185185cd0b17d0c8dc" + integrity sha512-zbARubNdogI9j7WY4nQJBiNqQf3sLS3wCP4WfOidu+p28LofJqDH1tcXypGrcmMHhDk2t9wGhCsYe/+szLTy1g== dependencies: cssesc "^3.0.0" util-deprecate "^1.0.2" @@ -8360,10 +8455,10 @@ postcss@^7.0.35: picocolors "^0.2.1" source-map "^0.6.1" -postcss@^8.3.5, postcss@^8.4.17, postcss@^8.4.4, postcss@^8.4.7: - version "8.4.18" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.18.tgz#6d50046ea7d3d66a85e0e782074e7203bc7fbca2" - integrity sha512-Wi8mWhncLJm11GATDaQKobXSNEYGUHeQLiQqDFG1qQ5UTDPTEvKw0Xt5NsTpktGTwLps3ByrWsBrG0rB8YQ9oA== +postcss@^8.3.5, postcss@^8.4.18, postcss@^8.4.19, postcss@^8.4.4: + version "8.4.20" + resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.20.tgz#64c52f509644cecad8567e949f4081d98349dc56" + integrity sha512-6Q04AXR1212bXr5fh03u8aAwbLxAQNGQ/Q1LNa0VfOI06ZAlhPHtQvE4OIdpj4kLThXilalPnmDSOD65DcHt+g== dependencies: nanoid "^3.3.4" picocolors "^1.0.0" @@ -8411,10 +8506,10 @@ pretty-format@^28.1.3: ansi-styles "^5.0.0" react-is "^18.0.0" -pretty-format@^29.0.0, pretty-format@^29.2.1: - version "29.2.1" - resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-29.2.1.tgz#86e7748fe8bbc96a6a4e04fa99172630907a9611" - integrity sha512-Y41Sa4aLCtKAXvwuIpTvcFBkyeYp2gdFWzXGA+ZNES3VwURIB165XO/z7CjETwzCCS53MjW/rLMyyqEnTtaOfA== +pretty-format@^29.0.0, pretty-format@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-29.3.1.tgz#1841cac822b02b4da8971dacb03e8a871b4722da" + integrity sha512-FyLnmb1cYJV8biEIiRyzRFvs2lry7PPIvOqKVe1GCUEYg4YGmlx1qG9EJNMxArYm7piII4qb8UV1Pncq5dxmcg== dependencies: "@jest/schemas" "^29.0.0" ansi-styles "^5.0.0" @@ -8431,9 +8526,9 @@ process@^0.11.10: integrity sha512-cdGef/drWFoydD1JsMzuFf8100nZl+GT+yacc2bEced5f9Rjk4z+WtFUTBu9PhOi9j/jfmBPu0mMEY4wIdAF8A== promise@^8.1.0: - 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version "2.2.2" - resolved "https://registry.yarnpkg.com/recursive-readdir/-/recursive-readdir-2.2.2.tgz#9946fb3274e1628de6e36b2f6714953b4845094f" - integrity sha512-nRCcW9Sj7NuZwa2XvH9co8NPeXUBhZP7CRKJtU+cS6PW9FpCIFoI5ib0NT1ZrbNuPoRy0ylyCaUL8Gih4LSyFg== + version "2.2.3" + resolved "https://registry.yarnpkg.com/recursive-readdir/-/recursive-readdir-2.2.3.tgz#e726f328c0d69153bcabd5c322d3195252379372" + integrity sha512-8HrF5ZsXk5FAH9dgsx3BlUer73nIhuj+9OrQwEbLTPOBzGkL1lsFCR01am+v+0m2Cmbs1nP12hLDl5FA7EszKA== dependencies: - minimatch "3.0.4" + minimatch "^3.0.5" redent@^3.0.0: version "3.0.0" @@ -8861,15 +8956,15 @@ regenerate@^1.4.2: resolved "https://registry.yarnpkg.com/regenerate/-/regenerate-1.4.2.tgz#b9346d8827e8f5a32f7ba29637d398b69014848a" integrity sha512-zrceR/XhGYU/d/opr2EKO7aRHUeiBI8qjtfHqADTwZd6Szfy16la6kqD0MIUs5z5hx6AaKa+PixpPrR289+I0A== -regenerator-runtime@^0.13.4, regenerator-runtime@^0.13.9: - version "0.13.10" - resolved "https://registry.yarnpkg.com/regenerator-runtime/-/regenerator-runtime-0.13.10.tgz#ed07b19616bcbec5da6274ebc75ae95634bfc2ee" - 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version "5.2.1" - resolved "https://registry.yarnpkg.com/regexpu-core/-/regexpu-core-5.2.1.tgz#a69c26f324c1e962e9ffd0b88b055caba8089139" - integrity sha512-HrnlNtpvqP1Xkb28tMhBUO2EbyUHdQlsnlAhzWcwHy8WJR53UWr7/MAvqrsQKMbV4qdpv03oTMG8iIhfsPFktQ== +regexpu-core@^5.2.1: + version "5.2.2" + resolved "https://registry.yarnpkg.com/regexpu-core/-/regexpu-core-5.2.2.tgz#3e4e5d12103b64748711c3aad69934d7718e75fc" + integrity sha512-T0+1Zp2wjF/juXMrMxHxidqGYn8U4R+zleSJhX9tQ1PUsS8a9UtYfbsF9LdiVgNX3kiX8RNaKM42nfSgvFJjmw== dependencies: regenerate "^1.4.2" regenerate-unicode-properties "^10.1.0" regjsgen "^0.7.1" regjsparser "^0.9.1" unicode-match-property-ecmascript "^2.0.0" - unicode-match-property-value-ecmascript "^2.0.0" + unicode-match-property-value-ecmascript "^2.1.0" regjsgen@^0.7.1: version "0.7.1" @@ -8948,9 +9043,9 @@ requires-port@^1.0.0: integrity sha512-KigOCHcocU3XODJxsu8i/j8T9tzT4adHiecwORRQ0ZZFcp7ahwXuRU1m+yuO90C5ZUyGeGfocHDI14M3L3yDAQ== reselect@^4.1.6: - version "4.1.6" - resolved "https://registry.yarnpkg.com/reselect/-/reselect-4.1.6.tgz#19ca2d3d0b35373a74dc1c98692cdaffb6602656" - integrity sha512-ZovIuXqto7elwnxyXbBtCPo9YFEr3uJqj2rRbcOOog1bmu2Ag85M4hixSwFWyaBMKXNgvPaJ9OSu9SkBPIeJHQ== + version "4.1.7" + resolved "https://registry.yarnpkg.com/reselect/-/reselect-4.1.7.tgz#56480d9ff3d3188970ee2b76527bd94a95567a42" + integrity sha512-Zu1xbUt3/OPwsXL46hvOOoQrap2azE7ZQbokq61BQfiXvhewsKDwhMeZjTX9sX0nvw1t/U5Audyn1I9P/m9z0A== resolve-cwd@^3.0.0: version "3.0.0" @@ -9169,7 +9264,7 @@ semver@^6.0.0, semver@^6.1.1, semver@^6.1.2, semver@^6.3.0: resolved "https://registry.yarnpkg.com/semver/-/semver-6.3.0.tgz#ee0a64c8af5e8ceea67687b133761e1becbd1d3d" integrity sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw== -semver@^7.3.2, semver@^7.3.5, semver@^7.3.7: +semver@^7.3.2, semver@^7.3.5, semver@^7.3.7, semver@^7.3.8: version "7.3.8" resolved "https://registry.yarnpkg.com/semver/-/semver-7.3.8.tgz#07a78feafb3f7b32347d725e33de7e2a2df67798" integrity sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A== @@ -9342,9 +9437,9 @@ source-map-js@^1.0.1, source-map-js@^1.0.2: integrity sha512-R0XvVJ9WusLiqTCEiGCmICCMplcCkIwwR11mOSD9CR5u+IXYdiseeEuXCVAjS54zqwkLcPNnmU4OeJ6tUrWhDw== source-map-loader@^3.0.0: - 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es-abstract "^1.19.5" + es-abstract "^1.20.4" string_decoder@^1.1.1, string_decoder@^1.3.0: version "1.3.0" @@ -9594,18 +9689,18 @@ style-loader@^3.3.1: resolved "https://registry.yarnpkg.com/style-loader/-/style-loader-3.3.1.tgz#057dfa6b3d4d7c7064462830f9113ed417d38575" integrity sha512-GPcQ+LDJbrcxHORTRes6Jy2sfvK2kS6hpSfI/fXhPt+spVzxF6LJ1dHLN9zIGmVaaP044YKaIatFaufENRiDoQ== -stylehacks@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/stylehacks/-/stylehacks-5.1.0.tgz#a40066490ca0caca04e96c6b02153ddc39913520" - integrity sha512-SzLmvHQTrIWfSgljkQCw2++C9+Ne91d/6Sp92I8c5uHTcy/PgeHamwITIbBW9wnFTY/3ZfSXR9HIL6Ikqmcu6Q== +stylehacks@^5.1.1: + version "5.1.1" + resolved "https://registry.yarnpkg.com/stylehacks/-/stylehacks-5.1.1.tgz#7934a34eb59d7152149fa69d6e9e56f2fc34bcc9" + integrity sha512-sBpcd5Hx7G6seo7b1LkpttvTz7ikD0LlH5RmdcBNb6fFR0Fl7LQwHDFr300q4cwUqi+IYrFGmsIHieMBfnN/Bw== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" postcss-selector-parser "^6.0.4" -stylis@4.0.13: - 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postcss "^8.4.17" + postcss "^8.4.18" postcss-import "^14.1.0" postcss-js "^4.0.0" postcss-load-config "^3.1.4" @@ -9761,9 +9857,9 @@ terser-webpack-plugin@^5.1.3, terser-webpack-plugin@^5.2.5: terser "^5.14.1" terser@^5.0.0, terser@^5.10.0, terser@^5.14.1: - version "5.15.1" - resolved "https://registry.yarnpkg.com/terser/-/terser-5.15.1.tgz#8561af6e0fd6d839669c73b92bdd5777d870ed6c" - integrity sha512-K1faMUvpm/FBxjBXud0LWVAGxmvoPbZbfTCYbSgaaYQaIXI3/TdI7a7ZGA73Zrou6Q8Zmz3oeUTsp/dj+ag2Xw== + version "5.16.1" + resolved "https://registry.yarnpkg.com/terser/-/terser-5.16.1.tgz#5af3bc3d0f24241c7fb2024199d5c461a1075880" + integrity sha512-xvQfyfA1ayT0qdK47zskQgRZeWLoOQ8JQ6mIgRGVNwZKdQMU+5FkCBjmv4QjcrTzyZquRw2FVtlJSRUmMKQslw== dependencies: "@jridgewell/source-map" "^0.3.2" acorn "^8.5.0" @@ -9897,14 +9993,14 @@ tslib@^1.8.1, tslib@^1.9.0: integrity sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg== tslib@^2.0.3: - version "2.4.0" - resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.4.0.tgz#7cecaa7f073ce680a05847aa77be941098f36dc3" - 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es-abstract "^1.20.0" for-each "^0.3.3" + gopd "^1.0.1" has-tostringtag "^1.0.0" - is-typed-array "^1.1.9" + is-typed-array "^1.1.10" which@^1.3.1: version "1.3.1" @@ -10620,9 +10726,9 @@ ws@^7.4.6: integrity sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q== ws@^8.4.2: - version "8.9.0" - resolved "https://registry.yarnpkg.com/ws/-/ws-8.9.0.tgz#2a994bb67144be1b53fe2d23c53c028adeb7f45e" - integrity sha512-Ja7nszREasGaYUYCI2k4lCKIRTt+y7XuqVoHR44YpI49TtryyqbqvDMn5eqfW7e6HzTukDRIsXqzVHScqRcafg== + version "8.11.0" + resolved "https://registry.yarnpkg.com/ws/-/ws-8.11.0.tgz#6a0d36b8edfd9f96d8b25683db2f8d7de6e8e143" + integrity sha512-HPG3wQd9sNQoT9xHyNCXoDUa+Xw/VevmY9FoHyQ+g+rrMn4j6FB4np7Z0OhdTgjx6MgQLK7jwSy1YecU1+4Asg== xml-name-validator@^3.0.0: version "3.0.0" diff --git a/demos/jbrowse-react-circular-genome-view-vanillajs/README.md b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/README.md similarity index 53% rename from demos/jbrowse-react-circular-genome-view-vanillajs/README.md rename to embedded_demos/jbrowse-react-circular-genome-view-vanillajs/README.md index 14b32fca3e..6faf766581 100644 --- a/demos/jbrowse-react-circular-genome-view-vanillajs/README.md +++ b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/README.md @@ -2,7 +2,8 @@ See this app running at https://jbrowse.org/demos/cgv-vanillajs/. -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-vanillajs +Download this directory from the monorepo using +https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-circular-genome-view-vanillajs ## Usage diff --git a/demos/jbrowse-react-circular-genome-view-vanillajs/assembly.js b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/assembly.js similarity index 100% rename from demos/jbrowse-react-circular-genome-view-vanillajs/assembly.js rename to embedded_demos/jbrowse-react-circular-genome-view-vanillajs/assembly.js diff --git a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/defaultSession.js b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/defaultSession.js new file mode 100644 index 0000000000..582c6b2e64 --- /dev/null +++ b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/defaultSession.js @@ -0,0 +1,22 @@ +export default { + name: 'My session', + view: { + id: 'circularView', + type: 'CircularView', + bpPerPx: 5000000, + tracks: [ + { + id: 'uPdLKHik1', + type: 'VariantTrack', + configuration: 'pacbio_sv_vcf', + displays: [ + { + id: 'v9QVAR3oaB', + type: 'ChordVariantDisplay', + configuration: 'pacbio_sv_vcf-ChordVariantDisplay', + }, + ], + }, + ], + }, +} diff --git a/products/jbrowse-react-circular-genome-view/umd_example/genomeView.js b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js similarity index 92% rename from products/jbrowse-react-circular-genome-view/umd_example/genomeView.js rename to embedded_demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js index 25d26b402d..53647685c7 100644 --- a/products/jbrowse-react-circular-genome-view/umd_example/genomeView.js +++ b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/genomeView.js @@ -1,6 +1,7 @@ /* global JBrowseReactCircularGenomeView React, ReactDOM */ import assembly from './assembly.js' import tracks from './tracks.js' +import defaultSession from './defaultSession.js' const { createViewState, JBrowseCircularGenomeView } = JBrowseReactCircularGenomeView @@ -11,6 +12,7 @@ const updates = document.getElementById('update') const state = new createViewState({ assembly, tracks, + defaultSession, onChange: patch => { updates.innerHTML += JSON.stringify(patch) + '\n' }, diff --git a/demos/jbrowse-react-circular-genome-view-vanillajs/index.html b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/index.html similarity index 75% rename from demos/jbrowse-react-circular-genome-view-vanillajs/index.html rename to embedded_demos/jbrowse-react-circular-genome-view-vanillajs/index.html index 8118d6efa0..42d9f47762 100644 --- a/demos/jbrowse-react-circular-genome-view-vanillajs/index.html +++ b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/index.html @@ -23,6 +23,15 @@

Using JBrowse Circular Genome View!

+

Code

+ +

+ The code for this app is available at + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-view-vanillajs +

diff --git a/demos/jbrowse-react-circular-genome-view-vanillajs/package.json b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/package.json similarity index 91% rename from demos/jbrowse-react-circular-genome-view-vanillajs/package.json rename to embedded_demos/jbrowse-react-circular-genome-view-vanillajs/package.json index 4626a47e4e..bc84b3f156 100644 --- a/demos/jbrowse-react-circular-genome-view-vanillajs/package.json +++ b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/package.json @@ -1,4 +1,5 @@ { + "license": "MIT", "scripts": { "deploy": "aws s3 sync --delete . s3://jbrowse.org/demos/cgv-vanillajs/", "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/demos/cgv-vanillajs/*\"" diff --git a/demos/jbrowse-react-circular-genome-view-vanillajs/tracks.js b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/tracks.js similarity index 100% rename from demos/jbrowse-react-circular-genome-view-vanillajs/tracks.js rename to embedded_demos/jbrowse-react-circular-genome-view-vanillajs/tracks.js diff --git a/demos/jbrowse-react-circular-genome-view-vanillajs/yarn.lock b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/yarn.lock similarity index 100% rename from demos/jbrowse-react-circular-genome-view-vanillajs/yarn.lock rename to embedded_demos/jbrowse-react-circular-genome-view-vanillajs/yarn.lock diff --git a/demos/jbrowse-react-circular-genome-view/.env b/embedded_demos/jbrowse-react-circular-genome-view/.env similarity index 100% rename from demos/jbrowse-react-circular-genome-view/.env rename to embedded_demos/jbrowse-react-circular-genome-view/.env diff --git a/demos/jbrowse-react-circular-genome-view/.gitignore b/embedded_demos/jbrowse-react-circular-genome-view/.gitignore similarity index 100% rename from demos/jbrowse-react-circular-genome-view/.gitignore rename to embedded_demos/jbrowse-react-circular-genome-view/.gitignore diff --git a/demos/jbrowse-react-circular-genome-view/README.md b/embedded_demos/jbrowse-react-circular-genome-view/README.md similarity index 85% rename from demos/jbrowse-react-circular-genome-view/README.md rename to embedded_demos/jbrowse-react-circular-genome-view/README.md index c84ffc8275..3b183c8766 100644 --- a/demos/jbrowse-react-circular-genome-view/README.md +++ b/embedded_demos/jbrowse-react-circular-genome-view/README.md @@ -4,7 +4,7 @@ See this app running at https://jbrowse.org/demos/cgv/. This demo is originally by [@garrettjstevens](https://github.com/garrettjstevens/). -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view +Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-circular-genome-view ## Usage diff --git a/demos/jbrowse-react-circular-genome-view/package.json b/embedded_demos/jbrowse-react-circular-genome-view/package.json similarity index 94% rename from demos/jbrowse-react-circular-genome-view/package.json rename to embedded_demos/jbrowse-react-circular-genome-view/package.json index 75953cab8d..190d5e28a6 100644 --- a/demos/jbrowse-react-circular-genome-view/package.json +++ b/embedded_demos/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,7 @@ { "name": "jbrowse-react-circular-genome-view-demo", "version": "0.1.0", + "license": "MIT", "private": true, "dependencies": { "@fontsource/roboto": "^4.5.3", @@ -11,8 +12,8 @@ "@testing-library/user-event": "^12.1.10", "@types/jest": "^26.0.15", "@types/node": "^12.0.0", - "@types/react": "^17.0.0", - "@types/react-dom": "^17.0.0", + "@types/react": "^18.0.0", + "@types/react-dom": "^18.0.0", "react": "^17.0.2", "react-dom": "^17.0.2", "react-scripts": "4.0.3", diff --git a/demos/jbrowse-react-circular-genome-view/public/favicon.ico b/embedded_demos/jbrowse-react-circular-genome-view/public/favicon.ico similarity index 100% rename from demos/jbrowse-react-circular-genome-view/public/favicon.ico rename to embedded_demos/jbrowse-react-circular-genome-view/public/favicon.ico diff --git a/demos/jbrowse-react-circular-genome-view/public/index.html b/embedded_demos/jbrowse-react-circular-genome-view/public/index.html similarity index 100% rename from demos/jbrowse-react-circular-genome-view/public/index.html rename to embedded_demos/jbrowse-react-circular-genome-view/public/index.html diff --git a/demos/jbrowse-react-circular-genome-view/public/logo192.png b/embedded_demos/jbrowse-react-circular-genome-view/public/logo192.png similarity index 100% rename from demos/jbrowse-react-circular-genome-view/public/logo192.png rename to embedded_demos/jbrowse-react-circular-genome-view/public/logo192.png diff --git a/demos/jbrowse-react-circular-genome-view/public/logo512.png b/embedded_demos/jbrowse-react-circular-genome-view/public/logo512.png similarity index 100% rename from demos/jbrowse-react-circular-genome-view/public/logo512.png rename to embedded_demos/jbrowse-react-circular-genome-view/public/logo512.png diff --git a/demos/jbrowse-react-circular-genome-view/public/manifest.json b/embedded_demos/jbrowse-react-circular-genome-view/public/manifest.json similarity index 100% rename from demos/jbrowse-react-circular-genome-view/public/manifest.json rename to embedded_demos/jbrowse-react-circular-genome-view/public/manifest.json diff --git a/demos/jbrowse-react-circular-genome-view/public/robots.txt b/embedded_demos/jbrowse-react-circular-genome-view/public/robots.txt similarity index 100% rename from demos/jbrowse-react-circular-genome-view/public/robots.txt rename to embedded_demos/jbrowse-react-circular-genome-view/public/robots.txt diff --git a/demos/jbrowse-react-circular-genome-view/src/App.tsx b/embedded_demos/jbrowse-react-circular-genome-view/src/App.tsx similarity index 80% rename from demos/jbrowse-react-circular-genome-view/src/App.tsx rename to embedded_demos/jbrowse-react-circular-genome-view/src/App.tsx index 5e17bd3103..da85ee14be 100644 --- a/demos/jbrowse-react-circular-genome-view/src/App.tsx +++ b/embedded_demos/jbrowse-react-circular-genome-view/src/App.tsx @@ -7,33 +7,12 @@ import { import assembly from './assembly' import tracks from './tracks' +import defaultSession from './defaultSession' -const defaultSession = { - name: 'My session', - view: { - id: 'circularView', - type: 'CircularView', - bpPerPx: 5000000, - tracks: [ - { - id: 'uPdLKHik1', - type: 'VariantTrack', - configuration: 'pacbio_sv_vcf', - displays: [ - { - id: 'v9QVAR3oaB', - type: 'ChordVariantDisplay', - configuration: 'pacbio_sv_vcf-ChordVariantDisplay', - }, - ], - }, - ], - }, -} +type ViewModel = ReturnType function View() { - const [viewState, setViewState] = - useState>() + const [viewState, setViewState] = useState() const [patches, setPatches] = useState('') const [stateSnapshot, setStateSnapshot] = useState('') @@ -63,11 +42,11 @@ function View() {

The code for this app is available at{' '} - https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view .

diff --git a/products/jbrowse-react-linear-genome-view/umd_example/assembly.js b/embedded_demos/jbrowse-react-circular-genome-view/src/assembly.ts similarity index 53% rename from products/jbrowse-react-linear-genome-view/umd_example/assembly.js rename to embedded_demos/jbrowse-react-circular-genome-view/src/assembly.ts index 7fd62437ec..389e7c6777 100644 --- a/products/jbrowse-react-linear-genome-view/umd_example/assembly.js +++ b/embedded_demos/jbrowse-react-circular-genome-view/src/assembly.ts @@ -1,32 +1,34 @@ -export default { - name: 'GRCh38', +const assembly = { + name: 'hg19', + aliases: ['GRCh37'], sequence: { type: 'ReferenceSequenceTrack', - trackId: 'GRCh38-ReferenceSequenceTrack', + trackId: 'Pd8Wh30ei9R', adapter: { type: 'BgzipFastaAdapter', fastaLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz', + uri: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz', locationType: 'UriLocation', }, faiLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai', + uri: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai', locationType: 'UriLocation', }, gziLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi', + uri: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi', locationType: 'UriLocation', }, }, }, - aliases: ['hg38'], refNameAliases: { adapter: { type: 'RefNameAliasAdapter', location: { - uri: 'GRCh38.aliases.txt', + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg19_aliases.txt', locationType: 'UriLocation', }, }, }, } + +export default assembly diff --git a/demos/jbrowse-react-circular-genome-view/src/declare.d.ts b/embedded_demos/jbrowse-react-circular-genome-view/src/declare.d.ts similarity index 100% rename from demos/jbrowse-react-circular-genome-view/src/declare.d.ts rename to embedded_demos/jbrowse-react-circular-genome-view/src/declare.d.ts diff --git a/embedded_demos/jbrowse-react-circular-genome-view/src/defaultSession.ts b/embedded_demos/jbrowse-react-circular-genome-view/src/defaultSession.ts new file mode 100644 index 0000000000..582c6b2e64 --- /dev/null +++ b/embedded_demos/jbrowse-react-circular-genome-view/src/defaultSession.ts @@ -0,0 +1,22 @@ +export default { + name: 'My session', + view: { + id: 'circularView', + type: 'CircularView', + bpPerPx: 5000000, + tracks: [ + { + id: 'uPdLKHik1', + type: 'VariantTrack', + configuration: 'pacbio_sv_vcf', + displays: [ + { + id: 'v9QVAR3oaB', + type: 'ChordVariantDisplay', + configuration: 'pacbio_sv_vcf-ChordVariantDisplay', + }, + ], + }, + ], + }, +} diff --git a/demos/jbrowse-react-circular-genome-view/src/index.css b/embedded_demos/jbrowse-react-circular-genome-view/src/index.css similarity index 100% rename from demos/jbrowse-react-circular-genome-view/src/index.css rename to embedded_demos/jbrowse-react-circular-genome-view/src/index.css diff --git a/demos/jbrowse-react-circular-genome-view/src/index.tsx b/embedded_demos/jbrowse-react-circular-genome-view/src/index.tsx similarity index 100% rename from demos/jbrowse-react-circular-genome-view/src/index.tsx rename to embedded_demos/jbrowse-react-circular-genome-view/src/index.tsx diff --git a/demos/jbrowse-react-circular-genome-view/src/react-app-env.d.ts b/embedded_demos/jbrowse-react-circular-genome-view/src/react-app-env.d.ts similarity index 100% rename from demos/jbrowse-react-circular-genome-view/src/react-app-env.d.ts rename to embedded_demos/jbrowse-react-circular-genome-view/src/react-app-env.d.ts diff --git a/embedded_demos/jbrowse-react-circular-genome-view/src/tracks.ts b/embedded_demos/jbrowse-react-circular-genome-view/src/tracks.ts new file mode 100644 index 0000000000..b641868fff --- /dev/null +++ b/embedded_demos/jbrowse-react-circular-genome-view/src/tracks.ts @@ -0,0 +1,24 @@ +const tracks = [ + { + type: 'VariantTrack', + trackId: 'pacbio_sv_vcf', + name: 'HG002 Pacbio SV (VCF)', + assemblyNames: ['hg19'], + category: ['GIAB'], + adapter: { + type: 'VcfTabixAdapter', + vcfGzLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf.gz', + locationType: 'UriLocation', + }, + index: { + location: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf.gz.tbi', + locationType: 'UriLocation', + }, + }, + }, + }, +] + +export default tracks diff --git a/demos/jbrowse-react-circular-genome-view/tsconfig.json b/embedded_demos/jbrowse-react-circular-genome-view/tsconfig.json similarity index 95% rename from demos/jbrowse-react-circular-genome-view/tsconfig.json rename to embedded_demos/jbrowse-react-circular-genome-view/tsconfig.json index 9d379a3c4a..2d519b5ad9 100644 --- a/demos/jbrowse-react-circular-genome-view/tsconfig.json +++ b/embedded_demos/jbrowse-react-circular-genome-view/tsconfig.json @@ -1,6 +1,6 @@ { "compilerOptions": { - "target": "es5", + "target": "es2015", "lib": ["dom", "dom.iterable", "esnext"], "allowJs": true, "skipLibCheck": true, diff --git a/demos/jbrowse-react-circular-genome-view/yarn.lock b/embedded_demos/jbrowse-react-circular-genome-view/yarn.lock similarity index 92% rename from demos/jbrowse-react-circular-genome-view/yarn.lock rename to embedded_demos/jbrowse-react-circular-genome-view/yarn.lock index cff6a63dec..91c6b6116c 100644 --- a/demos/jbrowse-react-circular-genome-view/yarn.lock +++ b/embedded_demos/jbrowse-react-circular-genome-view/yarn.lock @@ -36,10 +36,10 @@ dependencies: "@babel/highlight" "^7.18.6" -"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.19.3", "@babel/compat-data@^7.19.4": - version "7.19.4" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.19.4.tgz#95c86de137bf0317f3a570e1b6e996b427299747" - integrity sha512-CHIGpJcUQ5lU9KrPHTjBMhVwQG6CQjxfg36fGXl3qk/Gik1WwWachaXFuo0uCWJT/mStOKtcbFJCaVLihC1CMw== +"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.20.0", "@babel/compat-data@^7.20.1": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.20.5.tgz#86f172690b093373a933223b4745deeb6049e733" + integrity sha512-KZXo2t10+/jxmkhNXc7pZTqRvSOIvVv/+lJwHS+B2rErwOyjuVRh60yVpb7liQ1U5t7lLJ1bz+t8tSypUZdm0g== "@babel/core@7.12.3": version "7.12.3" @@ -64,32 +64,32 @@ source-map "^0.5.0" "@babel/core@^7.1.0", "@babel/core@^7.12.3", "@babel/core@^7.16.0", "@babel/core@^7.7.5", "@babel/core@^7.8.4": - version "7.19.3" - resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.19.3.tgz#2519f62a51458f43b682d61583c3810e7dcee64c" - integrity sha512-WneDJxdsjEvyKtXKsaBGbDeiyOjR5vYq4HcShxnIbG0qixpoHjI3MqeZM9NDvsojNCEBItQE4juOo/bU6e72gQ== + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.20.5.tgz#45e2114dc6cd4ab167f81daf7820e8fa1250d113" + integrity 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"@babel/plugin-proposal-unicode-property-regex@^7.4.4": @@ -520,12 +520,12 @@ dependencies: "@babel/helper-plugin-utils" "^7.18.6" -"@babel/plugin-syntax-import-assertions@^7.18.6": - version "7.18.6" - resolved "https://registry.yarnpkg.com/@babel/plugin-syntax-import-assertions/-/plugin-syntax-import-assertions-7.18.6.tgz#cd6190500a4fa2fe31990a963ffab4b63e4505e4" - integrity sha512-/DU3RXad9+bZwrgWJQKbr39gYbJpLJHezqEzRzi/BHRlJ9zsQb4CK2CA/5apllXNomwA1qHwzvHl+AdEmC5krQ== +"@babel/plugin-syntax-import-assertions@^7.20.0": + version "7.20.0" + resolved "https://registry.yarnpkg.com/@babel/plugin-syntax-import-assertions/-/plugin-syntax-import-assertions-7.20.0.tgz#bb50e0d4bea0957235390641209394e87bdb9cc4" + integrity sha512-IUh1vakzNoWalR8ch/areW7qFopR2AEw03JlG7BbrDqmQ4X3q9uuipQwSGrUn7oGiemKjtSLDhNtQHzMHr1JdQ== dependencies: - "@babel/helper-plugin-utils" "^7.18.6" + "@babel/helper-plugin-utils" "^7.19.0" "@babel/plugin-syntax-import-meta@^7.8.3": version "7.10.4" @@ -604,12 +604,12 @@ 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"^7.8.3" - "@babel/plugin-syntax-import-assertions" "^7.18.6" + "@babel/plugin-syntax-import-assertions" "^7.20.0" "@babel/plugin-syntax-json-strings" "^7.8.3" "@babel/plugin-syntax-logical-assignment-operators" "^7.10.4" "@babel/plugin-syntax-nullish-coalescing-operator" "^7.8.3" @@ -977,10 +974,10 @@ "@babel/plugin-transform-arrow-functions" "^7.18.6" "@babel/plugin-transform-async-to-generator" "^7.18.6" "@babel/plugin-transform-block-scoped-functions" "^7.18.6" - "@babel/plugin-transform-block-scoping" "^7.19.4" - "@babel/plugin-transform-classes" "^7.19.0" + "@babel/plugin-transform-block-scoping" "^7.20.2" + "@babel/plugin-transform-classes" "^7.20.2" "@babel/plugin-transform-computed-properties" "^7.18.9" - "@babel/plugin-transform-destructuring" "^7.19.4" + "@babel/plugin-transform-destructuring" "^7.20.2" "@babel/plugin-transform-dotall-regex" "^7.18.6" "@babel/plugin-transform-duplicate-keys" "^7.18.9" "@babel/plugin-transform-exponentiation-operator" "^7.18.6" @@ -988,14 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"https://registry.yarnpkg.com/emojis-list/-/emojis-list-3.0.0.tgz#5570662046ad29e2e916e71aae260abdff4f6a78" @@ -5010,10 +5035,10 @@ error-stack-parser@^2.0.6: dependencies: stackframe "^1.3.4" -es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19.2, es-abstract@^1.19.5, es-abstract@^1.20.1: - version "1.20.4" - resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.4.tgz#1d103f9f8d78d4cf0713edcd6d0ed1a46eed5861" - integrity sha512-0UtvRN79eMe2L+UNEF1BwRe364sj/DXhQ/k5FmivgoSdpM90b8Jc0mDzKMGo7QS0BVbOP/bTwBKNnDc9rNzaPA== +es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.20.4: + version "1.20.5" + resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.5.tgz#e6dc99177be37cacda5988e692c3fa8b218e95d2" + integrity sha512-7h8MM2EQhsCA7pU/Nv78qOXFpD8Rhqd12gYiSJVkrH9+e8VuA8JlPJK/hQjjlLv6pJvx/z1iRFKzYb0XT/RuAQ== dependencies: call-bind "^1.0.2" es-to-primitive "^1.2.1" @@ -5021,6 +5046,7 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 function.prototype.name "^1.1.5" get-intrinsic "^1.1.3" get-symbol-description "^1.0.0" + gopd "^1.0.1" has "^1.0.3" has-property-descriptors "^1.0.0" has-symbols "^1.0.3" @@ -5036,8 +5062,8 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 object.assign "^4.1.4" regexp.prototype.flags "^1.4.3" safe-regex-test "^1.0.0" - string.prototype.trimend "^1.0.5" - string.prototype.trimstart "^1.0.5" + string.prototype.trimend "^1.0.6" + string.prototype.trimstart "^1.0.6" unbox-primitive "^1.0.2" es-array-method-boxes-properly@^1.0.0: @@ -5045,6 +5071,20 @@ es-array-method-boxes-properly@^1.0.0: resolved "https://registry.yarnpkg.com/es-array-method-boxes-properly/-/es-array-method-boxes-properly-1.0.0.tgz#873f3e84418de4ee19c5be752990b2e44718d09e" integrity sha512-wd6JXUmyHmt8T5a2xreUwKcGPq6f1f+WwIJkijUqiGcJz1qqnZgP6XIK+QyIWU5lT7imeNxUll48bziG+TSYcA== +es-get-iterator@^1.1.2: + version "1.1.2" + resolved 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@@ follow-redirects@^1.0.0: resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.15.2.tgz#b460864144ba63f2681096f274c4e57026da2c13" integrity sha512-VQLG33o04KaQ8uYi2tVNbdrWp1QWxNNea+nmIB4EVM28v0hmP17z7aG1+wAkNzVq4KeXTq3221ye5qTJP91JwA== +for-each@^0.3.3: + version "0.3.3" + resolved "https://registry.yarnpkg.com/for-each/-/for-each-0.3.3.tgz#69b447e88a0a5d32c3e7084f3f1710034b21376e" + integrity sha512-jqYfLp7mo9vIyQf8ykW2v7A+2N4QjeCeI5+Dz9XraiO1ign81wjiH7Fb9vSOWvQfNtmSa4H2RoQTrrXivdUZmw== + dependencies: + is-callable "^1.1.3" + for-in@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/for-in/-/for-in-1.0.2.tgz#81068d295a8142ec0ac726c6e2200c30fb6d5e80" @@ -5906,9 +5954,9 @@ functions-have-names@^1.2.2: integrity sha512-xckBUXyTIqT97tq2x2AMb+g163b5JFysYk0x4qxNFwbfQkmNZoiRHb6sPzI9/QV33WeuvVYBUIiD4NzNIyqaRQ== generic-filehandle@^3.0.0: - version "3.0.0" - resolved 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resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.4.tgz#8551e7baf74a7a6ba5f749cfb16aa60722f0d6f3" + integrity sha512-tA8URYccNzMo94s5MQZgH8NB/XTa6HsOo0MLfXTKKEnHVVdegzaQoFZ7Jp44bdvLvY2waT5dc+j5ICEswhi7UQ== dependencies: - get-intrinsic "^1.1.0" + get-intrinsic "^1.1.3" has "^1.0.3" side-channel "^1.0.4" @@ -6575,7 +6630,7 @@ is-accessor-descriptor@^1.0.0: dependencies: kind-of "^6.0.0" -is-arguments@^1.0.4: +is-arguments@^1.0.4, is-arguments@^1.1.0, is-arguments@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== @@ -6627,7 +6682,7 @@ is-buffer@^1.1.5: resolved "https://registry.yarnpkg.com/is-buffer/-/is-buffer-1.1.6.tgz#efaa2ea9daa0d7ab2ea13a97b2b8ad51fefbe8be" integrity sha512-NcdALwpXkTm5Zvvbk7owOUSvVvBKDgKP5/ewfXEznmQFfs4ZRmanOeKBTjRVjka3QFoN6XJ+9F3USqfHqTaU5w== -is-callable@^1.1.4, is-callable@^1.2.7: +is-callable@^1.1.3, is-callable@^1.1.4, is-callable@^1.2.7: version "1.2.7" resolved "https://registry.yarnpkg.com/is-callable/-/is-callable-1.2.7.tgz#3bc2a85ea742d9e36205dcacdd72ca1fdc51b055" integrity sha512-1BC0BVFhS/p0qtw6enp8e+8OD0UrK0oFLztSjNzhcKA3WDuJxxAPXzPuPtKkjEY9UUoEWlX/8fgKeu2S8i9JTA== @@ -6672,7 +6727,7 @@ is-data-descriptor@^1.0.0: dependencies: kind-of "^6.0.0" -is-date-object@^1.0.1: +is-date-object@^1.0.1, is-date-object@^1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/is-date-object/-/is-date-object-1.0.5.tgz#0841d5536e724c25597bf6ea62e1bd38298df31f" integrity sha512-9YQaSxsAiSwcvS33MBk3wTCVnWK+HhF8VZR2jRxehM16QcVOdHqPn4VPHmRK4lSr38n9JriurInLcP90xsYNfQ== @@ -6753,6 +6808,11 @@ is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: dependencies: is-extglob "^2.1.1" +is-map@^2.0.1, is-map@^2.0.2: + version "2.0.2" + resolved 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"https://registry.yarnpkg.com/is-shared-array-buffer/-/is-shared-array-buffer-1.0.2.tgz#8f259c573b60b6a32d4058a1a07430c0a7344c79" @@ -6887,11 +6952,27 @@ is-symbol@^1.0.2, is-symbol@^1.0.3: dependencies: has-symbols "^1.0.2" +is-typed-array@^1.1.10: + version "1.1.10" + resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.10.tgz#36a5b5cb4189b575d1a3e4b08536bfb485801e3f" + integrity sha512-PJqgEHiWZvMpaFZ3uTc8kHPM4+4ADTlDniuQL7cU/UDA0Ql7F70yGfHph3cLNe+c9toaigv+DFzTJKhc2CtO6A== + dependencies: + available-typed-arrays "^1.0.5" + call-bind "^1.0.2" + for-each "^0.3.3" + gopd "^1.0.1" + has-tostringtag "^1.0.0" + is-typedarray@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-typedarray/-/is-typedarray-1.0.0.tgz#e479c80858df0c1b11ddda6940f96011fcda4a9a" integrity sha512-cyA56iCMHAh5CdzjJIa4aohJyeO1YbwLi3Jc35MmRU6poroFjIGZzUzupGiRPOjgHg9TLu43xbpwXk523fMxKA== +is-weakmap@^2.0.1: + version "2.0.1" + resolved "https://registry.yarnpkg.com/is-weakmap/-/is-weakmap-2.0.1.tgz#5008b59bdc43b698201d18f62b37b2ca243e8cf2" + integrity sha512-NSBR4kH5oVj1Uwvv970ruUkCV7O1mzgVFO4/rev2cLRda9Tm9HrL70ZPut4rOHgY0FNrUu9BCbXA2sdQ+x0chA== + is-weakref@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-weakref/-/is-weakref-1.0.2.tgz#9529f383a9338205e89765e0392efc2f100f06f2" @@ -6899,6 +6980,14 @@ is-weakref@^1.0.2: dependencies: call-bind "^1.0.2" +is-weakset@^2.0.1: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-weakset/-/is-weakset-2.0.2.tgz#4569d67a747a1ce5a994dfd4ef6dcea76e7c0a1d" + integrity sha512-t2yVvttHkQktwnNNmBQ98AhENLdPUTDTE21uPqAQ0ARwQfGeQKRVS0NNurH7bTf7RrvcVn1OOge45CnBeHCSmg== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.1" + is-windows@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-windows/-/is-windows-1.0.2.tgz#d1850eb9791ecd18e6182ce12a30f396634bb19d" @@ -6921,6 +7010,11 @@ isarray@1.0.0, isarray@^1.0.0, isarray@~1.0.0: resolved "https://registry.yarnpkg.com/isarray/-/isarray-1.0.0.tgz#bb935d48582cba168c06834957a54a3e07124f11" integrity sha512-VLghIWNM6ELQzo7zwmcg0NmTVyWKYjvIeM83yjp0wRDTmUnrM678fQbcKBo6n2CJEF0szoG//ytg+TKla89ALQ== +isarray@^2.0.5: + version "2.0.5" + resolved "https://registry.yarnpkg.com/isarray/-/isarray-2.0.5.tgz#8af1e4c1221244cc62459faf38940d4e644a5723" + integrity sha512-xHjhDr3cNBK0BzdUJSPXZntQUx/mwMS5Rw4A7lPJ90XGAO6ISP/ePDNuo0vhqOZU+UD5JoodwCAAoZQd3FeAKw== + isexe@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/isexe/-/isexe-2.0.0.tgz#e8fbf374dc556ff8947a10dcb0572d633f2cfa10" @@ -7079,15 +7173,15 @@ jest-diff@^26.0.0, jest-diff@^26.6.2: jest-get-type "^26.3.0" pretty-format "^26.6.2" -jest-diff@^29.2.1: - version "29.2.1" - resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-29.2.1.tgz#027e42f5a18b693fb2e88f81b0ccab533c08faee" - integrity sha512-gfh/SMNlQmP3MOUgdzxPOd4XETDJifADpT937fN1iUGz+9DgOu2eUPHH25JDkLVcLwwqxv3GzVyK4VBUr9fjfA== +jest-diff@^29.3.1: + version 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"https://registry.yarnpkg.com/jest-matcher-utils/-/jest-matcher-utils-29.3.1.tgz#6e7f53512f80e817dfa148672bd2d5d04914a572" + integrity sha512-fkRMZUAScup3txIKfMe3AIZZmPEjWEdsPJFK3AIy5qRohWqQFg1qrmKfYXR9qEkNc7OdAu2N4KPHibEmy4HPeQ== dependencies: chalk "^4.0.0" - jest-diff "^29.2.1" + jest-diff "^29.3.1" jest-get-type "^29.2.0" - pretty-format "^29.2.1" + pretty-format "^29.3.1" jest-message-util@^26.6.0, jest-message-util@^26.6.2: version "26.6.2" @@ -7230,18 +7324,18 @@ jest-message-util@^26.6.0, jest-message-util@^26.6.2: slash "^3.0.0" stack-utils "^2.0.2" -jest-message-util@^29.2.1: - version "29.2.1" - resolved "https://registry.yarnpkg.com/jest-message-util/-/jest-message-util-29.2.1.tgz#3a51357fbbe0cc34236f17a90d772746cf8d9193" - integrity sha512-Dx5nEjw9V8C1/Yj10S/8ivA8F439VS8vTq1L7hEgwHFn9ovSKNpYW/kwNh7UglaEgXO42XxzKJB+2x0nSglFVw== +jest-message-util@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-message-util/-/jest-message-util-29.3.1.tgz#37bc5c468dfe5120712053dd03faf0f053bd6adb" + integrity sha512-lMJTbgNcDm5z+6KDxWtqOFWlGQxD6XaYwBqHR8kmpkP+WWWG90I35kdtQHY67Ay5CSuydkTBbJG+tH9JShFCyA== dependencies: "@babel/code-frame" "^7.12.13" - "@jest/types" "^29.2.1" + "@jest/types" "^29.3.1" "@types/stack-utils" "^2.0.0" chalk "^4.0.0" graceful-fs "^4.2.9" micromatch "^4.0.4" - pretty-format "^29.2.1" + pretty-format "^29.3.1" slash "^3.0.0" stack-utils "^2.0.3" @@ -7254,9 +7348,9 @@ jest-mock@^26.6.2: "@types/node" "*" jest-pnp-resolver@^1.2.2: - version "1.2.2" - resolved "https://registry.yarnpkg.com/jest-pnp-resolver/-/jest-pnp-resolver-1.2.2.tgz#b704ac0ae028a89108a4d040b3f919dfddc8e33c" - integrity sha512-olV41bKSMm8BdnuMsewT4jqlZ8+3TCARAXjZGT9jcoSnrfUnRCqnMoF9XEeoWjbzObpqF9dRhHQj0Xb9QdF6/w== + version "1.2.3" + resolved "https://registry.yarnpkg.com/jest-pnp-resolver/-/jest-pnp-resolver-1.2.3.tgz#930b1546164d4ad5937d5540e711d4d38d4cad2e" + 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sha512-Bdboy+l7tA3OGW6FjyFHWkP5LuByj1Tk33Ljyq0axyzdk9//JSi2u3fP1QSmd1KNwq6VOKYGlAu87CisVir6Pw== json-stable-stringify@^1.0.1: - version "1.0.1" - resolved "https://registry.yarnpkg.com/json-stable-stringify/-/json-stable-stringify-1.0.1.tgz#9a759d39c5f2ff503fd5300646ed445f88c4f9af" - integrity sha512-i/J297TW6xyj7sDFa7AmBPkQvLIxWr2kKPWI26tXydnZrzVAocNqn5DMNT1Mzk0vit1V5UkRM7C1KdVNp7Lmcg== + version "1.0.2" + resolved "https://registry.yarnpkg.com/json-stable-stringify/-/json-stable-stringify-1.0.2.tgz#e06f23128e0bbe342dc996ed5a19e28b57b580e0" + integrity sha512-eunSSaEnxV12z+Z73y/j5N37/In40GK4GmsSy+tEHJMxknvqnA7/djeYtAgW0GsWHUfg+847WJjKaEylk2y09g== dependencies: - jsonify "~0.0.0" + jsonify "^0.0.1" json5@^1.0.1: version "1.0.1" @@ -7589,9 +7683,9 @@ json5@^1.0.1: minimist "^1.2.0" json5@^2.1.2, json5@^2.2.1: - version "2.2.1" - resolved "https://registry.yarnpkg.com/json5/-/json5-2.2.1.tgz#655d50ed1e6f95ad1a3caababd2b0efda10b395c" - integrity sha512-1hqLFMSrGHRHxav9q9gNjJ5EXznIxGVO09xQRrwplcS8qs28pZ8s8hupZAmqDwZUmVZ2Qb2jnyPOWcDH8m8dlA== + version "2.2.2" + resolved "https://registry.yarnpkg.com/json5/-/json5-2.2.2.tgz#64471c5bdcc564c18f7c1d4df2e2297f2457c5ab" + integrity sha512-46Tk9JiOL2z7ytNQWFLpj99RZkVgeHf87yGQKsIkaPz1qSH9UczKH1rO7K3wgRselo0tYMUNfecYpm/p1vC7tQ== jsonfile@^4.0.0: version "4.0.0" @@ -7609,7 +7703,7 @@ jsonfile@^6.0.1: optionalDependencies: graceful-fs "^4.1.6" -jsonify@~0.0.0: +jsonify@^0.0.1: version "0.0.1" resolved "https://registry.yarnpkg.com/jsonify/-/jsonify-0.0.1.tgz#2aa3111dae3d34a0f151c63f3a45d995d9420978" integrity sha512-2/Ki0GcmuqSrgFyelQq9M05y7PS0mEwuIzrf3f1fPqkVDVRvZrPZtVSMHxdgo8Aq0sxAOb/cr2aqqA3LeWHVPg== @@ -7622,6 +7716,11 @@ jsonify@~0.0.0: array-includes "^3.1.5" object.assign "^4.1.3" +jwt-decode@^3.1.2: + version "3.1.2" + resolved "https://registry.yarnpkg.com/jwt-decode/-/jwt-decode-3.1.2.tgz#3fb319f3675a2df0c2895c8f5e9fa4b67b04ed59" + integrity 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integrity sha512-qJhlO9cGXi6hBGKoxEG/sKZDAHD5Hnu9Hs4WbOY3pCWXDhw0N8x1NenNzm2EnNLkLkk7J2SdxAkDSbb6ftT+UQ== + version "1.0.7" + resolved "https://registry.yarnpkg.com/language-tags/-/language-tags-1.0.7.tgz#41cc248730f3f12a452c2e2efe32bc0bbce67967" + integrity sha512-bSytju1/657hFjgUzPAPqszxH62ouE8nQFoFaVlIQfne4wO/wXC9A4+m8jYve7YBBvi59eq0SUpcshvG8h5Usw== dependencies: - language-subtag-registry "~0.3.2" + language-subtag-registry "^0.3.20" last-call-webpack-plugin@^3.0.0: version "3.0.0" @@ -7725,15 +7824,6 @@ loader-runner@^2.4.0: resolved "https://registry.yarnpkg.com/loader-runner/-/loader-runner-2.4.0.tgz#ed47066bfe534d7e84c4c7b9998c2a75607d9357" integrity sha512-Jsmr89RcXGIwivFY21FcRrisYZfvLMTWx5kOLc+JTxtpBOG6xML0vzbc6SEQG2FO9/4Fc3wW4LVcB5DmGflaRw== -loader-utils@1.2.3: - version "1.2.3" - resolved "https://registry.yarnpkg.com/loader-utils/-/loader-utils-1.2.3.tgz#1ff5dc6911c9f0a062531a4c04b609406108c2c7" - integrity 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@@ object-visit@^1.0.0: dependencies: isobject "^3.0.0" -object.assign@^4.1.0, object.assign@^4.1.3, object.assign@^4.1.4: +object.assign@^4.1.3, object.assign@^4.1.4: version "4.1.4" resolved "https://registry.yarnpkg.com/object.assign/-/object.assign-4.1.4.tgz#9673c7c7c351ab8c4d0b516f4343ebf4dfb7799f" integrity sha512-1mxKf0e58bvyjSCtKYY4sRe9itRk3PJpquJOjeIkz885CczcI4IvJJDLPS72oowuSh+pBxUFROpX+TU++hxhZQ== @@ -8514,41 +8611,41 @@ object.entries-ponyfill@^1.0.1: resolved "https://registry.yarnpkg.com/object.entries-ponyfill/-/object.entries-ponyfill-1.0.1.tgz#29abdf77cbfbd26566dd1aa24e9d88f65433d256" integrity sha512-j0ixssXc5GirDWhB2cLVPsOs9jx61G/iRndyMdToTsjMYY8BQmG1Ke6mwqXmpDiP8icye1YCR94NswNaa/yyzA== -object.entries@^1.1.0, object.entries@^1.1.5: - version "1.1.5" - resolved "https://registry.yarnpkg.com/object.entries/-/object.entries-1.1.5.tgz#e1acdd17c4de2cd96d5a08487cfb9db84d881861" - integrity 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-11621,14 +11718,14 @@ tslib@^1.8.1, tslib@^1.9.0: integrity sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg== tslib@^2.0.3: - version "2.4.0" - resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.4.0.tgz#7cecaa7f073ce680a05847aa77be941098f36dc3" - integrity sha512-d6xOpEDfsi2CZVlPQzGeux8XMwLT9hssAsaPYExaQMuYskwb+x1x7J371tWlbBdWHroy99KnVB6qIkUbs5X3UQ== + version "2.4.1" + resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.4.1.tgz#0d0bfbaac2880b91e22df0768e55be9753a5b17e" + integrity sha512-tGyy4dAjRIEwI7BzsB0lynWgOpfqjUdq91XXAlIWD2OwKBH7oCl/GZG/HT4BOHrTlPMOASlMQ7veyTqpmRcrNA== -tss-react@^3.7.0: - version "3.7.1" - resolved "https://registry.yarnpkg.com/tss-react/-/tss-react-3.7.1.tgz#119647731490f9e7e62c7f6a38a78df981929a4b" - integrity sha512-dfWUoxBlKZfIG9UC1A2h02OmcE/Ni0itCmmZu94E9g+KyBhKMHKcsKvUm0bNlRqTmYjXiCgPJDmj5fyc8CSrLg== +tss-react@^4.4.1: + version "4.4.5" + resolved "https://registry.yarnpkg.com/tss-react/-/tss-react-4.4.5.tgz#0d1ba3892cc79eb7f9f73e016041c329fe5f588f" + integrity sha512-yKKwAuaTKyJf0R1Kn7o0T3RVw/Q3lufQQy2Cic2ZFiD1wnamjYCfPgDjQ44Wyk0lyVJGnTXHbUOwh7dhP5lTsA== dependencies: "@emotion/cache" "*" "@emotion/serialize" "*" @@ -11721,9 +11818,9 @@ typedarray@^0.0.6: integrity sha512-/aCDEGatGvZ2BIk+HmLf4ifCJFwvKFNb9/JeZPMulfgFracn9QFcAf5GO8B/mweUjSoblS5In0cWhqpfs/5PQA== typescript@^4.1.2: - version "4.8.4" - resolved "https://registry.yarnpkg.com/typescript/-/typescript-4.8.4.tgz#c464abca159669597be5f96b8943500b238e60e6" - integrity sha512-QCh+85mCy+h0IGff8r5XWzOVSbBO+KfeYrMQh7NJ58QujwcE22u+NUSmUxqF+un70P9GXKxa2HCNiTTMJknyjQ== + version "4.9.4" + resolved "https://registry.yarnpkg.com/typescript/-/typescript-4.9.4.tgz#a2a3d2756c079abda241d75f149df9d561091e78" + integrity sha512-Uz+dTXYzxXXbsFpM86Wh3dKCxrQqUcVMxwU54orwlJjOpO3ao8L7j5lH+dWfTwgCwIuM9GQ2kvVotzYJMXTBZg== unbox-primitive@^1.0.2: version "1.0.2" @@ -11748,10 +11845,10 @@ unicode-match-property-ecmascript@^2.0.0: unicode-canonical-property-names-ecmascript "^2.0.0" unicode-property-aliases-ecmascript "^2.0.0" -unicode-match-property-value-ecmascript@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.0.0.tgz#1a01aa57247c14c568b89775a54938788189a714" - integrity sha512-7Yhkc0Ye+t4PNYzOGKedDhXbYIBe1XEQYQxOPyhcXNMJ0WCABqqj6ckydd6pWRZTHV4GuCPKdBAUiMc60tsKVw== +unicode-match-property-value-ecmascript@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.1.0.tgz#cb5fffdcd16a05124f5a4b0bf7c3770208acbbe0" + integrity sha512-qxkjQt6qjg/mYscYMC0XKRn3Rh0wFPlfxB0xkt9CfyTvpX1Ra0+rAmdX2QyAobptSEvuy4RtpPRui6XkV+8wjA== unicode-property-aliases-ecmascript@^2.0.0: version "2.1.0" @@ -12218,11 +12315,33 @@ which-boxed-primitive@^1.0.2: is-string "^1.0.5" is-symbol "^1.0.3" +which-collection@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/which-collection/-/which-collection-1.0.1.tgz#70eab71ebbbd2aefaf32f917082fc62cdcb70906" + integrity sha512-W8xeTUwaln8i3K/cY1nGXzdnVZlidBcagyNFtBdD5kxnb4TvGKR7FfSIS3mYpwWS1QUCutfKz8IY8RjftB0+1A== + dependencies: + is-map "^2.0.1" + is-set "^2.0.1" + is-weakmap "^2.0.1" + is-weakset "^2.0.1" + which-module@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/which-module/-/which-module-2.0.0.tgz#d9ef07dce77b9902b8a3a8fa4b31c3e3f7e6e87a" integrity sha512-B+enWhmw6cjfVC7kS8Pj9pCrKSc5txArRyaYGe088shv/FGWH+0Rjx/xPgtsWfsUtS27FkP697E4DDhgrgoc0Q== +which-typed-array@^1.1.8: + version "1.1.9" + resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.9.tgz#307cf898025848cf995e795e8423c7f337efbde6" + integrity sha512-w9c4xkx6mPidwp7180ckYWfMmvxpjlZuIudNtDf4N/tTAUB8VJbX25qZoAsrtGuYNnGw3pa0AXgbGKRB8/EceA== + dependencies: + available-typed-arrays "^1.0.5" + call-bind "^1.0.2" + for-each "^0.3.3" + gopd "^1.0.1" + has-tostringtag "^1.0.0" + is-typed-array "^1.1.10" + which@^1.2.9, which@^1.3.1: version "1.3.1" resolved "https://registry.yarnpkg.com/which/-/which-1.3.1.tgz#a45043d54f5805316da8d62f9f50918d3da70b0a" diff --git a/demos/jbrowse-react-linear-genome-view-cra5/.gitignore b/embedded_demos/jbrowse-react-linear-genome-view-cra5/.gitignore similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/.gitignore rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/.gitignore diff --git a/demos/jbrowse-react-linear-genome-view-cra5/README.md b/embedded_demos/jbrowse-react-linear-genome-view-cra5/README.md similarity index 63% rename from demos/jbrowse-react-linear-genome-view-cra5/README.md rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/README.md index b418e01f84..f35e736897 100644 --- a/demos/jbrowse-react-linear-genome-view-cra5/README.md +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/README.md @@ -1,14 +1,17 @@ # jbrowse-react-linear-genome-view-cra5 -This is a demo of using the linear genome view with create-react-app v5 (which uses webpack 5) +This is a demo of using the linear genome view with create-react-app v5 (which +uses webpack 5) -It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill, etc) +It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill, +etc) # Demo of `@jbrowse/react-linear-genome-view` with CRA 5 See this app running at https://jbrowse.org/demos/lgv-cra5/. -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-cra5 +Download this directory from the monorepo using +https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-cra5 ## Usage diff --git a/demos/jbrowse-react-linear-genome-view-cra5/craco.config.js b/embedded_demos/jbrowse-react-linear-genome-view-cra5/craco.config.js similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/craco.config.js rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/craco.config.js diff --git a/demos/jbrowse-react-linear-genome-view-cra5/package.json b/embedded_demos/jbrowse-react-linear-genome-view-cra5/package.json similarity index 74% rename from demos/jbrowse-react-linear-genome-view-cra5/package.json rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/package.json index a842a53cc2..80ff30fd3e 100644 --- a/demos/jbrowse-react-linear-genome-view-cra5/package.json +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/package.json @@ -1,24 +1,25 @@ { "name": "jbrowse-react-linear-genome-view-cra5", "version": "0.1.0", + "license": "MIT", "private": true, "dependencies": { "@craco/craco": "^6.4.3", "@fontsource/roboto": "^4.5.5", - "@jbrowse/react-linear-genome-view": "^2.0.0", + "@jbrowse/react-linear-genome-view": "^2.2.0", "@testing-library/jest-dom": "^5.16.4", - "@testing-library/react": "^12.1.4", - "@testing-library/user-event": "^13.5.0", - "@types/jest": "^27.4.1", - "@types/node": "^16.11.26", - "@types/react": "^17.0.44", - "@types/react-dom": "^17.0.15", - "node-polyfill-webpack-plugin": "^1.1.4", + "@testing-library/react": "^13.4.0", + "@testing-library/user-event": "^14.4.3", + "@types/jest": "^29.2.2", + "@types/node": "^18.11.9", + "@types/react": "^18.0.25", + "@types/react-dom": "^18.0.8", + "node-polyfill-webpack-plugin": "^2.0.1", "react": "^18.0.0", "react-dom": "^18.0.0", "react-scripts": "^5.0.1", "typescript": "^4.6.3", - "web-vitals": "^2.1.4" + "web-vitals": "^3.0.4" }, "scripts": { "start": "craco start", diff --git a/demos/jbrowse-react-linear-genome-view-cra5/public/favicon.ico b/embedded_demos/jbrowse-react-linear-genome-view-cra5/public/favicon.ico similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/public/favicon.ico rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/public/favicon.ico diff --git a/demos/jbrowse-react-linear-genome-view-cra5/public/index.html b/embedded_demos/jbrowse-react-linear-genome-view-cra5/public/index.html similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/public/index.html rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/public/index.html diff --git a/demos/jbrowse-react-linear-genome-view-cra5/public/logo192.png b/embedded_demos/jbrowse-react-linear-genome-view-cra5/public/logo192.png similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/public/logo192.png rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/public/logo192.png diff --git a/demos/jbrowse-react-linear-genome-view-cra5/public/logo512.png b/embedded_demos/jbrowse-react-linear-genome-view-cra5/public/logo512.png similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/public/logo512.png rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/public/logo512.png diff --git a/demos/jbrowse-react-linear-genome-view-cra5/public/manifest.json b/embedded_demos/jbrowse-react-linear-genome-view-cra5/public/manifest.json similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/public/manifest.json rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/public/manifest.json diff --git a/demos/jbrowse-react-linear-genome-view-cra5/public/robots.txt b/embedded_demos/jbrowse-react-linear-genome-view-cra5/public/robots.txt similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/public/robots.txt rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/public/robots.txt diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/App.tsx b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/App.tsx similarity index 62% rename from demos/jbrowse-react-linear-genome-view-cra5/src/App.tsx rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/src/App.tsx index 559a2b1e19..8c293a5e1b 100644 --- a/demos/jbrowse-react-linear-genome-view-cra5/src/App.tsx +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/App.tsx @@ -8,64 +8,7 @@ import makeWorkerInstance from '@jbrowse/react-linear-genome-view/esm/makeWorker import assembly from './assembly' import tracks from './tracks' - -const defaultSession = { - name: 'this session', - view: { - id: 'linearGenomeView', - type: 'LinearGenomeView', - tracks: [ - { - id: '7PWx6ki1_', - type: 'ReferenceSequenceTrack', - configuration: 'GRCh38-ReferenceSequenceTrack', - displays: [ - { - id: 'pa_7lx6FDh', - type: 'LinearReferenceSequenceDisplay', - height: 210, - configuration: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - }, - ], - }, - { - id: 'KHwe41KXk', - type: 'AlignmentsTrack', - configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', - displays: [ - { - id: '_-kwYVczT8', - type: 'LinearAlignmentsDisplay', - PileupDisplay: { - id: '1HTk32IDZJ', - type: 'LinearPileupDisplay', - height: 100, - configuration: { - type: 'LinearPileupDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_pileup_xyz', - }, - }, - SNPCoverageDisplay: { - id: 'ZBXRXmuDrc', - type: 'LinearSNPCoverageDisplay', - height: 45, - configuration: { - type: 'LinearSNPCoverageDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', - }, - }, - configuration: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', - height: 250, - }, - ], - }, - ], - }, -} +import defaultSession from './defaultSession' type ViewModel = ReturnType @@ -78,7 +21,6 @@ function View() { const state = createViewState({ assembly, tracks, - location: '10:29,838,655..29,838,737', onChange: (patch: any) => { setPatches(previous => previous + JSON.stringify(patch) + '\n') }, @@ -107,11 +49,11 @@ function View() {

The code for this app is available at{' '} - https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view-cra5 + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-cra5 .

diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts similarity index 75% rename from demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts index 5c26ea9164..af9f6755d9 100644 --- a/demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/assembly.ts @@ -16,16 +16,6 @@ const assembly = { uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', }, }, - displays: [ - { - type: 'LinearReferenceSequenceDisplay', - displayId: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - renderer: { - type: 'DivSequenceRenderer', - }, - }, - ], }, refNameAliases: { adapter: { diff --git a/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/defaultSession.ts b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/defaultSession.ts new file mode 100644 index 0000000000..d9e0281ccc --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/defaultSession.ts @@ -0,0 +1,130 @@ +export default { + name: 'this session', + margin: 0, + view: { + id: 'linearGenomeView', + minimized: false, + type: 'LinearGenomeView', + offsetPx: 191980240, + bpPerPx: 0.1554251851851852, + displayedRegions: [ + { + refName: '10', + start: 0, + end: 133797422, + reversed: false, + assemblyName: 'GRCh38', + }, + ], + tracks: [ + { + id: '4aZAiE-A3', + type: 'ReferenceSequenceTrack', + configuration: 'GRCh38-ReferenceSequenceTrack', + minimized: false, + displays: [ + { + id: 'AD3gqvG0_6', + type: 'LinearReferenceSequenceDisplay', + height: 180, + configuration: + 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', + showForward: true, + showReverse: true, + showTranslation: true, + }, + ], + }, + { + id: 'T6uhrtY40O', + type: 'AlignmentsTrack', + configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + minimized: false, + displays: [ + { + id: 'FinKswChSr', + type: 'LinearAlignmentsDisplay', + PileupDisplay: { + id: 'YAAaF494z', + type: 'LinearPileupDisplay', + height: 134, + configuration: { + type: 'LinearPileupDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz', + }, + showSoftClipping: false, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + SNPCoverageDisplay: { + id: 'VTQ_VGbAVJ', + type: 'LinearSNPCoverageDisplay', + height: 45, + configuration: { + type: 'LinearSNPCoverageDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', + }, + selectedRendering: '', + resolution: 1, + constraints: {}, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + snpCovHeight: 45, + configuration: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', + height: 179, + lowerPanelType: 'LinearPileupDisplay', + }, + ], + }, + { + id: 'EUnTnpVI6', + type: 'QuantitativeTrack', + configuration: 'hg38.100way.phyloP100way', + minimized: false, + displays: [ + { + id: 'mrlawr9Wtg', + type: 'LinearWiggleDisplay', + height: 100, + configuration: 'hg38.100way.phyloP100way-LinearWiggleDisplay', + selectedRendering: '', + resolution: 1, + constraints: {}, + }, + ], + }, + { + id: 'Cbnwl72EX', + type: 'VariantTrack', + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + minimized: false, + displays: [ + { + id: 'dvXz01Wf6w', + type: 'LinearVariantDisplay', + height: 100, + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay', + }, + ], + }, + ], + hideHeader: false, + hideHeaderOverview: false, + hideNoTracksActive: false, + trackSelectorType: 'hierarchical', + trackLabels: 'overlapping', + showCenterLine: false, + showCytobandsSetting: true, + showGridlines: true, + }, +} diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/index.css b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/index.css similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/src/index.css rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/src/index.css diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/index.tsx b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/index.tsx similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/src/index.tsx rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/src/index.tsx diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/react-app-env.d.ts b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/react-app-env.d.ts similarity index 100% rename from demos/jbrowse-react-linear-genome-view-cra5/src/react-app-env.d.ts rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/src/react-app-env.d.ts diff --git a/demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts similarity index 68% rename from demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts index 2afda9019d..fb6422b271 100644 --- a/demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/src/tracks.ts @@ -1,8 +1,7 @@ const tracks = [ { - type: 'BasicTrack', - trackId: - 'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff', + type: 'FeatureTrack', + trackId: 'genes', name: 'NCBI RefSeq Genes', assemblyNames: ['GRCh38'], category: ['Genes'], @@ -17,8 +16,23 @@ const tracks = [ }, }, }, + textSearching: { + textSearchAdapter: { + type: 'TrixTextSearchAdapter', + textSearchAdapterId: 'gff3tabix_genes-index', + ixFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix', + }, + ixxFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx', + }, + metaFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json', + }, + assemblyNames: ['GRCh38'], + }, + }, }, - { type: 'FeatureTrack', trackId: 'repeats_hg38', @@ -61,7 +75,6 @@ const tracks = [ }, }, }, - { type: 'VariantTrack', trackId: @@ -81,6 +94,20 @@ const tracks = [ }, }, }, + { + type: 'QuantitativeTrack', + trackId: 'hg38.100way.phyloP100way', + name: 'hg38.100way.phyloP100way', + category: ['Conservation'], + assemblyNames: ['hg38'], + adapter: { + type: 'BigWigAdapter', + bigWigLocation: { + uri: 'https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw', + locationType: 'UriLocation', + }, + }, + }, ] export default tracks diff --git a/demos/jbrowse-react-linear-genome-view/tsconfig.json b/embedded_demos/jbrowse-react-linear-genome-view-cra5/tsconfig.json similarity index 95% rename from demos/jbrowse-react-linear-genome-view/tsconfig.json rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/tsconfig.json index 9d379a3c4a..42c57d41a1 100644 --- a/demos/jbrowse-react-linear-genome-view/tsconfig.json +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/tsconfig.json @@ -1,6 +1,6 @@ { "compilerOptions": { - "target": "es5", + "target": "es2018", "lib": ["dom", "dom.iterable", "esnext"], "allowJs": true, "skipLibCheck": true, diff --git a/demos/jbrowse-react-linear-genome-view-cra5/yarn.lock b/embedded_demos/jbrowse-react-linear-genome-view-cra5/yarn.lock similarity index 88% rename from demos/jbrowse-react-linear-genome-view-cra5/yarn.lock rename to embedded_demos/jbrowse-react-linear-genome-view-cra5/yarn.lock index 449fb57b8e..c40f857952 100644 --- a/demos/jbrowse-react-linear-genome-view-cra5/yarn.lock +++ b/embedded_demos/jbrowse-react-linear-genome-view-cra5/yarn.lock @@ -31,26 +31,26 @@ dependencies: "@babel/highlight" "^7.18.6" -"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.19.3", "@babel/compat-data@^7.19.4": - version "7.19.4" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.19.4.tgz#95c86de137bf0317f3a570e1b6e996b427299747" - integrity sha512-CHIGpJcUQ5lU9KrPHTjBMhVwQG6CQjxfg36fGXl3qk/Gik1WwWachaXFuo0uCWJT/mStOKtcbFJCaVLihC1CMw== +"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.20.0", "@babel/compat-data@^7.20.1": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.20.5.tgz#86f172690b093373a933223b4745deeb6049e733" + integrity sha512-KZXo2t10+/jxmkhNXc7pZTqRvSOIvVv/+lJwHS+B2rErwOyjuVRh60yVpb7liQ1U5t7lLJ1bz+t8tSypUZdm0g== "@babel/core@^7.1.0", "@babel/core@^7.11.1", "@babel/core@^7.12.3", "@babel/core@^7.16.0", "@babel/core@^7.7.2", "@babel/core@^7.8.0": - version "7.19.3" - resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.19.3.tgz#2519f62a51458f43b682d61583c3810e7dcee64c" - integrity sha512-WneDJxdsjEvyKtXKsaBGbDeiyOjR5vYq4HcShxnIbG0qixpoHjI3MqeZM9NDvsojNCEBItQE4juOo/bU6e72gQ== + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.20.5.tgz#45e2114dc6cd4ab167f81daf7820e8fa1250d113" + integrity sha512-UdOWmk4pNWTm/4DlPUl/Pt4Gz4rcEMb7CY0Y3eJl5Yz1vI8ZJGmHWaVE55LoxRjdpx0z259GE9U5STA9atUinQ== dependencies: "@ampproject/remapping" "^2.1.0" "@babel/code-frame" "^7.18.6" - "@babel/generator" "^7.19.3" - "@babel/helper-compilation-targets" "^7.19.3" - "@babel/helper-module-transforms" "^7.19.0" - "@babel/helpers" "^7.19.0" - "@babel/parser" "^7.19.3" + "@babel/generator" "^7.20.5" + "@babel/helper-compilation-targets" "^7.20.0" + "@babel/helper-module-transforms" "^7.20.2" + "@babel/helpers" "^7.20.5" + "@babel/parser" "^7.20.5" "@babel/template" "^7.18.10" - "@babel/traverse" "^7.19.3" - "@babel/types" "^7.19.3" + "@babel/traverse" "^7.20.5" + "@babel/types" "^7.20.5" convert-source-map "^1.7.0" debug "^4.1.0" gensync "^1.0.0-beta.2" @@ -66,12 +66,12 @@ eslint-visitor-keys "^2.1.0" semver "^6.3.0" -"@babel/generator@^7.19.3", "@babel/generator@^7.19.4", "@babel/generator@^7.7.2": - version "7.19.5" - resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.19.5.tgz#da3f4b301c8086717eee9cab14da91b1fa5dcca7" - integrity sha512-DxbNz9Lz4aMZ99qPpO1raTbcrI1ZeYh+9NR9qhfkQIbFtVEqotHojEBxHzmxhVONkGt6VyrqVQcgpefMy9pqcg== +"@babel/generator@^7.20.5", "@babel/generator@^7.7.2": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.20.5.tgz#cb25abee3178adf58d6814b68517c62bdbfdda95" + integrity sha512-jl7JY2Ykn9S0yj4DQP82sYvPU+T3g0HFcWTqDLqiuA9tGRNIj9VfbtXGAYTTkyNEnQk1jkMGOdYka8aG/lulCA== dependencies: - "@babel/types" "^7.19.4" + "@babel/types" "^7.20.5" "@jridgewell/gen-mapping" "^0.3.2" jsesc "^2.5.1" @@ -90,36 +90,36 @@ "@babel/helper-explode-assignable-expression" "^7.18.6" "@babel/types" "^7.18.9" -"@babel/helper-compilation-targets@^7.17.7", "@babel/helper-compilation-targets@^7.18.9", "@babel/helper-compilation-targets@^7.19.0", "@babel/helper-compilation-targets@^7.19.3": - version "7.19.3" - resolved "https://registry.yarnpkg.com/@babel/helper-compilation-targets/-/helper-compilation-targets-7.19.3.tgz#a10a04588125675d7c7ae299af86fa1b2ee038ca" - integrity sha512-65ESqLGyGmLvgR0mst5AdW1FkNlj9rQsCKduzEoEPhBCDFGXvz2jW6bXFG6i0/MrV2s7hhXjjb2yAzcPuQlLwg== +"@babel/helper-compilation-targets@^7.17.7", "@babel/helper-compilation-targets@^7.18.9", "@babel/helper-compilation-targets@^7.20.0": + version "7.20.0" + resolved "https://registry.yarnpkg.com/@babel/helper-compilation-targets/-/helper-compilation-targets-7.20.0.tgz#6bf5374d424e1b3922822f1d9bdaa43b1a139d0a" + integrity sha512-0jp//vDGp9e8hZzBc6N/KwA5ZK3Wsm/pfm4CrY7vzegkVxc65SgSn6wYOnwHe9Js9HRQ1YTCKLGPzDtaS3RoLQ== dependencies: - "@babel/compat-data" "^7.19.3" + "@babel/compat-data" "^7.20.0" "@babel/helper-validator-option" "^7.18.6" browserslist "^4.21.3" semver "^6.3.0" -"@babel/helper-create-class-features-plugin@^7.18.6", "@babel/helper-create-class-features-plugin@^7.19.0": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.19.0.tgz#bfd6904620df4e46470bae4850d66be1054c404b" - integrity sha512-NRz8DwF4jT3UfrmUoZjd0Uph9HQnP30t7Ash+weACcyNkiYTywpIjDBgReJMKgr+n86sn2nPVVmJ28Dm053Kqw== +"@babel/helper-create-class-features-plugin@^7.18.6", "@babel/helper-create-class-features-plugin@^7.20.2", "@babel/helper-create-class-features-plugin@^7.20.5": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.20.5.tgz#327154eedfb12e977baa4ecc72e5806720a85a06" + integrity sha512-3RCdA/EmEaikrhayahwToF0fpweU/8o2p8vhc1c/1kftHOdTKuC65kik/TLc+qfbS8JKw4qqJbne4ovICDhmww== dependencies: "@babel/helper-annotate-as-pure" "^7.18.6" "@babel/helper-environment-visitor" "^7.18.9" "@babel/helper-function-name" "^7.19.0" "@babel/helper-member-expression-to-functions" "^7.18.9" "@babel/helper-optimise-call-expression" "^7.18.6" - "@babel/helper-replace-supers" "^7.18.9" + "@babel/helper-replace-supers" "^7.19.1" "@babel/helper-split-export-declaration" "^7.18.6" -"@babel/helper-create-regexp-features-plugin@^7.18.6", "@babel/helper-create-regexp-features-plugin@^7.19.0": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.19.0.tgz#7976aca61c0984202baca73d84e2337a5424a41b" - integrity sha512-htnV+mHX32DF81amCDrwIDr8nrp1PTm+3wfBN9/v8QJOLEioOCOG7qNyq0nHeFiWbT3Eb7gsPwEmV64UCQ1jzw== +"@babel/helper-create-regexp-features-plugin@^7.18.6", "@babel/helper-create-regexp-features-plugin@^7.20.5": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.20.5.tgz#5ea79b59962a09ec2acf20a963a01ab4d076ccca" + integrity sha512-m68B1lkg3XDGX5yCvGO0kPx3v9WIYLnzjKfPcQiwntEQa5ZeRkPmo2X/ISJc8qxWGfwUr+kvZAeEzAwLec2r2w== dependencies: "@babel/helper-annotate-as-pure" "^7.18.6" - regexpu-core "^5.1.0" + regexpu-core "^5.2.1" "@babel/helper-define-polyfill-provider@^0.3.3": version "0.3.3" @@ -174,19 +174,19 @@ dependencies: "@babel/types" "^7.18.6" -"@babel/helper-module-transforms@^7.18.6", "@babel/helper-module-transforms@^7.19.0": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-module-transforms/-/helper-module-transforms-7.19.0.tgz#309b230f04e22c58c6a2c0c0c7e50b216d350c30" 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"@babel/helper-optimise-call-expression@^7.18.6": version "7.18.6" @@ -195,10 +195,10 @@ dependencies: "@babel/types" "^7.18.6" -"@babel/helper-plugin-utils@^7.0.0", "@babel/helper-plugin-utils@^7.10.4", "@babel/helper-plugin-utils@^7.12.13", "@babel/helper-plugin-utils@^7.14.5", "@babel/helper-plugin-utils@^7.16.7", "@babel/helper-plugin-utils@^7.18.6", "@babel/helper-plugin-utils@^7.18.9", "@babel/helper-plugin-utils@^7.19.0", "@babel/helper-plugin-utils@^7.8.0", "@babel/helper-plugin-utils@^7.8.3": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-plugin-utils/-/helper-plugin-utils-7.19.0.tgz#4796bb14961521f0f8715990bee2fb6e51ce21bf" - integrity sha512-40Ryx7I8mT+0gaNxm8JGTZFUITNqdLAgdg0hXzeVZxVD6nFsdhQvip6v8dqkRHzsz1VFpFAaOCHNn0vKBL7Czw== +"@babel/helper-plugin-utils@^7.0.0", "@babel/helper-plugin-utils@^7.10.4", "@babel/helper-plugin-utils@^7.12.13", "@babel/helper-plugin-utils@^7.14.5", "@babel/helper-plugin-utils@^7.16.7", 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+"@jbrowse/plugin-gccontent@^2.3.2": + version "2.3.2" + resolved "https://registry.yarnpkg.com/@jbrowse/plugin-gccontent/-/plugin-gccontent-2.3.2.tgz#9197b2ac02b83b472c9a15cf7bcc36f970ce79dc" + integrity sha512-mYSkdnHX6WcUvIxtMv1hHqsg2FE47HlmqcVxQHXbBU2rgjZxsIpG2M5RlIm2M8gqIGEsNyW0v9lLTSI6o0CZEg== + +"@jbrowse/plugin-gff3@^2.3.2": + version "2.3.2" + resolved "https://registry.yarnpkg.com/@jbrowse/plugin-gff3/-/plugin-gff3-2.3.2.tgz#a2ce40f9937253e1dfd75efeaf6cb9b15ea0841f" + integrity sha512-G1N684D2TaO64JfsWJDD732cos/Zs0qorxzBrTN0zob8nrPyTpL6YuN8Z9CMOgs3oo1orB6lupOAdM302uU6jg== dependencies: "@flatten-js/interval-tree" "^1.0.15" "@gmod/bgzf-filehandle" "^1.4.3" - "@gmod/gff" "^1.2.3" + "@gmod/gff" "^1.3.0" "@gmod/tabix" "^1.5.2" -"@jbrowse/plugin-legacy-jbrowse@^2.1.7": - version "2.1.7" - resolved "https://registry.yarnpkg.com/@jbrowse/plugin-legacy-jbrowse/-/plugin-legacy-jbrowse-2.1.7.tgz#26a215f2b96df424ff431dd8cc71d49cf50104d6" - integrity 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find-up "^5.0.0" html-entities "^2.1.0" - loader-utils "^2.0.0" + loader-utils "^2.0.4" schema-utils "^3.0.0" source-map "^0.7.3" @@ -2212,14 +2228,14 @@ integrity sha512-sXo/qW2/pAcmT43VoRKOJbDOfV3cYpq3szSVfIThQXNt+E4DfKj361vaAt3c88U5tPUxzEswam7GW48PJqtKAg== "@sinclair/typebox@^0.24.1": - version "0.24.47" - resolved "https://registry.yarnpkg.com/@sinclair/typebox/-/typebox-0.24.47.tgz#530b67163714356f93e82bdb871e7db4b7bc564e" - integrity sha512-J4Xw0xYK4h7eC34MNOPQi6IkNxGRck6n4VJpWDzXIFVTW8I/D43Gf+NfWz/v/7NHlzWOPd3+T4PJ4OqklQ2u7A== + version "0.24.51" + resolved "https://registry.yarnpkg.com/@sinclair/typebox/-/typebox-0.24.51.tgz#645f33fe4e02defe26f2f5c0410e1c094eac7f5f" + integrity sha512-1P1OROm/rdubP5aFDSZQILU0vrLCJ4fvHt6EoqHEM+2D/G5MK3bIaymUKLit8Js9gbns5UyJnkP/TZROLw4tUA== "@sinonjs/commons@^1.7.0": - version "1.8.3" - resolved "https://registry.yarnpkg.com/@sinonjs/commons/-/commons-1.8.3.tgz#3802ddd21a50a949b6721ddd72da36e67e7f1b2d" - integrity 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es-array-method-boxes-properly "^1.0.0" is-string "^1.0.7" +array.prototype.tosorted@^1.1.1: + version "1.1.1" + resolved "https://registry.yarnpkg.com/array.prototype.tosorted/-/array.prototype.tosorted-1.1.1.tgz#ccf44738aa2b5ac56578ffda97c03fd3e23dd532" + integrity sha512-pZYPXPRl2PqWcsUs6LOMn+1f1532nEoPTYowBtqLwAW+W8vSVhkIGnmOX1t/UQjD6YGI0vcD2B1U7ZFGQH9jnQ== + dependencies: + call-bind "^1.0.2" + define-properties "^1.1.4" + es-abstract "^1.20.4" + es-shim-unscopables "^1.0.0" + get-intrinsic "^1.1.3" + asap@~2.0.6: version "2.0.6" resolved "https://registry.yarnpkg.com/asap/-/asap-2.0.6.tgz#e50347611d7e690943208bbdafebcbc2fb866d46" @@ -3308,13 +3321,13 @@ at-least-node@^1.0.0: resolved "https://registry.yarnpkg.com/at-least-node/-/at-least-node-1.0.0.tgz#602cd4b46e844ad4effc92a8011a3c46e0238dc2" integrity sha512-+q/t7Ekv1EDY2l6Gda6LLiX14rU9TV20Wa3ofeQmwPFZbOMo9DXrLbOjFaaclkXKWidIaopwAObQDqwWtGUjqg== -autoprefixer@^10.4.11: - version "10.4.12" - resolved 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ci-info@^3.2.0: - version "3.5.0" - resolved "https://registry.yarnpkg.com/ci-info/-/ci-info-3.5.0.tgz#bfac2a29263de4c829d806b1ab478e35091e171f" - integrity sha512-yH4RezKOGlOhxkmhbeNuC4eYZKAUsEaGtBuBzDDP1eFUKiccDWzBABxBfOx31IDwDIXMTxWuwAxUGModvkbuVw== + version "3.7.0" + resolved "https://registry.yarnpkg.com/ci-info/-/ci-info-3.7.0.tgz#6d01b3696c59915b6ce057e4aa4adfc2fa25f5ef" + integrity sha512-2CpRNYmImPx+RXKLq6jko/L07phmS9I02TyqkcNU20GCF/GgaWvc58hPtjxDX8lPpkdwc9sNh72V9k00S7ezog== cipher-base@^1.0.0, cipher-base@^1.0.1, cipher-base@^1.0.3: version "1.0.4" @@ -4083,28 +4089,28 @@ cookie@0.5.0: integrity sha512-YZ3GUyn/o8gfKJlnlX7g7xq4gyO6OSuhGPKaaGssGB2qgDUS0gPgtTvoyZLTt9Ab6dC4hfc9dV5arkvc/OCmrw== copy-to-clipboard@^3.3.1: - version "3.3.2" - resolved "https://registry.yarnpkg.com/copy-to-clipboard/-/copy-to-clipboard-3.3.2.tgz#5b263ec2366224b100181dded7ce0579b340c107" - integrity sha512-Vme1Z6RUDzrb6xAI7EZlVZ5uvOk2F//GaxKUxajDqm9LhOVM1inxNAD2vy+UZDYsd0uyA9s7b3/FVZPSxqrCfg== + version "3.3.3" + resolved "https://registry.yarnpkg.com/copy-to-clipboard/-/copy-to-clipboard-3.3.3.tgz#55ac43a1db8ae639a4bd99511c148cdd1b83a1b0" + integrity sha512-2KV8NhB5JqC3ky0r9PMCAZKbUHSwtEo4CwCs0KXgruG43gX5PMqDEBbVU4OUzw2MuAWUfsuFmWvEKG5QRfSnJA== dependencies: toggle-selection "^1.0.6" core-js-compat@^3.25.1: - version "3.25.5" - resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.25.5.tgz#0016e8158c904f7b059486639e6e82116eafa7d9" - integrity sha512-ovcyhs2DEBUIE0MGEKHP4olCUW/XYte3Vroyxuh38rD1wAO4dHohsovUC4eAOuzFxE6b+RXvBU3UZ9o0YhUTkA== + version "3.26.1" + resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.26.1.tgz#0e710b09ebf689d719545ac36e49041850f943df" + integrity sha512-622/KzTudvXCDLRw70iHW4KKs1aGpcRcowGWyYJr2DEBfRrd6hNJybxSWJFuZYD4ma86xhrwDDHxmDaIq4EA8A== dependencies: browserslist "^4.21.4" core-js-pure@^3.23.3, core-js-pure@^3.25.1: - version "3.25.5" - resolved 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@@ -4131,9 +4137,9 @@ cosmiconfig@^6.0.0: yaml "^1.7.2" cosmiconfig@^7, cosmiconfig@^7.0.0, cosmiconfig@^7.0.1: - version "7.0.1" - resolved "https://registry.yarnpkg.com/cosmiconfig/-/cosmiconfig-7.0.1.tgz#714d756522cace867867ccb4474c5d01bbae5d6d" - integrity sha512-a1YWNUV2HwGimB7dU2s1wUMurNKjpx60HxBB6xUM8Re+2s1g1IIfJvFR0/iCF+XHdE0GMTKTuLR32UQff4TEyQ== + version "7.1.0" + resolved "https://registry.yarnpkg.com/cosmiconfig/-/cosmiconfig-7.1.0.tgz#1443b9afa596b670082ea46cbd8f6a62b84635f6" + integrity sha512-AdmX6xUzdNASswsFtmwSt7Vj8po9IuqXm0UXz7QKPuEUmPB4XyjGfaAr2PSuELMwkRMVH1EpIkX5bTZGRB3eCA== dependencies: "@types/parse-json" "^4.0.0" import-fresh "^3.2.1" @@ -4227,7 +4233,7 @@ css-blank-pseudo@^3.0.3: dependencies: postcss-selector-parser "^6.0.9" -css-declaration-sorter@^6.3.0: +css-declaration-sorter@^6.3.1: version "6.3.1" resolved "https://registry.yarnpkg.com/css-declaration-sorter/-/css-declaration-sorter-6.3.1.tgz#be5e1d71b7a992433fb1c542c7a1b835e45682ec" integrity sha512-fBffmak0bPAnyqc/HO8C3n2sHrp9wcqQz6ES9koRF2/mLOVAx9zIQ3Y7R29sYCteTPqMCwns4WYQoCX91Xl3+w== @@ -4240,18 +4246,18 @@ css-has-pseudo@^3.0.4: postcss-selector-parser "^6.0.9" css-loader@^6.5.1: - version "6.7.1" - resolved "https://registry.yarnpkg.com/css-loader/-/css-loader-6.7.1.tgz#e98106f154f6e1baf3fc3bc455cb9981c1d5fd2e" - integrity sha512-yB5CNFa14MbPJcomwNh3wLThtkZgcNyI2bNMRt8iE5Z8Vwl7f8vQXFAzn2HDOJvtDq2NTZBUGMSUNNyrv3/+cw== + version "6.7.3" + resolved "https://registry.yarnpkg.com/css-loader/-/css-loader-6.7.3.tgz#1e8799f3ccc5874fdd55461af51137fcc5befbcd" + integrity sha512-qhOH1KlBMnZP8FzRO6YCH9UHXQhVMcEGLyNdb7Hv2cpcmJbW0YrddO+tG1ab5nT41KpHIYGsbeHqxB9xPu1pKQ== dependencies: icss-utils "^5.1.0" - postcss "^8.4.7" + postcss "^8.4.19" postcss-modules-extract-imports "^3.0.0" postcss-modules-local-by-default "^4.0.0" postcss-modules-scope "^3.0.0" postcss-modules-values "^4.0.0" postcss-value-parser "^4.2.0" - semver "^7.3.5" + semver "^7.3.8" css-minimizer-webpack-plugin@^3.2.0: version "3.4.1" @@ -4327,35 +4333,35 @@ css.escape@^1.5.1: resolved "https://registry.yarnpkg.com/css.escape/-/css.escape-1.5.1.tgz#42e27d4fa04ae32f931a4b4d4191fa9cddee97cb" integrity sha512-YUifsXXuknHlUsmlgyY0PKzgPOr7/FjCePfHNt0jxm83wHZi44VDMQ7/fGNkjY3/jV1MC+1CmZbaHzugyeRtpg== -cssdb@^7.0.1: - version "7.0.2" - resolved "https://registry.yarnpkg.com/cssdb/-/cssdb-7.0.2.tgz#e1cadfe2be318797bd02ca929d2b3c7bac332abc" - integrity sha512-Vm4b6P/PifADu0a76H0DKRNVWq3Rq9xa/Nx6oEMUBJlwTUuZoZ3dkZxo8Gob3UEL53Cq+Ma1GBgISed6XEBs3w== +cssdb@^7.1.0: + version "7.2.0" + resolved "https://registry.yarnpkg.com/cssdb/-/cssdb-7.2.0.tgz#f44bd4abc430f0ff7f4c64b8a1fb857a753f77a8" + integrity sha512-JYlIsE7eKHSi0UNuCyo96YuIDFqvhGgHw4Ck6lsN+DP0Tp8M64UTDT2trGbkMDqnCoEjks7CkS0XcjU0rkvBdg== cssesc@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/cssesc/-/cssesc-3.0.0.tgz#37741919903b868565e1c09ea747445cd18983ee" integrity sha512-/Tb/JcjK111nNScGob5MNtsntNM1aCNUDipB/TkwZFhyDrrE47SOx/18wF2bbjgc3ZzCSKW1T5nt5EbFoAz/Vg== -cssnano-preset-default@^5.2.12: - version "5.2.12" - resolved "https://registry.yarnpkg.com/cssnano-preset-default/-/cssnano-preset-default-5.2.12.tgz#ebe6596ec7030e62c3eb2b3c09f533c0644a9a97" - integrity sha512-OyCBTZi+PXgylz9HAA5kHyoYhfGcYdwFmyaJzWnzxuGRtnMw/kR6ilW9XzlzlRAtB6PLT/r+prYgkef7hngFew== +cssnano-preset-default@^5.2.13: + version "5.2.13" + resolved "https://registry.yarnpkg.com/cssnano-preset-default/-/cssnano-preset-default-5.2.13.tgz#e7353b0c57975d1bdd97ac96e68e5c1b8c68e990" + integrity sha512-PX7sQ4Pb+UtOWuz8A1d+Rbi+WimBIxJTRyBdgGp1J75VU0r/HFQeLnMYgHiCAp6AR4rqrc7Y4R+1Rjk3KJz6DQ== dependencies: - css-declaration-sorter "^6.3.0" + css-declaration-sorter "^6.3.1" cssnano-utils "^3.1.0" postcss-calc "^8.2.3" postcss-colormin "^5.3.0" - postcss-convert-values "^5.1.2" + postcss-convert-values "^5.1.3" postcss-discard-comments "^5.1.2" postcss-discard-duplicates "^5.1.0" postcss-discard-empty "^5.1.1" postcss-discard-overridden "^5.1.0" - postcss-merge-longhand "^5.1.6" - postcss-merge-rules "^5.1.2" + postcss-merge-longhand "^5.1.7" + postcss-merge-rules "^5.1.3" postcss-minify-font-values "^5.1.0" postcss-minify-gradients "^5.1.1" - postcss-minify-params "^5.1.3" + postcss-minify-params "^5.1.4" postcss-minify-selectors "^5.2.1" postcss-normalize-charset "^5.1.0" postcss-normalize-display-values "^5.1.0" @@ -4363,11 +4369,11 @@ cssnano-preset-default@^5.2.12: postcss-normalize-repeat-style "^5.1.1" postcss-normalize-string "^5.1.0" postcss-normalize-timing-functions "^5.1.0" - postcss-normalize-unicode "^5.1.0" + postcss-normalize-unicode "^5.1.1" postcss-normalize-url "^5.1.0" postcss-normalize-whitespace "^5.1.1" postcss-ordered-values "^5.1.3" - postcss-reduce-initial "^5.1.0" + postcss-reduce-initial "^5.1.1" postcss-reduce-transforms "^5.1.0" postcss-svgo "^5.1.0" postcss-unique-selectors "^5.1.1" @@ -4378,11 +4384,11 @@ cssnano-utils@^3.1.0: integrity sha512-JQNR19/YZhz4psLX/rQ9M83e3z2Wf/HdJbryzte4a3NSuafyp9w/I4U+hx5C2S9g41qlstH7DEWnZaaj83OuEA== cssnano@^5.0.6: - version "5.1.13" - resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-5.1.13.tgz#83d0926e72955332dc4802a7070296e6258efc0a" - integrity sha512-S2SL2ekdEz6w6a2epXn4CmMKU4K3KpcyXLKfAYc9UQQqJRkD/2eLUG0vJ3Db/9OvO5GuAdgXw3pFbR6abqghDQ== + version "5.1.14" + resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-5.1.14.tgz#07b0af6da73641276fe5a6d45757702ebae2eb05" + integrity sha512-Oou7ihiTocbKqi0J1bB+TRJIQX5RMR3JghA8hcWSw9mjBLQ5Y3RWqEDoYG3sRNlAbCIXpqMoZGbq5KDR3vdzgw== dependencies: - cssnano-preset-default "^5.2.12" + cssnano-preset-default "^5.2.13" lilconfig "^2.0.3" yaml "^1.10.2" @@ -4510,15 +4516,36 @@ debug@^3.2.7: ms "^2.1.1" decimal.js@^10.2.1: - version "10.4.2" - resolved "https://registry.yarnpkg.com/decimal.js/-/decimal.js-10.4.2.tgz#0341651d1d997d86065a2ce3a441fbd0d8e8b98e" - integrity 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"^1.1.4" + isarray "^2.0.5" + object-is "^1.1.5" + object-keys "^1.1.1" + object.assign "^4.1.4" + regexp.prototype.flags "^1.4.3" + side-channel "^1.0.4" + which-boxed-primitive "^1.0.2" + which-collection "^1.0.1" + which-typed-array "^1.1.8" + deep-is@^0.1.3, deep-is@~0.1.3: version "0.1.4" resolved "https://registry.yarnpkg.com/deep-is/-/deep-is-0.1.4.tgz#a6f2dce612fadd2ef1f519b73551f17e85199831" @@ -4619,10 +4646,10 @@ diff-sequences@^27.5.1: resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-27.5.1.tgz#eaecc0d327fd68c8d9672a1e64ab8dccb2ef5327" integrity sha512-k1gCAXAsNgLwEL+Y8Wvl+M6oEFj5bgazfZULpS5CneoPPXRaCCW7dm+q21Ky2VEE5X+VeRDBVg1Pcvvsr4TtNQ== -diff-sequences@^29.2.0: - version "29.2.0" - resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-29.2.0.tgz#4c55b5b40706c7b5d2c5c75999a50c56d214e8f6" - integrity sha512-413SY5JpYeSBZxmenGEmCVQ8mCgtFJF0w9PROdaS6z987XC2Pd2GOKqOITLtMftmyFZqgtCOb/QA7/Z3ZXfzIw== +diff-sequences@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-29.3.1.tgz#104b5b95fe725932421a9c6e5b4bef84c3f2249e" + integrity sha512-hlM3QR272NXCi4pq+N4Kok4kOp6EsgOM3ZSpJI7Da3UAs+Ttsi8MRmB6trM/lhyzUxGfOgnpkHtgqm5Q/CTcfQ== diff@^4.0.1: version "4.0.2" @@ -4713,7 +4740,7 @@ dom-serializer@^1.0.1: domhandler "^4.2.0" entities "^2.0.0" -domain-browser@^4.19.0: +domain-browser@^4.22.0: version "4.22.0" resolved "https://registry.yarnpkg.com/domain-browser/-/domain-browser-4.22.0.tgz#6ddd34220ec281f9a65d3386d267ddd35c491f9f" integrity sha512-IGBwjF7tNk3cwypFNH/7bfzBcgSCbaMOD3GsaY1AU/JRrnHnYgEM0+9kQt52iZxjNsjBtJYtao146V+f8jFZNw== @@ -4743,9 +4770,9 @@ domhandler@^4.0.0, domhandler@^4.2.0, domhandler@^4.3.1: domelementtype "^2.2.0" dompurify@^2.3.4: - version "2.4.0" - resolved "https://registry.yarnpkg.com/dompurify/-/dompurify-2.4.0.tgz#c9c88390f024c2823332615c9e20a453cf3825dd" - integrity 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-4885,6 +4912,7 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 function.prototype.name "^1.1.5" get-intrinsic "^1.1.3" get-symbol-description "^1.0.0" + gopd "^1.0.1" has "^1.0.3" has-property-descriptors "^1.0.0" has-symbols "^1.0.3" @@ -4900,8 +4928,8 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 object.assign "^4.1.4" regexp.prototype.flags "^1.4.3" safe-regex-test "^1.0.0" - string.prototype.trimend "^1.0.5" - string.prototype.trimstart "^1.0.5" + string.prototype.trimend "^1.0.6" + string.prototype.trimstart "^1.0.6" unbox-primitive "^1.0.2" es-array-method-boxes-properly@^1.0.0: @@ -4909,6 +4937,20 @@ es-array-method-boxes-properly@^1.0.0: resolved "https://registry.yarnpkg.com/es-array-method-boxes-properly/-/es-array-method-boxes-properly-1.0.0.tgz#873f3e84418de4ee19c5be752990b2e44718d09e" integrity sha512-wd6JXUmyHmt8T5a2xreUwKcGPq6f1f+WwIJkijUqiGcJz1qqnZgP6XIK+QyIWU5lT7imeNxUll48bziG+TSYcA== +es-get-iterator@^1.1.2: + version "1.1.2" + resolved "https://registry.yarnpkg.com/es-get-iterator/-/es-get-iterator-1.1.2.tgz#9234c54aba713486d7ebde0220864af5e2b283f7" + integrity sha512-+DTO8GYwbMCwbywjimwZMHp8AuYXOS2JZFWoi2AlPOS3ebnII9w/NLpNZtA7A0YLaVDw+O7KFCeoIV7OPvM7hQ== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.0" + has-symbols "^1.0.1" + is-arguments "^1.1.0" + is-map "^2.0.2" + is-set "^2.0.2" + is-string "^1.0.5" + isarray "^2.0.5" + es-module-lexer@^0.9.0: version "0.9.3" resolved "https://registry.yarnpkg.com/es-module-lexer/-/es-module-lexer-0.9.3.tgz#6f13db00cc38417137daf74366f535c8eb438f19" @@ -4935,7 +4977,7 @@ es6-object-assign@^1.1.0: resolved "https://registry.yarnpkg.com/es6-object-assign/-/es6-object-assign-1.1.0.tgz#c2c3582656247c39ea107cb1e6652b6f9f24523c" integrity sha512-MEl9uirslVwqQU369iHNWZXsI8yaZYGg/D65aOgZkeyFJwHYSxilf7rQzXKI7DdDuBPrBXbfk3sl9hJhmd5AUw== -es6-promisify@^6.0.1, es6-promisify@^6.1.1: +es6-promisify@^6.1.1: version "6.1.1" resolved "https://registry.yarnpkg.com/es6-promisify/-/es6-promisify-6.1.1.tgz#46837651b7b06bf6fff893d03f29393668d01621" integrity sha512-HBL8I3mIki5C1Cc9QjKUenHtnG0A5/xA8Q/AllRcfiwl2CZFXGK7ddBiCoRwAix4i2KxcQfjtIVcrVbB3vbmwg== @@ -5076,29 +5118,30 @@ eslint-plugin-react-hooks@^4.3.0: integrity sha512-oFc7Itz9Qxh2x4gNHStv3BqJq54ExXmfC+a1NjAta66IAN87Wu0R/QArgIS9qKzX3dXKPI9H5crl9QchNMY9+g== eslint-plugin-react@^7.27.1: - version "7.31.10" - resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.10.tgz#6782c2c7fe91c09e715d536067644bbb9491419a" - integrity sha512-e4N/nc6AAlg4UKW/mXeYWd3R++qUano5/o+t+wnWxIf+bLsOaH3a4q74kX3nDjYym3VBN4HyO9nEn1GcAqgQOA== + version "7.31.11" + resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.11.tgz#011521d2b16dcf95795df688a4770b4eaab364c8" + integrity sha512-TTvq5JsT5v56wPa9OYHzsrOlHzKZKjV+aLgS+55NJP/cuzdiQPC7PfYoUjMoxlffKtvijpk7vA/jmuqRb9nohw== dependencies: - array-includes "^3.1.5" - array.prototype.flatmap "^1.3.0" + array-includes "^3.1.6" + array.prototype.flatmap "^1.3.1" + array.prototype.tosorted "^1.1.1" doctrine "^2.1.0" estraverse "^5.3.0" jsx-ast-utils "^2.4.1 || ^3.0.0" minimatch "^3.1.2" - object.entries "^1.1.5" - object.fromentries "^2.0.5" - object.hasown "^1.1.1" - object.values "^1.1.5" + object.entries "^1.1.6" + object.fromentries "^2.0.6" + object.hasown "^1.1.2" + object.values "^1.1.6" prop-types "^15.8.1" resolve "^2.0.0-next.3" semver "^6.3.0" - string.prototype.matchall "^4.0.7" + string.prototype.matchall "^4.0.8" eslint-plugin-testing-library@^5.0.1: - version "5.8.0" - resolved "https://registry.yarnpkg.com/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.8.0.tgz#0faed7695ba76c0021fde3aeda9b90748995d2f2" - integrity sha512-QzOKgu4x8WmNq4LdbHb8lz5nBR+KX5kSg5VvIdr/5f1BvHx2IoO1B/tgDa5pD/ng2LsiQ0/HIH6gsUuxpbcrkQ== + version "5.9.1" + resolved "https://registry.yarnpkg.com/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.9.1.tgz#12e4bd34c48683ee98af4df2e3318ec9f51dcf8a" + integrity sha512-6BQp3tmb79jLLasPHJmy8DnxREe+2Pgf7L+7o09TSWPfdqqtQfRZmZNetr5mOs3yqZk/MRNxpN3RUpJe0wB4LQ== dependencies: "@typescript-eslint/utils" "^5.13.0" @@ -5147,13 +5190,14 @@ eslint-webpack-plugin@^3.1.1: schema-utils "^4.0.0" eslint@^8.3.0: - version "8.25.0" - resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.25.0.tgz#00eb962f50962165d0c4ee3327708315eaa8058b" - integrity sha512-DVlJOZ4Pn50zcKW5bYH7GQK/9MsoQG2d5eDH0ebEkE8PbgzTTmtt/VTH9GGJ4BfeZCpBLqFfvsjX35UacUL83A== + version "8.30.0" + resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.30.0.tgz#83a506125d089eef7c5b5910eeea824273a33f50" + integrity sha512-MGADB39QqYuzEGov+F/qb18r4i7DohCDOfatHaxI2iGlPuC65bwG2gxgO+7DkyL38dRFaRH7RaRAgU6JKL9rMQ== dependencies: - "@eslint/eslintrc" "^1.3.3" - "@humanwhocodes/config-array" "^0.10.5" + "@eslint/eslintrc" "^1.4.0" + "@humanwhocodes/config-array" "^0.11.8" "@humanwhocodes/module-importer" "^1.0.1" + "@nodelib/fs.walk" "^1.2.8" ajv "^6.10.0" chalk "^4.0.0" cross-spawn "^7.0.2" @@ -5169,14 +5213,14 @@ eslint@^8.3.0: fast-deep-equal "^3.1.3" file-entry-cache "^6.0.1" find-up "^5.0.0" - glob-parent "^6.0.1" - globals "^13.15.0" - globby "^11.1.0" + glob-parent "^6.0.2" + globals "^13.19.0" grapheme-splitter "^1.0.4" ignore "^5.2.0" import-fresh "^3.0.0" imurmurhash "^0.1.4" is-glob "^4.0.0" + is-path-inside "^3.0.3" js-sdsl "^4.1.4" js-yaml "^4.1.0" json-stable-stringify-without-jsonify "^1.0.1" @@ -5191,9 +5235,9 @@ eslint@^8.3.0: text-table "^0.2.0" espree@^9.4.0: - version "9.4.0" - resolved "https://registry.yarnpkg.com/espree/-/espree-9.4.0.tgz#cd4bc3d6e9336c433265fc0aa016fc1aaf182f8a" - integrity sha512-DQmnRpLj7f6TgN/NYb0MTzJXL+vJF9h3pHy4JhCIs3zwcgez8xmGg3sXHcEO97BrmO2OSvCwMdfdlyl+E9KjOw== + version "9.4.1" + resolved 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jest-message-util "^27.5.1" expect@^29.0.0: - version "29.2.1" - resolved "https://registry.yarnpkg.com/expect/-/expect-29.2.1.tgz#25752d0df92d3daa5188dc8804de1f30759658cf" - integrity sha512-BJtA754Fba0YWRWHgjKUMTA3ltWarKgITXHQnbZ2mTxTXC4yMQlR0FI7HkB3fJYkhWBf4qjNiqvg3LDtXCcVRQ== + version "29.3.1" + resolved "https://registry.yarnpkg.com/expect/-/expect-29.3.1.tgz#92877aad3f7deefc2e3f6430dd195b92295554a6" + integrity sha512-gGb1yTgU30Q0O/tQq+z30KBWv24ApkMgFUpvKBkyLUBL68Wv8dHdJxTBZFl/iT8K/bqDHvUYRH6IIN3rToopPA== dependencies: - "@jest/expect-utils" "^29.2.1" + "@jest/expect-utils" "^29.3.1" jest-get-type "^29.2.0" - jest-matcher-utils "^29.2.1" - jest-message-util "^29.2.1" - jest-util "^29.2.1" + jest-matcher-utils "^29.3.1" + jest-message-util "^29.3.1" + jest-util "^29.3.1" express@^4.17.3: version "4.18.2" @@ -5366,9 +5415,9 @@ fast-levenshtein@^2.0.6, fast-levenshtein@~2.0.6: integrity sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw== fastq@^1.6.0: - version "1.13.0" - resolved "https://registry.yarnpkg.com/fastq/-/fastq-1.13.0.tgz#616760f88a7526bdfc596b7cab8c18938c36b98c" - integrity sha512-YpkpUnK8od0o1hmeSc7UUs/eB/vIPWJYjKck2QKIzAf71Vm1AAQ3EbuZB3g2JIy+pg+ERD0vqI79KyZiB2e2Nw== + version "1.14.0" + resolved "https://registry.yarnpkg.com/fastq/-/fastq-1.14.0.tgz#107f69d7295b11e0fccc264e1fc6389f623731ce" + integrity sha512-eR2D+V9/ExcbF9ls441yIuN6TI2ED1Y2ZcA5BmMtJsOkWOFRJQ0Jt0g1UwqXJJVAb+V+umH5Dfr8oh4EVP7VVg== dependencies: reusify "^1.0.4" @@ -5603,9 +5652,9 @@ functions-have-names@^1.2.2: integrity sha512-xckBUXyTIqT97tq2x2AMb+g163b5JFysYk0x4qxNFwbfQkmNZoiRHb6sPzI9/QV33WeuvVYBUIiD4NzNIyqaRQ== generic-filehandle@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.0.0.tgz#10d5ddc4adf105de616224dba58370f3dcc3877c" - integrity sha512-THrFJ1fq7wjwMmSN7sdp0JnQKZDVE7aooVwHTWREKHrCGVJGKKiD5BSaboNHiFU84RIzJ+oBOqQsN//ISWj1ZQ== + version "3.0.1" + resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.0.1.tgz#9bea8ad8f572bb07c16097df6fccc05a87ec77ff" + integrity sha512-E0eVkls2Ni7fUQ47VxYJN45/ow821pITHcgyaMZXBUt1czZUionT6HSqE0t+bcAozt5MYeJCxVxIrlTxoASXuQ== dependencies: es6-promisify "^6.1.1" @@ -5665,7 +5714,7 @@ glob-parent@^5.1.2, glob-parent@~5.1.2: dependencies: is-glob "^4.0.1" -glob-parent@^6.0.1, glob-parent@^6.0.2: +glob-parent@^6.0.2: version "6.0.2" resolved "https://registry.yarnpkg.com/glob-parent/-/glob-parent-6.0.2.tgz#6d237d99083950c79290f24c7642a3de9a28f9e3" integrity sha512-XxwI8EOhVQgWp6iDL+3b0r86f4d6AX6zSU55HfB4ydCEuXLXc5FcYeOu+nnGftS4TEju/11rt4KJPTMgbfmv4A== @@ -5710,10 +5759,10 @@ globals@^11.1.0: resolved "https://registry.yarnpkg.com/globals/-/globals-11.12.0.tgz#ab8795338868a0babd8525758018c2a7eb95c42e" integrity sha512-WOBp/EEGUiIsJSp7wcv/y6MO+lV9UoncWqxuFfm8eBwzWNgyfBd6Gz+IeKQ9jCmyhoH99g15M3T+QaVHFjizVA== -globals@^13.15.0: - version "13.17.0" - resolved "https://registry.yarnpkg.com/globals/-/globals-13.17.0.tgz#902eb1e680a41da93945adbdcb5a9f361ba69bd4" - integrity sha512-1C+6nQRb1GwGMKm2dH/E7enFAMxGTmGI7/dEdhy/DNelv85w9B72t3uc5frtMNXIbzrarJJ/lTCjcaZwbLJmyw== +globals@^13.19.0: + version "13.19.0" + resolved "https://registry.yarnpkg.com/globals/-/globals-13.19.0.tgz#7a42de8e6ad4f7242fbcca27ea5b23aca367b5c8" + integrity sha512-dkQ957uSRWHw7CFXLUtUHQI3g3aWApYhfNR2O6jn/907riyTYKVBmxYVROkBcY614FSSeSJh7Xm7SrUWCxvJMQ== dependencies: type-fest "^0.20.2" @@ -5729,6 +5778,13 @@ globby@^11.0.4, globby@^11.1.0: merge2 "^1.4.1" slash "^3.0.0" +gopd@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/gopd/-/gopd-1.0.1.tgz#29ff76de69dac7489b7c0918a5788e56477c332c" + integrity sha512-d65bNlIadxvpb/A2abVdlqKqV563juRnZ1Wtk6s1sIR8uNsXR70xqIzVqxVf1eTqDunwT2MkczEeaezCKTZhwA== + dependencies: + get-intrinsic "^1.1.3" + graceful-fs@^4.1.2, graceful-fs@^4.1.6, graceful-fs@^4.2.0, graceful-fs@^4.2.4, graceful-fs@^4.2.6, graceful-fs@^4.2.9: version "4.2.10" resolved "https://registry.yarnpkg.com/graceful-fs/-/graceful-fs-4.2.10.tgz#147d3a006da4ca3ce14728c7aefc287c367d7a6c" @@ -6010,9 +6066,9 @@ icss-utils@^5.0.0, icss-utils@^5.1.0: integrity sha512-soFhflCVWLfRNOPU3iv5Z9VUdT44xFRbzjLsEzSr5AQmgqPMTHdU3PMT1Cf1ssx8fLNJDA1juftYl+PUcv3MqA== idb@^7.0.1: - version "7.1.0" - resolved "https://registry.yarnpkg.com/idb/-/idb-7.1.0.tgz#2cc886be57738419e57f9aab58f647e5e2160270" - integrity sha512-Wsk07aAxDsntgYJY4h0knZJuTxM73eQ4reRAO+Z1liOh8eMCJ/MoDS8fCui1vGT9mnjtl1sOu3I2i/W1swPYZg== + version "7.1.1" + resolved "https://registry.yarnpkg.com/idb/-/idb-7.1.1.tgz#d910ded866d32c7ced9befc5bfdf36f572ced72b" + integrity sha512-gchesWBzyvGHRO9W8tzUWFDycow5gwjvFKfyV9FF32Y7F50yZMp7mP+T2mJIWFx49zicqyC4uefHM17o6xKIVQ== identity-obj-proxy@^3.0.0: version "3.0.0" @@ -6027,14 +6083,14 @@ ieee754@^1.2.1: integrity sha512-dcyqhDvX1C46lXZcVqCpK+FtMRQVdIMN6/Df5js2zouUsqG7I6sFxitIC+7KYK29KdXOLHdu9zL4sFnoVQnqaA== ignore@^5.2.0: - version "5.2.0" - resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.2.0.tgz#6d3bac8fa7fe0d45d9f9be7bac2fc279577e345a" - integrity sha512-CmxgYGiEPCLhfLnpPp1MoRmifwEIOgjcHXxOBjv7mY96c+eWScsOP9c112ZyLdWHi0FxHjI+4uVhKYp/gcdRmQ== + version "5.2.4" + resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.2.4.tgz#a291c0c6178ff1b960befe47fcdec301674a6324" + integrity sha512-MAb38BcSbH0eHNBxn7ql2NH/kX33OkB3lZ1BNdh7ENeRChHTYsTvWrMubiIAMNS2llXEEgZ1MUOBtXChP3kaFQ== immer@^9.0.7: - version "9.0.15" - resolved "https://registry.yarnpkg.com/immer/-/immer-9.0.15.tgz#0b9169e5b1d22137aba7d43f8a81a495dd1b62dc" - integrity sha512-2eB/sswms9AEUSkOm4SbV5Y7Vmt/bKRwByd52jfLkW4OLYeaTP3EEiJ9agqU0O/tq6Dk62Zfj+TJSqfm1rLVGQ== + version "9.0.16" + resolved "https://registry.yarnpkg.com/immer/-/immer-9.0.16.tgz#8e7caab80118c2b54b37ad43e05758cdefad0198" + integrity sha512-qenGE7CstVm1NrHQbMh8YaSzTZTFNP3zPqr3YU0S0UY441j4bJTg4A2Hh5KAhwgaiU6ZZ1Ar6y/2f4TblnMReQ== import-fresh@^3.0.0, import-fresh@^3.1.0, import-fresh@^3.2.1: version "3.3.0" @@ -6086,11 +6142,11 @@ ini@^1.3.5: integrity sha512-JV/yugV2uzW5iMRSiZAyDtQd+nxtUnjeLt0acNdw98kKLrvuRVyB80tsREOE7yvGVgalhZ6RNXCmEHkUKBKxew== internal-slot@^1.0.3: - version "1.0.3" - resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.3.tgz#7347e307deeea2faac2ac6205d4bc7d34967f59c" - integrity sha512-O0DB1JC/sPyZl7cIo78n5dR7eUSwwpYPiXRhTzNxZVAMUuB8vlnRFyLxdrVToks6XPLVnFfbzaVd5WLjhgg+vA== + version "1.0.4" + resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.4.tgz#8551e7baf74a7a6ba5f749cfb16aa60722f0d6f3" + integrity sha512-tA8URYccNzMo94s5MQZgH8NB/XTa6HsOo0MLfXTKKEnHVVdegzaQoFZ7Jp44bdvLvY2waT5dc+j5ICEswhi7UQ== dependencies: - get-intrinsic "^1.1.0" + get-intrinsic "^1.1.3" has "^1.0.3" side-channel "^1.0.4" @@ -6109,7 +6165,7 @@ ipaddr.js@^2.0.1: resolved "https://registry.yarnpkg.com/ipaddr.js/-/ipaddr.js-2.0.1.tgz#eca256a7a877e917aeb368b0a7497ddf42ef81c0" integrity sha512-1qTgH9NG+IIJ4yfKs2e6Pp1bZg8wbDbKHT21HrLIeYBTRLgMYKnMTPAuI3Lcs61nfx5h1xlXnbJtH1kX5/d/ng== -is-arguments@^1.0.4: +is-arguments@^1.0.4, is-arguments@^1.1.0, is-arguments@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== @@ -6166,7 +6222,7 @@ is-core-module@^2.8.1, is-core-module@^2.9.0: dependencies: has "^1.0.3" -is-date-object@^1.0.1: +is-date-object@^1.0.1, is-date-object@^1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/is-date-object/-/is-date-object-1.0.5.tgz#0841d5536e724c25597bf6ea62e1bd38298df31f" integrity sha512-9YQaSxsAiSwcvS33MBk3wTCVnWK+HhF8VZR2jRxehM16QcVOdHqPn4VPHmRK4lSr38n9JriurInLcP90xsYNfQ== @@ -6207,6 +6263,11 @@ is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: dependencies: is-extglob "^2.1.1" +is-map@^2.0.1, is-map@^2.0.2: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-map/-/is-map-2.0.2.tgz#00922db8c9bf73e81b7a335827bc2a43f2b91127" + integrity sha512-cOZFQQozTha1f4MxLFzlgKYPTyj26picdZTx82hbc/Xf4K/tZOOXSCkMvU4pKioRXGDLJRn0GM7Upe7kR721yg== + is-module@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-module/-/is-module-1.0.0.tgz#3258fb69f78c14d5b815d664336b4cffb6441591" @@ -6247,6 +6308,11 @@ is-object@^1.0.1: resolved "https://registry.yarnpkg.com/is-object/-/is-object-1.0.2.tgz#a56552e1c665c9e950b4a025461da87e72f86fcf" integrity sha512-2rRIahhZr2UWb45fIOuvZGpFtz0TyOZLf32KxBbSoUCeZR495zCKlWUKKUByk3geS2eAs7ZAABt0Y/Rx0GiQGA== +is-path-inside@^3.0.3: + version "3.0.3" + resolved "https://registry.yarnpkg.com/is-path-inside/-/is-path-inside-3.0.3.tgz#d231362e53a07ff2b0e0ea7fed049161ffd16283" + integrity sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ== + is-plain-obj@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/is-plain-obj/-/is-plain-obj-3.0.0.tgz#af6f2ea14ac5a646183a5bbdb5baabbc156ad9d7" @@ -6287,6 +6353,11 @@ is-root@^2.1.0: resolved "https://registry.yarnpkg.com/is-root/-/is-root-2.1.0.tgz#809e18129cf1129644302a4f8544035d51984a9c" integrity sha512-AGOriNp96vNBd3HtU+RzFEc75FfR5ymiYv8E553I71SCeXBiMsVDUtdio1OEFvrPyLIQ9tVR5RxXIFe5PUFjMg== +is-set@^2.0.1, is-set@^2.0.2: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-set/-/is-set-2.0.2.tgz#90755fa4c2562dc1c5d4024760d6119b94ca18ec" + integrity sha512-+2cnTEZeY5z/iXGbLhPrOAaK/Mau5k5eXq9j14CpRTftq0pAJu2MwVRSZhyZWBzx3o6X795Lz6Bpb6R0GKf37g== + is-shared-array-buffer@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-shared-array-buffer/-/is-shared-array-buffer-1.0.2.tgz#8f259c573b60b6a32d4058a1a07430c0a7344c79" @@ -6313,15 +6384,15 @@ is-symbol@^1.0.2, is-symbol@^1.0.3: dependencies: has-symbols "^1.0.2" -is-typed-array@^1.1.3, is-typed-array@^1.1.9: - version "1.1.9" - resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.9.tgz#246d77d2871e7d9f5aeb1d54b9f52c71329ece67" - integrity sha512-kfrlnTTn8pZkfpJMUgYD7YZ3qzeJgWUn8XfVYBARc4wnmNOmLbmuuaAs3q5fvB0UJOn6yHAKaGTPM7d6ezoD/A== +is-typed-array@^1.1.10, is-typed-array@^1.1.3: + version "1.1.10" + resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.10.tgz#36a5b5cb4189b575d1a3e4b08536bfb485801e3f" + integrity sha512-PJqgEHiWZvMpaFZ3uTc8kHPM4+4ADTlDniuQL7cU/UDA0Ql7F70yGfHph3cLNe+c9toaigv+DFzTJKhc2CtO6A== dependencies: available-typed-arrays "^1.0.5" call-bind "^1.0.2" - es-abstract "^1.20.0" for-each "^0.3.3" + gopd "^1.0.1" has-tostringtag "^1.0.0" is-typedarray@^1.0.0: @@ -6329,6 +6400,11 @@ is-typedarray@^1.0.0: resolved "https://registry.yarnpkg.com/is-typedarray/-/is-typedarray-1.0.0.tgz#e479c80858df0c1b11ddda6940f96011fcda4a9a" integrity sha512-cyA56iCMHAh5CdzjJIa4aohJyeO1YbwLi3Jc35MmRU6poroFjIGZzUzupGiRPOjgHg9TLu43xbpwXk523fMxKA== +is-weakmap@^2.0.1: + version "2.0.1" + resolved "https://registry.yarnpkg.com/is-weakmap/-/is-weakmap-2.0.1.tgz#5008b59bdc43b698201d18f62b37b2ca243e8cf2" + integrity sha512-NSBR4kH5oVj1Uwvv970ruUkCV7O1mzgVFO4/rev2cLRda9Tm9HrL70ZPut4rOHgY0FNrUu9BCbXA2sdQ+x0chA== + is-weakref@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-weakref/-/is-weakref-1.0.2.tgz#9529f383a9338205e89765e0392efc2f100f06f2" @@ -6336,6 +6412,14 @@ is-weakref@^1.0.2: dependencies: call-bind "^1.0.2" +is-weakset@^2.0.1: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-weakset/-/is-weakset-2.0.2.tgz#4569d67a747a1ce5a994dfd4ef6dcea76e7c0a1d" + integrity sha512-t2yVvttHkQktwnNNmBQ98AhENLdPUTDTE21uPqAQ0ARwQfGeQKRVS0NNurH7bTf7RrvcVn1OOge45CnBeHCSmg== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.1" + is-wsl@^2.2.0: version "2.2.0" resolved "https://registry.yarnpkg.com/is-wsl/-/is-wsl-2.2.0.tgz#74a4c76e77ca9fd3f932f290c17ea326cd157271" @@ -6343,6 +6427,11 @@ is-wsl@^2.2.0: dependencies: is-docker "^2.0.0" +isarray@^2.0.5: + version "2.0.5" + resolved "https://registry.yarnpkg.com/isarray/-/isarray-2.0.5.tgz#8af1e4c1221244cc62459faf38940d4e644a5723" + integrity sha512-xHjhDr3cNBK0BzdUJSPXZntQUx/mwMS5Rw4A7lPJ90XGAO6ISP/ePDNuo0vhqOZU+UD5JoodwCAAoZQd3FeAKw== + isarray@~1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/isarray/-/isarray-1.0.0.tgz#bb935d48582cba168c06834957a54a3e07124f11" @@ -6502,15 +6591,15 @@ jest-diff@^27.5.1: jest-get-type "^27.5.1" pretty-format "^27.5.1" -jest-diff@^29.2.1: - version "29.2.1" - resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-29.2.1.tgz#027e42f5a18b693fb2e88f81b0ccab533c08faee" - integrity sha512-gfh/SMNlQmP3MOUgdzxPOd4XETDJifADpT937fN1iUGz+9DgOu2eUPHH25JDkLVcLwwqxv3GzVyK4VBUr9fjfA== +jest-diff@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-29.3.1.tgz#d8215b72fed8f1e647aed2cae6c752a89e757527" + integrity 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-7429,14 +7523,7 @@ minimalistic-crypto-utils@^1.0.1: resolved "https://registry.yarnpkg.com/minimalistic-crypto-utils/-/minimalistic-crypto-utils-1.0.1.tgz#f6c00c1c0b082246e5c4d99dfb8c7c083b2b582a" integrity sha512-JIYlbt6g8i5jKfJ3xz7rF0LXmv2TkDxBLUkiBeZ7bAx4GnnNMr8xFpGnOxn6GhTEHx3SjRrZEoU+j04prX1ktg== -minimatch@3.0.4: - version "3.0.4" - resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-3.0.4.tgz#5166e286457f03306064be5497e8dbb0c3d32083" - integrity sha512-yJHVQEhyqPLUTgt9B83PXu6W3rx4MvvHvSUvToogpwoGDOUQ+yDrR0HRot+yOCdCO7u4hX3pWft6kWBBcqh0UA== - dependencies: - brace-expansion "^1.1.7" - -minimatch@^3.0.4, minimatch@^3.1.1, minimatch@^3.1.2: +minimatch@^3.0.4, minimatch@^3.0.5, minimatch@^3.1.1, minimatch@^3.1.2: version "3.1.2" resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-3.1.2.tgz#19cd194bfd3e428f049a70817c038d89ab4be35b" integrity sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw== @@ -7444,9 +7531,9 @@ 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"https://registry.yarnpkg.com/node-polyfill-webpack-plugin/-/node-polyfill-webpack-plugin-2.0.1.tgz#141d86f177103a8517c71d99b7c6a46edbb1bb58" + integrity sha512-ZUMiCnZkP1LF0Th2caY6J/eKKoA0TefpoVa68m/LQU1I/mE8rGt4fNYGgNuCcK+aG8P8P43nbeJ2RqJMOL/Y1A== dependencies: assert "^2.0.0" browserify-zlib "^0.2.0" @@ -7568,7 +7660,7 @@ node-polyfill-webpack-plugin@^1.1.4: console-browserify "^1.2.0" constants-browserify "^1.0.0" crypto-browserify "^3.12.0" - domain-browser "^4.19.0" + domain-browser "^4.22.0" events "^3.3.0" filter-obj "^2.0.2" https-browserify "^1.0.0" @@ -7577,20 +7669,21 @@ node-polyfill-webpack-plugin@^1.1.4: process "^0.11.10" punycode "^2.1.1" querystring-es3 "^0.2.1" - readable-stream "^3.6.0" + readable-stream "^4.0.0" stream-browserify "^3.0.0" stream-http "^3.2.0" string_decoder "^1.3.0" timers-browserify "^2.0.12" tty-browserify "^0.0.1" + type-fest "^2.14.0" url "^0.11.0" util "^0.12.4" vm-browserify "^1.1.2" node-releases@^2.0.6: - version "2.0.6" - resolved 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dependencies: define-properties "^1.1.4" - es-abstract "^1.19.5" + es-abstract "^1.20.4" -object.values@^1.1.0, object.values@^1.1.5: - version "1.1.5" - resolved "https://registry.yarnpkg.com/object.values/-/object.values-1.1.5.tgz#959f63e3ce9ef108720333082131e4a459b716ac" - integrity sha512-QUZRW0ilQ3PnPpbNtgdNV1PDbEqLIiSFB3l+EnGtBQ/8SUTLj1PZwtQHABZtLgwpJZTSZhuGLOGk57Drx2IvYg== +object.values@^1.1.0, object.values@^1.1.5, object.values@^1.1.6: + version "1.1.6" + resolved "https://registry.yarnpkg.com/object.values/-/object.values-1.1.6.tgz#4abbaa71eba47d63589d402856f908243eea9b1d" + integrity sha512-FVVTkD1vENCsAcwNs9k6jea2uHC/X0+JcjG8YA60FN5CMaJmG95wT9jek/xX9nornqGRrBkKtzuAu2wuHpKqvw== dependencies: call-bind "^1.0.2" - define-properties "^1.1.3" - es-abstract "^1.19.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" obuf@^1.0.0, obuf@^1.1.2: version "1.1.2" @@ -7849,9 +7942,9 @@ pako@^1.0.11, pako@^1.0.4, pako@~1.0.5: integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw== pako@^2.0.0: - version "2.0.4" - resolved "https://registry.yarnpkg.com/pako/-/pako-2.0.4.tgz#6cebc4bbb0b6c73b0d5b8d7e8476e2b2fbea576d" - integrity sha512-v8tweI900AUkZN6heMU/4Uy4cXRc2AYNRggVmTR+dEncawDJgCdLMximOVA2p4qO57WMynangsfGRb5WD6L1Bg== + version "2.1.0" + resolved "https://registry.yarnpkg.com/pako/-/pako-2.1.0.tgz#266cc37f98c7d883545d11335c00fbd4062c9a86" + integrity sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug== param-case@^3.0.4: version "3.0.4" @@ -8065,12 +8158,12 @@ postcss-colormin@^5.3.0: colord "^2.9.1" postcss-value-parser "^4.2.0" -postcss-convert-values@^5.1.2: - version "5.1.2" - resolved "https://registry.yarnpkg.com/postcss-convert-values/-/postcss-convert-values-5.1.2.tgz#31586df4e184c2e8890e8b34a0b9355313f503ab" - integrity sha512-c6Hzc4GAv95B7suy4udszX9Zy4ETyMCgFPUDtWjdFTKH1SE9eFY/jEpHSwTH1QPuwxHpWslhckUQWbNRM4ho5g== +postcss-convert-values@^5.1.3: + version "5.1.3" + resolved "https://registry.yarnpkg.com/postcss-convert-values/-/postcss-convert-values-5.1.3.tgz#04998bb9ba6b65aa31035d669a6af342c5f9d393" + integrity sha512-82pC1xkJZtcJEfiLw6UXnXVXScgtBrjlO5CBmuDQc+dlb88ZYheFsjTn40+zBVi3DkfF7iezO0nJUPLcJK3pvA== dependencies: - browserslist "^4.20.3" + browserslist "^4.21.4" postcss-value-parser "^4.2.0" postcss-custom-media@^8.0.2: @@ -8080,10 +8173,10 @@ postcss-custom-media@^8.0.2: dependencies: postcss-value-parser "^4.2.0" -postcss-custom-properties@^12.1.9: - version "12.1.9" - resolved "https://registry.yarnpkg.com/postcss-custom-properties/-/postcss-custom-properties-12.1.9.tgz#0883429a7ef99f1ba239d1fea29ce84906daa8bd" - integrity sha512-/E7PRvK8DAVljBbeWrcEQJPG72jaImxF3vvCNFwv9cC8CzigVoNIpeyfnJzphnN3Fd8/auBf5wvkw6W9MfmTyg== +postcss-custom-properties@^12.1.10: + version "12.1.11" + resolved 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cssnano-utils "^3.1.0" postcss-selector-parser "^6.0.5" @@ -8262,12 +8355,12 @@ postcss-minify-gradients@^5.1.1: cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" -postcss-minify-params@^5.1.3: - version "5.1.3" - resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.3.tgz#ac41a6465be2db735099bbd1798d85079a6dc1f9" - integrity sha512-bkzpWcjykkqIujNL+EVEPOlLYi/eZ050oImVtHU7b4lFS82jPnsCb44gvC6pxaNt38Els3jWYDHTjHKf0koTgg== +postcss-minify-params@^5.1.4: + version "5.1.4" + resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.4.tgz#c06a6c787128b3208b38c9364cfc40c8aa5d7352" + integrity sha512-+mePA3MgdmVmv6g+30rn57USjOGSAyuxUmkfiWpzalZ8aiBkdPYjXWtHuwJGm1v5Ojy0Z0LaSYhHaLJQB0P8Jw== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" @@ -8361,12 +8454,12 @@ postcss-normalize-timing-functions@^5.1.0: dependencies: postcss-value-parser "^4.2.0" -postcss-normalize-unicode@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/postcss-normalize-unicode/-/postcss-normalize-unicode-5.1.0.tgz#3d23aede35e160089a285e27bf715de11dc9db75" - integrity sha512-J6M3MizAAZ2dOdSjy2caayJLQT8E8K9XjLce8AUQMwOrCvjCHv24aLC/Lps1R1ylOfol5VIDMaM/Lo9NGlk1SQ== +postcss-normalize-unicode@^5.1.1: + version "5.1.1" + resolved "https://registry.yarnpkg.com/postcss-normalize-unicode/-/postcss-normalize-unicode-5.1.1.tgz#f67297fca3fea7f17e0d2caa40769afc487aa030" + integrity sha512-qnCL5jzkNUmKVhZoENp1mJiGNPcsJCs1aaRmURmeJGES23Z/ajaln+EPTD+rBeNkSryI+2WTdW+lwcVdOikrpA== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" postcss-value-parser "^4.2.0" postcss-normalize-url@^5.1.0: @@ -8394,9 +8487,9 @@ postcss-normalize@^10.0.1: sanitize.css "*" postcss-opacity-percentage@^1.1.2: - version "1.1.2" - resolved 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pretty-format@^27.0.2, pretty-format@^27.5.1: +pretty-format@^27.0.2, pretty-format@^27.5.1: version "27.5.1" resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-27.5.1.tgz#2181879fdea51a7a5851fb39d920faa63f01d88e" integrity sha512-Qb1gy5OrP5+zDf2Bvnzdl3jsTf1qXVMazbvCoKhtKqVs4/YK4ozX4gKQJJVyNe+cajNPn0KoC0MC3FUmaHWEmQ== @@ -8601,10 +8694,10 @@ pretty-format@^28.1.3: ansi-styles "^5.0.0" react-is "^18.0.0" -pretty-format@^29.0.0, pretty-format@^29.2.1: - version "29.2.1" - resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-29.2.1.tgz#86e7748fe8bbc96a6a4e04fa99172630907a9611" - integrity sha512-Y41Sa4aLCtKAXvwuIpTvcFBkyeYp2gdFWzXGA+ZNES3VwURIB165XO/z7CjETwzCCS53MjW/rLMyyqEnTtaOfA== +pretty-format@^29.0.0, pretty-format@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-29.3.1.tgz#1841cac822b02b4da8971dacb03e8a871b4722da" + integrity 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"@babel/runtime" "^7.0.0" memoize-one ">=3.1.1 <6" @@ -9017,6 +9110,16 @@ readable-stream@^3.0.6, readable-stream@^3.5.0, readable-stream@^3.6.0: string_decoder "^1.1.1" util-deprecate "^1.0.1" +readable-stream@^4.0.0: + version "4.2.0" + resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-4.2.0.tgz#a7ef523d3b39e4962b0db1a1af22777b10eeca46" + integrity sha512-gJrBHsaI3lgBoGMW/jHZsQ/o/TIWiu5ENCJG1BB7fuCKzpFM8GaS2UoBVt9NO+oI+3FcrBNbUkl3ilDe09aY4A== + dependencies: + abort-controller "^3.0.0" + buffer "^6.0.3" + events "^3.3.0" + process "^0.11.10" + readdirp@~3.6.0: version "3.6.0" resolved "https://registry.yarnpkg.com/readdirp/-/readdirp-3.6.0.tgz#74a370bd857116e245b29cc97340cd431a02a6c7" @@ -9025,11 +9128,11 @@ readdirp@~3.6.0: picomatch "^2.2.1" recursive-readdir@^2.2.2: - version "2.2.2" - resolved "https://registry.yarnpkg.com/recursive-readdir/-/recursive-readdir-2.2.2.tgz#9946fb3274e1628de6e36b2f6714953b4845094f" - integrity 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semver@^7.3.7, semver@^7.3.8: version "7.3.8" resolved "https://registry.yarnpkg.com/semver/-/semver-7.3.8.tgz#07a78feafb3f7b32347d725e33de7e2a2df67798" integrity sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A== @@ -9540,9 +9643,9 @@ source-map-js@^1.0.1, source-map-js@^1.0.2: integrity sha512-R0XvVJ9WusLiqTCEiGCmICCMplcCkIwwR11mOSD9CR5u+IXYdiseeEuXCVAjS54zqwkLcPNnmU4OeJ6tUrWhDw== source-map-loader@^3.0.0: - version "3.0.1" - resolved "https://registry.yarnpkg.com/source-map-loader/-/source-map-loader-3.0.1.tgz#9ae5edc7c2d42570934be4c95d1ccc6352eba52d" - integrity sha512-Vp1UsfyPvgujKQzi4pyDiTOnE3E4H+yHvkVRN3c/9PJmQS4CQJExvcDvaX/D+RV+xQben9HJ56jMJS3CgUeWyA== + version "3.0.2" + resolved "https://registry.yarnpkg.com/source-map-loader/-/source-map-loader-3.0.2.tgz#af23192f9b344daa729f6772933194cc5fa54fee" + integrity sha512-BokxPoLjyl3iOrgkWaakaxqnelAJSS+0V+De0kKIq6lyWrXuiPgYTGp6z3iHmqljKAaLXwZa+ctD8GccRJeVvg== dependencies: abab "^2.0.5" 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+string.prototype.trimstart@^1.0.6: + version "1.0.6" + resolved "https://registry.yarnpkg.com/string.prototype.trimstart/-/string.prototype.trimstart-1.0.6.tgz#e90ab66aa8e4007d92ef591bbf3cd422c56bdcf4" + integrity sha512-omqjMDaY92pbn5HOX7f9IccLA+U1tA9GvtU4JrodiXFfYB7jPzzHpRzpglLAjtUV6bB557zwClJezTqnAiYnQA== dependencies: call-bind "^1.0.2" define-properties "^1.1.4" - es-abstract "^1.19.5" + es-abstract "^1.20.4" string_decoder@^1.1.1, string_decoder@^1.3.0: version "1.3.0" @@ -9792,18 +9895,18 @@ style-loader@^3.3.1: resolved "https://registry.yarnpkg.com/style-loader/-/style-loader-3.3.1.tgz#057dfa6b3d4d7c7064462830f9113ed417d38575" integrity sha512-GPcQ+LDJbrcxHORTRes6Jy2sfvK2kS6hpSfI/fXhPt+spVzxF6LJ1dHLN9zIGmVaaP044YKaIatFaufENRiDoQ== -stylehacks@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/stylehacks/-/stylehacks-5.1.0.tgz#a40066490ca0caca04e96c6b02153ddc39913520" - integrity 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"^3.1.4" @@ -9959,9 +10063,9 @@ terser-webpack-plugin@^5.1.3, terser-webpack-plugin@^5.2.5: terser "^5.14.1" terser@^5.0.0, terser@^5.10.0, terser@^5.14.1: - version "5.15.1" - resolved "https://registry.yarnpkg.com/terser/-/terser-5.15.1.tgz#8561af6e0fd6d839669c73b92bdd5777d870ed6c" - integrity sha512-K1faMUvpm/FBxjBXud0LWVAGxmvoPbZbfTCYbSgaaYQaIXI3/TdI7a7ZGA73Zrou6Q8Zmz3oeUTsp/dj+ag2Xw== + version "5.16.1" + resolved "https://registry.yarnpkg.com/terser/-/terser-5.16.1.tgz#5af3bc3d0f24241c7fb2024199d5c461a1075880" + integrity sha512-xvQfyfA1ayT0qdK47zskQgRZeWLoOQ8JQ6mIgRGVNwZKdQMU+5FkCBjmv4QjcrTzyZquRw2FVtlJSRUmMKQslw== dependencies: "@jridgewell/source-map" "^0.3.2" acorn "^8.5.0" @@ -10095,14 +10199,14 @@ tslib@^1.8.1, tslib@^1.9.0: integrity sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg== tslib@^2.0.3: - version "2.4.0" - resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.4.0.tgz#7cecaa7f073ce680a05847aa77be941098f36dc3" - 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-10486,9 +10595,9 @@ webpack-sources@^3.2.3: integrity sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w== webpack@^5.64.4: - version "5.74.0" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.74.0.tgz#02a5dac19a17e0bb47093f2be67c695102a55980" - integrity sha512-A2InDwnhhGN4LYctJj6M1JEaGL7Luj6LOmyBHjcI8529cm5p6VXiTIW2sn6ffvEAKmveLzvu4jrihwXtPojlAA== + version "5.75.0" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.75.0.tgz#1e440468647b2505860e94c9ff3e44d5b582c152" + integrity sha512-piaIaoVJlqMsPtX/+3KTTO6jfvrSYgauFVdt8cr9LTHKmcq/AMd4mhzsiP7ZF/PGRNPGA8336jldh9l2Kt2ogQ== dependencies: "@types/eslint-scope" "^3.7.3" "@types/estree" "^0.0.51" @@ -10583,17 +10692,27 @@ which-boxed-primitive@^1.0.2: is-string "^1.0.5" is-symbol "^1.0.3" -which-typed-array@^1.1.2: - version "1.1.8" - resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.8.tgz#0cfd53401a6f334d90ed1125754a42ed663eb01f" - integrity 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version "1.3.1" @@ -10818,9 +10937,9 @@ ws@^7.4.6: integrity sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q== ws@^8.4.2: - version "8.9.0" - resolved "https://registry.yarnpkg.com/ws/-/ws-8.9.0.tgz#2a994bb67144be1b53fe2d23c53c028adeb7f45e" - integrity sha512-Ja7nszREasGaYUYCI2k4lCKIRTt+y7XuqVoHR44YpI49TtryyqbqvDMn5eqfW7e6HzTukDRIsXqzVHScqRcafg== + version "8.11.0" + resolved "https://registry.yarnpkg.com/ws/-/ws-8.11.0.tgz#6a0d36b8edfd9f96d8b25683db2f8d7de6e8e143" + integrity sha512-HPG3wQd9sNQoT9xHyNCXoDUa+Xw/VevmY9FoHyQ+g+rrMn4j6FB4np7Z0OhdTgjx6MgQLK7jwSy1YecU1+4Asg== xml-name-validator@^3.0.0: version "3.0.0" diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/.eslintrc.json b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/.eslintrc.json similarity index 100% rename from demos/jbrowse-react-linear-genome-view-nextjs/.eslintrc.json rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/.eslintrc.json diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/.gitignore b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/.gitignore similarity index 100% rename from demos/jbrowse-react-linear-genome-view-nextjs/.gitignore rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/.gitignore diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/README.md b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/README.md similarity index 56% rename from demos/jbrowse-react-linear-genome-view-nextjs/README.md rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/README.md index 4eb631c000..3c7fc24725 100644 --- a/demos/jbrowse-react-linear-genome-view-nextjs/README.md +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/README.md @@ -1,12 +1,14 @@ # jbrowse-react-linear-genome-view-nextjs -This is a demo of using the linear genome view with next.js 11 (which uses webpack 5) +This is a demo of using the linear genome view with next.js 11 (which uses +webpack 5) # Demo of `@jbrowse/react-linear-genome-view` with next.js See this app running at https://jbrowse.org/demos/lgv-nextjs/. -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-nextjs +Download this directory from the monorepo using +https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-nextjs ## Getting Started @@ -20,4 +22,5 @@ yarn dev ## Deploy -This page is deployed to https://jbrowse.org/demos/lgv-nextjs (uses `yarn build && yarn export` to create static build with no server side) +This page is deployed to https://jbrowse.org/demos/lgv-nextjs (uses +`yarn build && yarn export` to create static build with no server side) diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/next-env.d.ts b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/next-env.d.ts similarity index 100% rename from demos/jbrowse-react-linear-genome-view-nextjs/next-env.d.ts rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/next-env.d.ts diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/next.config.js b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/next.config.js similarity index 100% rename from demos/jbrowse-react-linear-genome-view-nextjs/next.config.js rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/next.config.js diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/package.json b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/package.json similarity index 68% rename from demos/jbrowse-react-linear-genome-view-nextjs/package.json rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/package.json index 814e73d14f..faaab8ecf9 100644 --- a/demos/jbrowse-react-linear-genome-view-nextjs/package.json +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/package.json @@ -2,6 +2,7 @@ "name": "jbrowse-react-linear-genome-view-next", "version": "0.1.0", "private": true, + "license": "MIT", "scripts": { "dev": "next dev", "build": "next build", @@ -14,14 +15,16 @@ "dependencies": { "@fontsource/roboto": "^4.5.7", "@jbrowse/react-linear-genome-view": "^2.0.0", - "next": "^12.1.0", - "react": "^17.0.0", - "react-dom": "^17.0.0" + "next": "^13.0.7", + "react": "^18.2.0", + "react-dom": "^18.2.0" }, "devDependencies": { - "@types/node": "17.0.41", - "@types/react": "^17.0.0", - "@types/react-dom": "^17.0.0", - "typescript": "4.7.3" + "@types/node": "18.11.9", + "@types/react": "^18.0.25", + "@types/react-dom": "^18.0.9", + "eslint": "8.28.0", + "eslint-config-next": "13.0.4", + "typescript": "4.9.3" } } diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/pages/index.tsx b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/pages/index.tsx similarity index 60% rename from demos/jbrowse-react-linear-genome-view-nextjs/pages/index.tsx rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/pages/index.tsx index 936274d008..6a677baaa9 100644 --- a/demos/jbrowse-react-linear-genome-view-nextjs/pages/index.tsx +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/pages/index.tsx @@ -7,64 +7,7 @@ import { import assembly from '../utils/assembly' import tracks from '../utils/tracks' - -const defaultSession = { - name: 'this session', - view: { - id: 'linearGenomeView', - type: 'LinearGenomeView', - tracks: [ - { - id: '7PWx6ki1_', - type: 'ReferenceSequenceTrack', - configuration: 'GRCh38-ReferenceSequenceTrack', - displays: [ - { - id: 'pa_7lx6FDh', - type: 'LinearReferenceSequenceDisplay', - height: 210, - configuration: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - }, - ], - }, - { - id: 'KHwe41KXk', - type: 'AlignmentsTrack', - configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', - displays: [ - { - id: '_-kwYVczT8', - type: 'LinearAlignmentsDisplay', - PileupDisplay: { - id: '1HTk32IDZJ', - type: 'LinearPileupDisplay', - height: 100, - configuration: { - type: 'LinearPileupDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_pileup_xyz', - }, - }, - SNPCoverageDisplay: { - id: 'ZBXRXmuDrc', - type: 'LinearSNPCoverageDisplay', - height: 45, - configuration: { - type: 'LinearSNPCoverageDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', - }, - }, - configuration: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', - height: 250, - }, - ], - }, - ], - }, -} +import defaultSession from '../utils/defaultSession' type ViewModel = ReturnType @@ -77,7 +20,6 @@ function View() { const state = createViewState({ assembly, tracks, - location: '10:29,838,655..29,838,737', onChange: (patch: any) => { setPatches(previous => previous + JSON.stringify(patch) + '\n') }, @@ -98,11 +40,11 @@ function View() {

The code for this app is available at{' '} - https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view-nextjs + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-nextjs .

diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/public/favicon.ico b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/public/favicon.ico similarity index 100% rename from demos/jbrowse-react-linear-genome-view-nextjs/public/favicon.ico rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/public/favicon.ico diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/public/vercel.svg b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/public/vercel.svg similarity index 100% rename from demos/jbrowse-react-linear-genome-view-nextjs/public/vercel.svg rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/public/vercel.svg diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/tsconfig.json b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/tsconfig.json similarity index 95% rename from demos/jbrowse-react-linear-genome-view-nextjs/tsconfig.json rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/tsconfig.json index 99710e8578..921df2f209 100644 --- a/demos/jbrowse-react-linear-genome-view-nextjs/tsconfig.json +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/tsconfig.json @@ -1,6 +1,6 @@ { "compilerOptions": { - "target": "es5", + "target": "es2018", "lib": ["dom", "dom.iterable", "esnext"], "allowJs": true, "skipLibCheck": true, diff --git a/demos/jbrowse-react-linear-genome-view/src/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts similarity index 75% rename from demos/jbrowse-react-linear-genome-view/src/assembly.ts rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts index 5c26ea9164..af9f6755d9 100644 --- a/demos/jbrowse-react-linear-genome-view/src/assembly.ts +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts @@ -16,16 +16,6 @@ const assembly = { uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', }, }, - displays: [ - { - type: 'LinearReferenceSequenceDisplay', - displayId: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - renderer: { - type: 'DivSequenceRenderer', - }, - }, - ], }, refNameAliases: { adapter: { diff --git a/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/defaultSession.ts b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/defaultSession.ts new file mode 100644 index 0000000000..d9e0281ccc --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/defaultSession.ts @@ -0,0 +1,130 @@ +export default { + name: 'this session', + margin: 0, + view: { + id: 'linearGenomeView', + minimized: false, + type: 'LinearGenomeView', + offsetPx: 191980240, + bpPerPx: 0.1554251851851852, + displayedRegions: [ + { + refName: '10', + start: 0, + end: 133797422, + reversed: false, + assemblyName: 'GRCh38', + }, + ], + tracks: [ + { + id: '4aZAiE-A3', + type: 'ReferenceSequenceTrack', + configuration: 'GRCh38-ReferenceSequenceTrack', + minimized: false, + displays: [ + { + id: 'AD3gqvG0_6', + type: 'LinearReferenceSequenceDisplay', + height: 180, + configuration: + 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', + showForward: true, + showReverse: true, + showTranslation: true, + }, + ], + }, + { + id: 'T6uhrtY40O', + type: 'AlignmentsTrack', + configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + minimized: false, + displays: [ + { + id: 'FinKswChSr', + type: 'LinearAlignmentsDisplay', + PileupDisplay: { + id: 'YAAaF494z', + type: 'LinearPileupDisplay', + height: 134, + configuration: { + type: 'LinearPileupDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz', + }, + showSoftClipping: false, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + SNPCoverageDisplay: { + id: 'VTQ_VGbAVJ', + type: 'LinearSNPCoverageDisplay', + height: 45, + configuration: { + type: 'LinearSNPCoverageDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', + }, + selectedRendering: '', + resolution: 1, + constraints: {}, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + snpCovHeight: 45, + configuration: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', + height: 179, + lowerPanelType: 'LinearPileupDisplay', + }, + ], + }, + { + id: 'EUnTnpVI6', + type: 'QuantitativeTrack', + configuration: 'hg38.100way.phyloP100way', + minimized: false, + displays: [ + { + id: 'mrlawr9Wtg', + type: 'LinearWiggleDisplay', + height: 100, + configuration: 'hg38.100way.phyloP100way-LinearWiggleDisplay', + selectedRendering: '', + resolution: 1, + constraints: {}, + }, + ], + }, + { + id: 'Cbnwl72EX', + type: 'VariantTrack', + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + minimized: false, + displays: [ + { + id: 'dvXz01Wf6w', + type: 'LinearVariantDisplay', + height: 100, + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay', + }, + ], + }, + ], + hideHeader: false, + hideHeaderOverview: false, + hideNoTracksActive: false, + trackSelectorType: 'hierarchical', + trackLabels: 'overlapping', + showCenterLine: false, + showCytobandsSetting: true, + showGridlines: true, + }, +} diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts similarity index 60% rename from demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts rename to embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts index c3489ea36a..fb6422b271 100644 --- a/demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/utils/tracks.ts @@ -1,8 +1,7 @@ const tracks = [ { - type: 'BasicTrack', - trackId: - 'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff', + type: 'FeatureTrack', + trackId: 'genes', name: 'NCBI RefSeq Genes', assemblyNames: ['GRCh38'], category: ['Genes'], @@ -17,6 +16,36 @@ const tracks = [ }, }, }, + textSearching: { + textSearchAdapter: { + type: 'TrixTextSearchAdapter', + textSearchAdapterId: 'gff3tabix_genes-index', + ixFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix', + }, + ixxFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx', + }, + metaFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json', + }, + assemblyNames: ['GRCh38'], + }, + }, + }, + { + type: 'FeatureTrack', + trackId: 'repeats_hg38', + name: 'Repeats', + assemblyNames: ['hg38'], + category: ['Annotation'], + adapter: { + type: 'BigBedAdapter', + bigBedLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb', + locationType: 'UriLocation', + }, + }, }, { type: 'AlignmentsTrack', @@ -65,6 +94,20 @@ const tracks = [ }, }, }, + { + type: 'QuantitativeTrack', + trackId: 'hg38.100way.phyloP100way', + name: 'hg38.100way.phyloP100way', + category: ['Conservation'], + assemblyNames: ['hg38'], + adapter: { + type: 'BigWigAdapter', + bigWigLocation: { + uri: 'https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw', + locationType: 'UriLocation', + }, + }, + }, ] export default tracks diff --git a/embedded_demos/jbrowse-react-linear-genome-view-nextjs/yarn.lock b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/yarn.lock new file mode 100644 index 0000000000..d13de9f585 --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view-nextjs/yarn.lock @@ -0,0 +1,3286 @@ +# THIS IS AN AUTOGENERATED FILE. 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"0.1.0" + resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" + integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== diff --git a/demos/jbrowse-react-linear-genome-view-vanillajs/README.md b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/README.md similarity index 53% rename from demos/jbrowse-react-linear-genome-view-vanillajs/README.md rename to embedded_demos/jbrowse-react-linear-genome-view-vanillajs/README.md index 19de7967b9..62a07ccabd 100644 --- a/demos/jbrowse-react-linear-genome-view-vanillajs/README.md +++ b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/README.md @@ -2,7 +2,8 @@ See this app running at https://jbrowse.org/demos/lgv-vanillajs/. -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vanillajs +Download this directory from the monorepo using +https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-vanillajs ## Usage diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/assembly.js b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/assembly.js new file mode 100644 index 0000000000..af9f6755d9 --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/assembly.js @@ -0,0 +1,30 @@ +const assembly = { + name: 'GRCh38', + aliases: ['hg38'], + sequence: { + type: 'ReferenceSequenceTrack', + trackId: 'GRCh38-ReferenceSequenceTrack', + adapter: { + type: 'BgzipFastaAdapter', + fastaLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz', + }, + faiLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai', + }, + gziLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', + }, + }, + }, + refNameAliases: { + adapter: { + type: 'RefNameAliasAdapter', + location: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt', + }, + }, + }, +} + +export default assembly diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/defaultSession.js b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/defaultSession.js new file mode 100644 index 0000000000..d9e0281ccc --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/defaultSession.js @@ -0,0 +1,130 @@ +export default { + name: 'this session', + margin: 0, + view: { + id: 'linearGenomeView', + minimized: false, + type: 'LinearGenomeView', + offsetPx: 191980240, + bpPerPx: 0.1554251851851852, + displayedRegions: [ + { + refName: '10', + start: 0, + end: 133797422, + reversed: false, + assemblyName: 'GRCh38', + }, + ], + tracks: [ + { + id: '4aZAiE-A3', + type: 'ReferenceSequenceTrack', + configuration: 'GRCh38-ReferenceSequenceTrack', + minimized: false, + displays: [ + { + id: 'AD3gqvG0_6', + type: 'LinearReferenceSequenceDisplay', + height: 180, + configuration: + 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', + showForward: true, + showReverse: true, + showTranslation: true, + }, + ], + }, + { + id: 'T6uhrtY40O', + type: 'AlignmentsTrack', + configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + minimized: false, + displays: [ + { + id: 'FinKswChSr', + type: 'LinearAlignmentsDisplay', + PileupDisplay: { + id: 'YAAaF494z', + type: 'LinearPileupDisplay', + height: 134, + configuration: { + type: 'LinearPileupDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz', + }, + showSoftClipping: false, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + SNPCoverageDisplay: { + id: 'VTQ_VGbAVJ', + type: 'LinearSNPCoverageDisplay', + height: 45, + configuration: { + type: 'LinearSNPCoverageDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', + }, + selectedRendering: '', + resolution: 1, + constraints: {}, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + snpCovHeight: 45, + configuration: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', + height: 179, + lowerPanelType: 'LinearPileupDisplay', + }, + ], + }, + { + id: 'EUnTnpVI6', + type: 'QuantitativeTrack', + configuration: 'hg38.100way.phyloP100way', + minimized: false, + displays: [ + { + id: 'mrlawr9Wtg', + type: 'LinearWiggleDisplay', + height: 100, + configuration: 'hg38.100way.phyloP100way-LinearWiggleDisplay', + selectedRendering: '', + resolution: 1, + constraints: {}, + }, + ], + }, + { + id: 'Cbnwl72EX', + type: 'VariantTrack', + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + minimized: false, + displays: [ + { + id: 'dvXz01Wf6w', + type: 'LinearVariantDisplay', + height: 100, + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay', + }, + ], + }, + ], + hideHeader: false, + hideHeaderOverview: false, + hideNoTracksActive: false, + trackSelectorType: 'hierarchical', + trackLabels: 'overlapping', + showCenterLine: false, + showCytobandsSetting: true, + showGridlines: true, + }, +} diff --git a/products/jbrowse-react-linear-genome-view/umd_example/genomeView.js b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/genomeView.js similarity index 84% rename from products/jbrowse-react-linear-genome-view/umd_example/genomeView.js rename to embedded_demos/jbrowse-react-linear-genome-view-vanillajs/genomeView.js index ee06a2b3d6..1d1b20f6b0 100644 --- a/products/jbrowse-react-linear-genome-view/umd_example/genomeView.js +++ b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/genomeView.js @@ -1,17 +1,17 @@ /* global JBrowseReactLinearGenomeView React, ReactDOM */ import assembly from './assembly.js' import tracks from './tracks.js' +import defaultSession from './defaultSession.js' const { createViewState, JBrowseLinearGenomeView } = JBrowseReactLinearGenomeView -const { createElement } = React -const { render } = ReactDOM const updates = document.getElementById('update') + const state = new createViewState({ assembly, tracks, - location: '1:100,987,269..100,987,368', + defaultSession, onChange: patch => { updates.innerHTML += JSON.stringify(patch) + '\n' }, @@ -33,7 +33,7 @@ document.getElementById('showviewstate').addEventListener('click', () => { }) const domContainer = document.getElementById('jbrowse_linear_genome_view') -render( - createElement(JBrowseLinearGenomeView, { viewState: state }), +ReactDOM.render( + React.createElement(JBrowseLinearGenomeView, { viewState: state }), domContainer, ) diff --git a/demos/jbrowse-react-linear-genome-view-vanillajs/index.html b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/index.html similarity index 79% rename from demos/jbrowse-react-linear-genome-view-vanillajs/index.html rename to embedded_demos/jbrowse-react-linear-genome-view-vanillajs/index.html index 386549300b..4854242f5b 100644 --- a/demos/jbrowse-react-linear-genome-view-vanillajs/index.html +++ b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/index.html @@ -28,6 +28,13 @@

Using JBrowse Linear Genome View!

BRCA2
+

+ The code for this app is available at + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-view-vanillajs +

diff --git a/demos/jbrowse-react-linear-genome-view-vanillajs/package.json b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/package.json similarity index 91% rename from demos/jbrowse-react-linear-genome-view-vanillajs/package.json rename to embedded_demos/jbrowse-react-linear-genome-view-vanillajs/package.json index b26b4e6c42..ea3fe9c080 100644 --- a/demos/jbrowse-react-linear-genome-view-vanillajs/package.json +++ b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/package.json @@ -1,4 +1,5 @@ { + "license": "MIT", "scripts": { "deploy": "aws s3 sync --delete . s3://jbrowse.org/demos/lgv-vanillajs/", "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/demos/lgv-vanillajs/*\"" diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js new file mode 100644 index 0000000000..fb6422b271 --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js @@ -0,0 +1,113 @@ +const tracks = [ + { + type: 'FeatureTrack', + trackId: 'genes', + name: 'NCBI RefSeq Genes', + assemblyNames: ['GRCh38'], + category: ['Genes'], + adapter: { + type: 'Gff3TabixAdapter', + gffGzLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz', + }, + index: { + location: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.tbi', + }, + }, + }, + textSearching: { + textSearchAdapter: { + type: 'TrixTextSearchAdapter', + textSearchAdapterId: 'gff3tabix_genes-index', + ixFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix', + }, + ixxFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx', + }, + metaFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json', + }, + assemblyNames: ['GRCh38'], + }, + }, + }, + { + type: 'FeatureTrack', + trackId: 'repeats_hg38', + name: 'Repeats', + assemblyNames: ['hg38'], + category: ['Annotation'], + adapter: { + type: 'BigBedAdapter', + bigBedLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb', + locationType: 'UriLocation', + }, + }, + }, + { + type: 'AlignmentsTrack', + trackId: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + name: 'NA12878 Exome', + assemblyNames: ['GRCh38'], + category: ['1000 Genomes', 'Alignments'], + adapter: { + type: 'CramAdapter', + cramLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram', + }, + craiLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai', + }, + sequenceAdapter: { + type: 'BgzipFastaAdapter', + fastaLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz', + }, + faiLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai', + }, + gziLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', + }, + }, + }, + }, + { + type: 'VariantTrack', + trackId: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + name: '1000 Genomes Variant Calls', + assemblyNames: ['GRCh38'], + category: ['1000 Genomes', 'Variants'], + adapter: { + type: 'VcfTabixAdapter', + vcfGzLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz', + }, + index: { + location: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz.tbi', + }, + }, + }, + }, + { + type: 'QuantitativeTrack', + trackId: 'hg38.100way.phyloP100way', + name: 'hg38.100way.phyloP100way', + category: ['Conservation'], + assemblyNames: ['hg38'], + adapter: { + type: 'BigWigAdapter', + bigWigLocation: { + uri: 'https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw', + locationType: 'UriLocation', + }, + }, + }, +] + +export default tracks diff --git a/demos/jbrowse-react-linear-genome-view-vanillajs/yarn.lock b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/yarn.lock similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vanillajs/yarn.lock rename to embedded_demos/jbrowse-react-linear-genome-view-vanillajs/yarn.lock diff --git a/demos/jbrowse-react-linear-genome-view-vite/.gitignore b/embedded_demos/jbrowse-react-linear-genome-view-vite/.gitignore similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/.gitignore rename to embedded_demos/jbrowse-react-linear-genome-view-vite/.gitignore diff --git a/demos/jbrowse-react-linear-genome-view-vite/README.md b/embedded_demos/jbrowse-react-linear-genome-view-vite/README.md similarity index 56% rename from demos/jbrowse-react-linear-genome-view-vite/README.md rename to embedded_demos/jbrowse-react-linear-genome-view-vite/README.md index 80430555e7..f22011de90 100644 --- a/demos/jbrowse-react-linear-genome-view-vite/README.md +++ b/embedded_demos/jbrowse-react-linear-genome-view-vite/README.md @@ -1,18 +1,23 @@ # vite with @jbrowse/react-linear-genome-view -Based on https://codesandbox.io/s/ylt4t?file=/vite.config.ts:478-540 by @garrettjstevens +Based on https://codesandbox.io/s/ylt4t?file=/vite.config.ts:478-540 by +@garrettjstevens -This is a demo of using the linear genome view with vite (see https://vitejs.dev/) +This is a demo of using the linear genome view with vite (see +https://vitejs.dev/) -Vite is a build system that is very fast and becoming more popular, using esbuild and rollup instead of webpack +Vite is a build system that is very fast and becoming more popular, using +esbuild and rollup instead of webpack -This particular demo includes several polyfills that are needed for JBrowse including the Buffer polyfill +This particular demo includes several polyfills that are needed for JBrowse +including the Buffer polyfill # Demo of `@jbrowse/react-linear-genome-view` with vite See this app running at https://jbrowse.org/demos/lgv-vite/. -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vite +Download this directory from the monorepo using +https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-vite ## Usage diff --git a/demos/jbrowse-react-linear-genome-view-vite/index.html b/embedded_demos/jbrowse-react-linear-genome-view-vite/index.html similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/index.html rename to embedded_demos/jbrowse-react-linear-genome-view-vite/index.html diff --git a/demos/jbrowse-react-linear-genome-view-vite/package.json b/embedded_demos/jbrowse-react-linear-genome-view-vite/package.json similarity index 73% rename from demos/jbrowse-react-linear-genome-view-vite/package.json rename to embedded_demos/jbrowse-react-linear-genome-view-vite/package.json index e93b689244..6f023f175c 100644 --- a/demos/jbrowse-react-linear-genome-view-vite/package.json +++ b/embedded_demos/jbrowse-react-linear-genome-view-vite/package.json @@ -1,6 +1,7 @@ { "name": "vite-react-lgv", "version": "0.0.0", + "license": "MIT", "scripts": { "dev": "vite", "build": "vite build", @@ -13,19 +14,19 @@ "@fontsource/roboto": "^4.5.3", "@jbrowse/core": "^2.0.0", "@jbrowse/react-linear-genome-view": "^2.0.0", - "@types/node": "^17.0.18", + "@types/node": "^18.11.12", "buffer": "^6.0.3", - "react": "^17.0.2", - "react-dom": "^17.0.2" + "react": "^18.2.0", + "react-dom": "^18.2.0" }, "devDependencies": { "@esbuild-plugins/node-globals-polyfill": "^0.1.1", "@esbuild-plugins/node-modules-polyfill": "^0.1.4", - "@types/react": "^17.0.33", - "@types/react-dom": "^17.0.10", - "@vitejs/plugin-react": "^1.0.0", + "@types/react": "^18.0.26", + "@types/react-dom": "^18.0.9", + "@vitejs/plugin-react": "^3.0.0", "stream-browserify": "^3.0.0", - "typescript": "^4.4.4", - "vite": "^3.0.0" + "typescript": "^4.9.4", + "vite": "^4.0.0" } } diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/App.tsx b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx similarity index 58% rename from demos/jbrowse-react-linear-genome-view-vite/src/App.tsx rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx index efeb8996f0..11cd54243e 100644 --- a/demos/jbrowse-react-linear-genome-view-vite/src/App.tsx +++ b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx @@ -7,68 +7,12 @@ import { import assembly from './assembly' import tracks from './tracks' +import defaultSession from './defaultSession' -const defaultSession = { - name: 'this session', - view: { - id: 'linearGenomeView', - type: 'LinearGenomeView', - tracks: [ - { - id: '7PWx6ki1_', - type: 'ReferenceSequenceTrack', - configuration: 'GRCh38-ReferenceSequenceTrack', - displays: [ - { - id: 'pa_7lx6FDh', - type: 'LinearReferenceSequenceDisplay', - height: 210, - configuration: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - }, - ], - }, - { - id: 'KHwe41KXk', - type: 'AlignmentsTrack', - configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', - displays: [ - { - id: '_-kwYVczT8', - type: 'LinearAlignmentsDisplay', - PileupDisplay: { - id: '1HTk32IDZJ', - type: 'LinearPileupDisplay', - height: 100, - configuration: { - type: 'LinearPileupDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_pileup_xyz', - }, - }, - SNPCoverageDisplay: { - id: 'ZBXRXmuDrc', - type: 'LinearSNPCoverageDisplay', - height: 45, - configuration: { - type: 'LinearSNPCoverageDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', - }, - }, - configuration: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', - height: 250, - }, - ], - }, - ], - }, -} +type ViewModel = ReturnType function View() { - const [viewState, setViewState] = - useState>() + const [viewState, setViewState] = useState() const [patches, setPatches] = useState('') const [stateSnapshot, setStateSnapshot] = useState('') @@ -76,11 +20,10 @@ function View() { const state = createViewState({ assembly, tracks, - location: '10:29,838,655..29,838,737', + defaultSession, onChange: patch => { setPatches(previous => previous + JSON.stringify(patch) + '\n') }, - defaultSession, }) setViewState(state) }, []) @@ -97,11 +40,11 @@ function View() {

The code for this app is available at{' '} - https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view-vite + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-vite .

diff --git a/demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts similarity index 75% rename from demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts index 5c26ea9164..af9f6755d9 100644 --- a/demos/jbrowse-react-linear-genome-view-nextjs/utils/assembly.ts +++ b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/assembly.ts @@ -16,16 +16,6 @@ const assembly = { uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', }, }, - displays: [ - { - type: 'LinearReferenceSequenceDisplay', - displayId: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - renderer: { - type: 'DivSequenceRenderer', - }, - }, - ], }, refNameAliases: { adapter: { diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/src/defaultSession.ts b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/defaultSession.ts new file mode 100644 index 0000000000..d9e0281ccc --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/defaultSession.ts @@ -0,0 +1,130 @@ +export default { + name: 'this session', + margin: 0, + view: { + id: 'linearGenomeView', + minimized: false, + type: 'LinearGenomeView', + offsetPx: 191980240, + bpPerPx: 0.1554251851851852, + displayedRegions: [ + { + refName: '10', + start: 0, + end: 133797422, + reversed: false, + assemblyName: 'GRCh38', + }, + ], + tracks: [ + { + id: '4aZAiE-A3', + type: 'ReferenceSequenceTrack', + configuration: 'GRCh38-ReferenceSequenceTrack', + minimized: false, + displays: [ + { + id: 'AD3gqvG0_6', + type: 'LinearReferenceSequenceDisplay', + height: 180, + configuration: + 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', + showForward: true, + showReverse: true, + showTranslation: true, + }, + ], + }, + { + id: 'T6uhrtY40O', + type: 'AlignmentsTrack', + configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + minimized: false, + displays: [ + { + id: 'FinKswChSr', + type: 'LinearAlignmentsDisplay', + PileupDisplay: { + id: 'YAAaF494z', + type: 'LinearPileupDisplay', + height: 134, + configuration: { + type: 'LinearPileupDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz', + }, + showSoftClipping: false, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + SNPCoverageDisplay: { + id: 'VTQ_VGbAVJ', + type: 'LinearSNPCoverageDisplay', + height: 45, + configuration: { + type: 'LinearSNPCoverageDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', + }, + selectedRendering: '', + resolution: 1, + constraints: {}, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + snpCovHeight: 45, + configuration: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', + height: 179, + lowerPanelType: 'LinearPileupDisplay', + }, + ], + }, + { + id: 'EUnTnpVI6', + type: 'QuantitativeTrack', + configuration: 'hg38.100way.phyloP100way', + minimized: false, + displays: [ + { + id: 'mrlawr9Wtg', + type: 'LinearWiggleDisplay', + height: 100, + configuration: 'hg38.100way.phyloP100way-LinearWiggleDisplay', + selectedRendering: '', + resolution: 1, + constraints: {}, + }, + ], + }, + { + id: 'Cbnwl72EX', + type: 'VariantTrack', + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + minimized: false, + displays: [ + { + id: 'dvXz01Wf6w', + type: 'LinearVariantDisplay', + height: 100, + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay', + }, + ], + }, + ], + hideHeader: false, + hideHeaderOverview: false, + hideNoTracksActive: false, + trackSelectorType: 'hierarchical', + trackLabels: 'overlapping', + showCenterLine: false, + showCytobandsSetting: true, + showGridlines: true, + }, +} diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/favicon.svg b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/favicon.svg similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/src/favicon.svg rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/favicon.svg diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/index.css b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/index.css similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/src/index.css rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/index.css diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/logo.svg b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/logo.svg similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/src/logo.svg rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/logo.svg diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/main.tsx b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/main.tsx similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/src/main.tsx rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/main.tsx diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts similarity index 60% rename from demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts index c3489ea36a..fb6422b271 100644 --- a/demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts +++ b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/tracks.ts @@ -1,8 +1,7 @@ const tracks = [ { - type: 'BasicTrack', - trackId: - 'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff', + type: 'FeatureTrack', + trackId: 'genes', name: 'NCBI RefSeq Genes', assemblyNames: ['GRCh38'], category: ['Genes'], @@ -17,6 +16,36 @@ const tracks = [ }, }, }, + textSearching: { + textSearchAdapter: { + type: 'TrixTextSearchAdapter', + textSearchAdapterId: 'gff3tabix_genes-index', + ixFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix', + }, + ixxFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx', + }, + metaFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json', + }, + assemblyNames: ['GRCh38'], + }, + }, + }, + { + type: 'FeatureTrack', + trackId: 'repeats_hg38', + name: 'Repeats', + assemblyNames: ['hg38'], + category: ['Annotation'], + adapter: { + type: 'BigBedAdapter', + bigBedLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb', + locationType: 'UriLocation', + }, + }, }, { type: 'AlignmentsTrack', @@ -65,6 +94,20 @@ const tracks = [ }, }, }, + { + type: 'QuantitativeTrack', + trackId: 'hg38.100way.phyloP100way', + name: 'hg38.100way.phyloP100way', + category: ['Conservation'], + assemblyNames: ['hg38'], + adapter: { + type: 'BigWigAdapter', + bigWigLocation: { + uri: 'https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw', + locationType: 'UriLocation', + }, + }, + }, ] export default tracks diff --git a/demos/jbrowse-react-linear-genome-view-vite/src/vite-env.d.ts b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/vite-env.d.ts similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/src/vite-env.d.ts rename to embedded_demos/jbrowse-react-linear-genome-view-vite/src/vite-env.d.ts diff --git a/demos/jbrowse-react-linear-genome-view-vite/tsconfig.json b/embedded_demos/jbrowse-react-linear-genome-view-vite/tsconfig.json similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/tsconfig.json rename to embedded_demos/jbrowse-react-linear-genome-view-vite/tsconfig.json diff --git a/demos/jbrowse-react-linear-genome-view-vite/vite.config.ts b/embedded_demos/jbrowse-react-linear-genome-view-vite/vite.config.ts similarity index 100% rename from demos/jbrowse-react-linear-genome-view-vite/vite.config.ts rename to embedded_demos/jbrowse-react-linear-genome-view-vite/vite.config.ts diff --git a/demos/jbrowse-react-linear-genome-view-vite/yarn.lock b/embedded_demos/jbrowse-react-linear-genome-view-vite/yarn.lock similarity index 70% rename from demos/jbrowse-react-linear-genome-view-vite/yarn.lock rename to embedded_demos/jbrowse-react-linear-genome-view-vite/yarn.lock index 3c2274e26d..2ea04c669c 100644 --- a/demos/jbrowse-react-linear-genome-view-vite/yarn.lock +++ b/embedded_demos/jbrowse-react-linear-genome-view-vite/yarn.lock @@ -17,54 +17,47 @@ dependencies: "@babel/highlight" "^7.18.6" -"@babel/compat-data@^7.19.3": - version "7.19.4" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.19.4.tgz#95c86de137bf0317f3a570e1b6e996b427299747" - integrity sha512-CHIGpJcUQ5lU9KrPHTjBMhVwQG6CQjxfg36fGXl3qk/Gik1WwWachaXFuo0uCWJT/mStOKtcbFJCaVLihC1CMw== +"@babel/compat-data@^7.20.0": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.20.5.tgz#86f172690b093373a933223b4745deeb6049e733" + integrity sha512-KZXo2t10+/jxmkhNXc7pZTqRvSOIvVv/+lJwHS+B2rErwOyjuVRh60yVpb7liQ1U5t7lLJ1bz+t8tSypUZdm0g== -"@babel/core@^7.17.10": - version "7.19.3" - resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.19.3.tgz#2519f62a51458f43b682d61583c3810e7dcee64c" - integrity sha512-WneDJxdsjEvyKtXKsaBGbDeiyOjR5vYq4HcShxnIbG0qixpoHjI3MqeZM9NDvsojNCEBItQE4juOo/bU6e72gQ== +"@babel/core@^7.20.5": + version 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"https://registry.yarnpkg.com/librpc-web-mod/-/librpc-web-mod-1.1.6.tgz#40cc6cedd7391f393654d36e5708b5ebfe8aff2f" @@ -1624,9 +1598,9 @@ long@^4.0.0: integrity sha512-XsP+KhQif4bjX1kbuSiySJFNAehNxgLb6hPRGJ9QsUr8ajHkuXGdrHmFUTUUXhDwVX2R5bY4JNZEwbUiMhV+MA== long@^5.1.0: - version "5.2.0" - resolved "https://registry.yarnpkg.com/long/-/long-5.2.0.tgz#2696dadf4b4da2ce3f6f6b89186085d94d52fd61" - integrity sha512-9RTUNjK60eJbx3uz+TEGF7fUr29ZDxR5QzXcyDpeSfeH28S9ycINflOgOlppit5U+4kNTe83KQnMEerw7GmE8w== + version "5.2.1" + resolved "https://registry.yarnpkg.com/long/-/long-5.2.1.tgz#e27595d0083d103d2fa2c20c7699f8e0c92b897f" + integrity sha512-GKSNGeNAtw8IryjjkhZxuKB3JzlcLTwjtiQCHKvqQet81I93kXslhDQruGI/QsddO83mcDToBVy7GqGS/zYf/A== loose-envify@^1.0.0, loose-envify@^1.1.0, loose-envify@^1.4.0: version "1.4.0" @@ -1642,6 +1616,13 @@ magic-string@^0.25.3: dependencies: sourcemap-codec "^1.4.8" +magic-string@^0.27.0: + version "0.27.0" + resolved 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-1736,9 +1717,9 @@ pako@^1.0.11, pako@^1.0.4: integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw== pako@^2.0.0: - version "2.0.4" - resolved "https://registry.yarnpkg.com/pako/-/pako-2.0.4.tgz#6cebc4bbb0b6c73b0d5b8d7e8476e2b2fbea576d" - integrity sha512-v8tweI900AUkZN6heMU/4Uy4cXRc2AYNRggVmTR+dEncawDJgCdLMximOVA2p4qO57WMynangsfGRb5WD6L1Bg== + version "2.1.0" + resolved "https://registry.yarnpkg.com/pako/-/pako-2.1.0.tgz#266cc37f98c7d883545d11335c00fbd4062c9a86" + integrity sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug== parent-module@^1.0.0: version "1.0.1" @@ -1772,20 +1753,15 @@ picocolors@^1.0.0: resolved "https://registry.yarnpkg.com/picocolors/-/picocolors-1.0.0.tgz#cb5bdc74ff3f51892236eaf79d68bc44564ab81c" integrity sha512-1fygroTLlHu66zi26VoTDv8yRgm0Fccecssto+MhsZ0D/DGW2sm8E8AjW7NU5VVTRt5GxbeZ5qBuJr+HyLYkjQ== -picomatch@^2.2.2: - version "2.3.1" - resolved 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nanoid "^3.3.4" picocolors "^1.0.0" @@ -1805,7 +1781,7 @@ quick-lru@^2.0.0: resolved "https://registry.yarnpkg.com/quick-lru/-/quick-lru-2.0.0.tgz#32b017b28d1784631c8ab0a1ed2978e094dbe181" integrity sha512-DqOtZziv7lDjEyuqyVQacRciAwMCEjTNrLYCHYEIIgjcE/tLEpBF82hiDIwCjRnEL9/hY2GJxA0T8ZvYvVVSSA== -quick-lru@^4.0.0: +quick-lru@^4.0.0, quick-lru@^4.0.1: version "4.0.1" resolved "https://registry.yarnpkg.com/quick-lru/-/quick-lru-4.0.1.tgz#5b8878f113a58217848c6482026c73e1ba57727f" integrity sha512-ARhCpm70fzdcvNQfPoy49IaanKkTlRWF2JMzqhcJbhSFRZv7nPTvZJdcY7301IPmvW+/p0RgIWnQDLJxifsQ7g== @@ -1827,14 +1803,13 @@ react-d3-axis-mod@^0.1.8: resolved "https://registry.yarnpkg.com/react-d3-axis-mod/-/react-d3-axis-mod-0.1.8.tgz#2876bf36b81e8b33b8cf03f299b48d6c0595bb3b" integrity sha512-6h9PcCwDyqrzIxmZNtV/BHxDhpTvU35PaL+mQrgZgfZrhR1/t/lPgUY8fnJIwGPInsXgsPJzAqplCWLVEhuPog== -react-dom@^17.0.2: - version "17.0.2" - resolved 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semver@^6.3.0: version "6.3.0" @@ -2077,10 +2050,10 @@ string_decoder@^1.1.1: dependencies: safe-buffer "~5.2.0" -stylis@4.0.13: - version "4.0.13" - resolved "https://registry.yarnpkg.com/stylis/-/stylis-4.0.13.tgz#f5db332e376d13cc84ecfe5dace9a2a51d954c91" - integrity sha512-xGPXiFVl4YED9Jh7Euv2V220mriG9u4B2TA6Ybjc1catrstKD2PpIdU3U0RKpkVBC2EhmL/F0sPCr9vrFTNRag== +stylis@4.1.3: + version "4.1.3" + resolved "https://registry.yarnpkg.com/stylis/-/stylis-4.1.3.tgz#fd2fbe79f5fed17c55269e16ed8da14c84d069f7" + integrity sha512-GP6WDNWf+o403jrEp9c5jibKavrtLW+/qYGhFxFrG8maXhwTBI7gLLhiBb0o7uFccWN+EOS9aMO6cGHWAO07OA== supports-color@^5.3.0: version "5.5.0" @@ -2119,10 +2092,10 @@ tslib@^1.9.0: resolved "https://registry.yarnpkg.com/tslib/-/tslib-1.14.1.tgz#cf2d38bdc34a134bcaf1091c41f6619e2f672d00" integrity sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg== -tss-react@^3.7.0: - version "3.7.1" - resolved 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"https://registry.yarnpkg.com/vite/-/vite-4.0.2.tgz#909beb07995048fe5a83b35b5e827d79627457c4" + integrity sha512-QJaY3R+tFlTagH0exVqbgkkw45B+/bXVBzF2ZD1KB5Z8RiAoiKo60vSUf6/r4c2Vh9jfGBKM4oBI9b4/1ZJYng== dependencies: - esbuild "^0.15.9" - postcss "^8.4.16" + esbuild "^0.16.3" + postcss "^8.4.20" resolve "^1.22.1" - rollup "~2.78.0" + rollup "^3.7.0" optionalDependencies: fsevents "~2.3.2" diff --git a/demos/jbrowse-react-linear-genome-view/.env b/embedded_demos/jbrowse-react-linear-genome-view/.env similarity index 100% rename from demos/jbrowse-react-linear-genome-view/.env rename to embedded_demos/jbrowse-react-linear-genome-view/.env diff --git a/demos/jbrowse-react-linear-genome-view/.gitignore b/embedded_demos/jbrowse-react-linear-genome-view/.gitignore similarity index 100% rename from demos/jbrowse-react-linear-genome-view/.gitignore rename to embedded_demos/jbrowse-react-linear-genome-view/.gitignore diff --git a/demos/jbrowse-react-linear-genome-view/README.md b/embedded_demos/jbrowse-react-linear-genome-view/README.md similarity index 85% rename from demos/jbrowse-react-linear-genome-view/README.md rename to embedded_demos/jbrowse-react-linear-genome-view/README.md index 09eed45f14..b3c0abee73 100644 --- a/demos/jbrowse-react-linear-genome-view/README.md +++ b/embedded_demos/jbrowse-react-linear-genome-view/README.md @@ -4,7 +4,7 @@ See this app running at https://jbrowse.org/demos/lgv/. This demo is originally by [@garrettjstevens](https://github.com/garrettjstevens/). -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view +Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view ## Usage diff --git a/demos/jbrowse-react-linear-genome-view/package.json b/embedded_demos/jbrowse-react-linear-genome-view/package.json similarity index 94% rename from demos/jbrowse-react-linear-genome-view/package.json rename to embedded_demos/jbrowse-react-linear-genome-view/package.json index b0bc31ff2d..caadf8d5d5 100644 --- a/demos/jbrowse-react-linear-genome-view/package.json +++ b/embedded_demos/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,7 @@ { "name": "jbrowse-react-linear-genome-view-demo-site", "version": "0.1.0", + "license": "MIT", "private": true, "dependencies": { "@fontsource/roboto": "^4.5.3", @@ -10,8 +11,8 @@ "@testing-library/user-event": "^12.1.10", "@types/jest": "^26.0.15", "@types/node": "^12.0.0", - "@types/react": "^17.0.0", - "@types/react-dom": "^17.0.0", + "@types/react": "^18.0.0", + "@types/react-dom": "^18.0.0", "react": "^17.0.2", "react-dom": "^17.0.2", "react-scripts": "4.0.3", diff --git a/demos/jbrowse-react-linear-genome-view/public/favicon.ico b/embedded_demos/jbrowse-react-linear-genome-view/public/favicon.ico similarity index 100% rename from demos/jbrowse-react-linear-genome-view/public/favicon.ico rename to embedded_demos/jbrowse-react-linear-genome-view/public/favicon.ico diff --git a/demos/jbrowse-react-linear-genome-view/public/index.html b/embedded_demos/jbrowse-react-linear-genome-view/public/index.html similarity index 100% rename from demos/jbrowse-react-linear-genome-view/public/index.html rename to embedded_demos/jbrowse-react-linear-genome-view/public/index.html diff --git a/demos/jbrowse-react-linear-genome-view/public/logo192.png b/embedded_demos/jbrowse-react-linear-genome-view/public/logo192.png similarity index 100% rename from demos/jbrowse-react-linear-genome-view/public/logo192.png rename to embedded_demos/jbrowse-react-linear-genome-view/public/logo192.png diff --git a/demos/jbrowse-react-linear-genome-view/public/logo512.png b/embedded_demos/jbrowse-react-linear-genome-view/public/logo512.png similarity index 100% rename from demos/jbrowse-react-linear-genome-view/public/logo512.png rename to embedded_demos/jbrowse-react-linear-genome-view/public/logo512.png diff --git a/demos/jbrowse-react-linear-genome-view/public/manifest.json b/embedded_demos/jbrowse-react-linear-genome-view/public/manifest.json similarity index 100% rename from demos/jbrowse-react-linear-genome-view/public/manifest.json rename to embedded_demos/jbrowse-react-linear-genome-view/public/manifest.json diff --git a/demos/jbrowse-react-linear-genome-view/public/robots.txt b/embedded_demos/jbrowse-react-linear-genome-view/public/robots.txt similarity index 100% rename from demos/jbrowse-react-linear-genome-view/public/robots.txt rename to embedded_demos/jbrowse-react-linear-genome-view/public/robots.txt diff --git a/demos/jbrowse-react-linear-genome-view/src/App.tsx b/embedded_demos/jbrowse-react-linear-genome-view/src/App.tsx similarity index 60% rename from demos/jbrowse-react-linear-genome-view/src/App.tsx rename to embedded_demos/jbrowse-react-linear-genome-view/src/App.tsx index 21e8bbce8a..7ed29782b5 100644 --- a/demos/jbrowse-react-linear-genome-view/src/App.tsx +++ b/embedded_demos/jbrowse-react-linear-genome-view/src/App.tsx @@ -7,64 +7,7 @@ import { import assembly from './assembly' import tracks from './tracks' - -const defaultSession = { - name: 'this session', - view: { - id: 'linearGenomeView', - type: 'LinearGenomeView', - tracks: [ - { - id: '7PWx6ki1_', - type: 'ReferenceSequenceTrack', - configuration: 'GRCh38-ReferenceSequenceTrack', - displays: [ - { - id: 'pa_7lx6FDh', - type: 'LinearReferenceSequenceDisplay', - height: 210, - configuration: - 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', - }, - ], - }, - { - id: 'KHwe41KXk', - type: 'AlignmentsTrack', - configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', - displays: [ - { - id: '_-kwYVczT8', - type: 'LinearAlignmentsDisplay', - PileupDisplay: { - id: '1HTk32IDZJ', - type: 'LinearPileupDisplay', - height: 100, - configuration: { - type: 'LinearPileupDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_pileup_xyz', - }, - }, - SNPCoverageDisplay: { - id: 'ZBXRXmuDrc', - type: 'LinearSNPCoverageDisplay', - height: 45, - configuration: { - type: 'LinearSNPCoverageDisplay', - displayId: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', - }, - }, - configuration: - 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', - height: 250, - }, - ], - }, - ], - }, -} +import defaultSession from './defaultSession' type ViewModel = ReturnType @@ -77,7 +20,6 @@ function View() { const state = createViewState({ assembly, tracks, - location: '10:29,838,655..29,838,737', onChange: (patch: any) => { setPatches((previous) => previous + JSON.stringify(patch) + '\n') }, @@ -100,11 +42,11 @@ function View() {

The code for this app is available at{' '} - https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view + https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view .

diff --git a/embedded_demos/jbrowse-react-linear-genome-view/src/assembly.ts b/embedded_demos/jbrowse-react-linear-genome-view/src/assembly.ts new file mode 100644 index 0000000000..af9f6755d9 --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view/src/assembly.ts @@ -0,0 +1,30 @@ +const assembly = { + name: 'GRCh38', + aliases: ['hg38'], + sequence: { + type: 'ReferenceSequenceTrack', + trackId: 'GRCh38-ReferenceSequenceTrack', + adapter: { + type: 'BgzipFastaAdapter', + fastaLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz', + }, + faiLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai', + }, + gziLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', + }, + }, + }, + refNameAliases: { + adapter: { + type: 'RefNameAliasAdapter', + location: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt', + }, + }, + }, +} + +export default assembly diff --git a/demos/jbrowse-react-linear-genome-view/src/declare.d.ts b/embedded_demos/jbrowse-react-linear-genome-view/src/declare.d.ts similarity index 100% rename from demos/jbrowse-react-linear-genome-view/src/declare.d.ts rename to embedded_demos/jbrowse-react-linear-genome-view/src/declare.d.ts diff --git a/embedded_demos/jbrowse-react-linear-genome-view/src/defaultSession.ts b/embedded_demos/jbrowse-react-linear-genome-view/src/defaultSession.ts new file mode 100644 index 0000000000..d9e0281ccc --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view/src/defaultSession.ts @@ -0,0 +1,130 @@ +export default { + name: 'this session', + margin: 0, + view: { + id: 'linearGenomeView', + minimized: false, + type: 'LinearGenomeView', + offsetPx: 191980240, + bpPerPx: 0.1554251851851852, + displayedRegions: [ + { + refName: '10', + start: 0, + end: 133797422, + reversed: false, + assemblyName: 'GRCh38', + }, + ], + tracks: [ + { + id: '4aZAiE-A3', + type: 'ReferenceSequenceTrack', + configuration: 'GRCh38-ReferenceSequenceTrack', + minimized: false, + displays: [ + { + id: 'AD3gqvG0_6', + type: 'LinearReferenceSequenceDisplay', + height: 180, + configuration: + 'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay', + showForward: true, + showReverse: true, + showTranslation: true, + }, + ], + }, + { + id: 'T6uhrtY40O', + type: 'AlignmentsTrack', + configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + minimized: false, + displays: [ + { + id: 'FinKswChSr', + type: 'LinearAlignmentsDisplay', + PileupDisplay: { + id: 'YAAaF494z', + type: 'LinearPileupDisplay', + height: 134, + configuration: { + type: 'LinearPileupDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz', + }, + showSoftClipping: false, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + SNPCoverageDisplay: { + id: 'VTQ_VGbAVJ', + type: 'LinearSNPCoverageDisplay', + height: 45, + configuration: { + type: 'LinearSNPCoverageDisplay', + displayId: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz', + }, + selectedRendering: '', + resolution: 1, + constraints: {}, + filterBy: { + flagInclude: 0, + flagExclude: 1540, + }, + }, + snpCovHeight: 45, + configuration: + 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay', + height: 179, + lowerPanelType: 'LinearPileupDisplay', + }, + ], + }, + { + id: 'EUnTnpVI6', + type: 'QuantitativeTrack', + configuration: 'hg38.100way.phyloP100way', + minimized: false, + displays: [ + { + id: 'mrlawr9Wtg', + type: 'LinearWiggleDisplay', + height: 100, + configuration: 'hg38.100way.phyloP100way-LinearWiggleDisplay', + selectedRendering: '', + resolution: 1, + constraints: {}, + }, + ], + }, + { + id: 'Cbnwl72EX', + type: 'VariantTrack', + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + minimized: false, + displays: [ + { + id: 'dvXz01Wf6w', + type: 'LinearVariantDisplay', + height: 100, + configuration: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay', + }, + ], + }, + ], + hideHeader: false, + hideHeaderOverview: false, + hideNoTracksActive: false, + trackSelectorType: 'hierarchical', + trackLabels: 'overlapping', + showCenterLine: false, + showCytobandsSetting: true, + showGridlines: true, + }, +} diff --git a/demos/jbrowse-react-linear-genome-view/src/index.css b/embedded_demos/jbrowse-react-linear-genome-view/src/index.css similarity index 100% rename from demos/jbrowse-react-linear-genome-view/src/index.css rename to embedded_demos/jbrowse-react-linear-genome-view/src/index.css diff --git a/demos/jbrowse-react-linear-genome-view/src/index.tsx b/embedded_demos/jbrowse-react-linear-genome-view/src/index.tsx similarity index 100% rename from demos/jbrowse-react-linear-genome-view/src/index.tsx rename to embedded_demos/jbrowse-react-linear-genome-view/src/index.tsx diff --git a/demos/jbrowse-react-linear-genome-view/src/react-app-env.d.ts b/embedded_demos/jbrowse-react-linear-genome-view/src/react-app-env.d.ts similarity index 100% rename from demos/jbrowse-react-linear-genome-view/src/react-app-env.d.ts rename to embedded_demos/jbrowse-react-linear-genome-view/src/react-app-env.d.ts diff --git a/embedded_demos/jbrowse-react-linear-genome-view/src/tracks.ts b/embedded_demos/jbrowse-react-linear-genome-view/src/tracks.ts new file mode 100644 index 0000000000..fb6422b271 --- /dev/null +++ b/embedded_demos/jbrowse-react-linear-genome-view/src/tracks.ts @@ -0,0 +1,113 @@ +const tracks = [ + { + type: 'FeatureTrack', + trackId: 'genes', + name: 'NCBI RefSeq Genes', + assemblyNames: ['GRCh38'], + category: ['Genes'], + adapter: { + type: 'Gff3TabixAdapter', + gffGzLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz', + }, + index: { + location: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.tbi', + }, + }, + }, + textSearching: { + textSearchAdapter: { + type: 'TrixTextSearchAdapter', + textSearchAdapterId: 'gff3tabix_genes-index', + ixFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix', + }, + ixxFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx', + }, + metaFilePath: { + uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json', + }, + assemblyNames: ['GRCh38'], + }, + }, + }, + { + type: 'FeatureTrack', + trackId: 'repeats_hg38', + name: 'Repeats', + assemblyNames: ['hg38'], + category: ['Annotation'], + adapter: { + type: 'BigBedAdapter', + bigBedLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb', + locationType: 'UriLocation', + }, + }, + }, + { + type: 'AlignmentsTrack', + trackId: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', + name: 'NA12878 Exome', + assemblyNames: ['GRCh38'], + category: ['1000 Genomes', 'Alignments'], + adapter: { + type: 'CramAdapter', + cramLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram', + }, + craiLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai', + }, + sequenceAdapter: { + type: 'BgzipFastaAdapter', + fastaLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz', + }, + faiLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai', + }, + gziLocation: { + uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', + }, + }, + }, + }, + { + type: 'VariantTrack', + trackId: + 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', + name: '1000 Genomes Variant Calls', + assemblyNames: ['GRCh38'], + category: ['1000 Genomes', 'Variants'], + adapter: { + type: 'VcfTabixAdapter', + vcfGzLocation: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz', + }, + index: { + location: { + uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz.tbi', + }, + }, + }, + }, + { + type: 'QuantitativeTrack', + trackId: 'hg38.100way.phyloP100way', + name: 'hg38.100way.phyloP100way', + category: ['Conservation'], + assemblyNames: ['hg38'], + adapter: { + type: 'BigWigAdapter', + bigWigLocation: { + uri: 'https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw', + locationType: 'UriLocation', + }, + }, + }, +] + +export default tracks diff --git a/demos/jbrowse-react-linear-genome-view-cra5/tsconfig.json b/embedded_demos/jbrowse-react-linear-genome-view/tsconfig.json similarity index 95% rename from demos/jbrowse-react-linear-genome-view-cra5/tsconfig.json rename to embedded_demos/jbrowse-react-linear-genome-view/tsconfig.json index 9d379a3c4a..42c57d41a1 100644 --- a/demos/jbrowse-react-linear-genome-view-cra5/tsconfig.json +++ b/embedded_demos/jbrowse-react-linear-genome-view/tsconfig.json @@ -1,6 +1,6 @@ { "compilerOptions": { - "target": "es5", + "target": "es2018", "lib": ["dom", "dom.iterable", "esnext"], "allowJs": true, "skipLibCheck": true, diff --git a/demos/jbrowse-react-linear-genome-view/yarn.lock b/embedded_demos/jbrowse-react-linear-genome-view/yarn.lock similarity index 91% rename from demos/jbrowse-react-linear-genome-view/yarn.lock rename to embedded_demos/jbrowse-react-linear-genome-view/yarn.lock index 9afd781230..c4156a74e4 100644 --- a/demos/jbrowse-react-linear-genome-view/yarn.lock +++ b/embedded_demos/jbrowse-react-linear-genome-view/yarn.lock @@ -36,10 +36,10 @@ dependencies: "@babel/highlight" "^7.18.6" -"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.19.3", "@babel/compat-data@^7.19.4": - version "7.19.4" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.19.4.tgz#95c86de137bf0317f3a570e1b6e996b427299747" - integrity sha512-CHIGpJcUQ5lU9KrPHTjBMhVwQG6CQjxfg36fGXl3qk/Gik1WwWachaXFuo0uCWJT/mStOKtcbFJCaVLihC1CMw== +"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.20.0", "@babel/compat-data@^7.20.1": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.20.5.tgz#86f172690b093373a933223b4745deeb6049e733" + integrity sha512-KZXo2t10+/jxmkhNXc7pZTqRvSOIvVv/+lJwHS+B2rErwOyjuVRh60yVpb7liQ1U5t7lLJ1bz+t8tSypUZdm0g== "@babel/core@7.12.3": version "7.12.3" @@ -64,32 +64,32 @@ source-map "^0.5.0" "@babel/core@^7.1.0", "@babel/core@^7.12.3", "@babel/core@^7.16.0", "@babel/core@^7.7.5", "@babel/core@^7.8.4": - version "7.19.3" - resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.19.3.tgz#2519f62a51458f43b682d61583c3810e7dcee64c" - integrity sha512-WneDJxdsjEvyKtXKsaBGbDeiyOjR5vYq4HcShxnIbG0qixpoHjI3MqeZM9NDvsojNCEBItQE4juOo/bU6e72gQ== + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/core/-/core-7.20.5.tgz#45e2114dc6cd4ab167f81daf7820e8fa1250d113" + integrity sha512-UdOWmk4pNWTm/4DlPUl/Pt4Gz4rcEMb7CY0Y3eJl5Yz1vI8ZJGmHWaVE55LoxRjdpx0z259GE9U5STA9atUinQ== dependencies: "@ampproject/remapping" "^2.1.0" "@babel/code-frame" "^7.18.6" - "@babel/generator" "^7.19.3" - "@babel/helper-compilation-targets" "^7.19.3" - "@babel/helper-module-transforms" "^7.19.0" - "@babel/helpers" "^7.19.0" - "@babel/parser" "^7.19.3" + "@babel/generator" "^7.20.5" + "@babel/helper-compilation-targets" "^7.20.0" + "@babel/helper-module-transforms" "^7.20.2" + "@babel/helpers" "^7.20.5" + "@babel/parser" "^7.20.5" "@babel/template" "^7.18.10" - "@babel/traverse" "^7.19.3" - "@babel/types" "^7.19.3" + "@babel/traverse" "^7.20.5" + "@babel/types" "^7.20.5" convert-source-map "^1.7.0" debug "^4.1.0" gensync "^1.0.0-beta.2" json5 "^2.2.1" semver "^6.3.0" -"@babel/generator@^7.12.1", "@babel/generator@^7.19.3", "@babel/generator@^7.19.4": - version "7.19.5" - resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.19.5.tgz#da3f4b301c8086717eee9cab14da91b1fa5dcca7" - integrity sha512-DxbNz9Lz4aMZ99qPpO1raTbcrI1ZeYh+9NR9qhfkQIbFtVEqotHojEBxHzmxhVONkGt6VyrqVQcgpefMy9pqcg== +"@babel/generator@^7.12.1", "@babel/generator@^7.20.5": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.20.5.tgz#cb25abee3178adf58d6814b68517c62bdbfdda95" + integrity sha512-jl7JY2Ykn9S0yj4DQP82sYvPU+T3g0HFcWTqDLqiuA9tGRNIj9VfbtXGAYTTkyNEnQk1jkMGOdYka8aG/lulCA== dependencies: - "@babel/types" "^7.19.4" + "@babel/types" "^7.20.5" "@jridgewell/gen-mapping" "^0.3.2" jsesc "^2.5.1" @@ -108,36 +108,36 @@ "@babel/helper-explode-assignable-expression" "^7.18.6" "@babel/types" "^7.18.9" -"@babel/helper-compilation-targets@^7.17.7", "@babel/helper-compilation-targets@^7.18.9", "@babel/helper-compilation-targets@^7.19.0", "@babel/helper-compilation-targets@^7.19.3": - version "7.19.3" - resolved "https://registry.yarnpkg.com/@babel/helper-compilation-targets/-/helper-compilation-targets-7.19.3.tgz#a10a04588125675d7c7ae299af86fa1b2ee038ca" - integrity sha512-65ESqLGyGmLvgR0mst5AdW1FkNlj9rQsCKduzEoEPhBCDFGXvz2jW6bXFG6i0/MrV2s7hhXjjb2yAzcPuQlLwg== +"@babel/helper-compilation-targets@^7.17.7", "@babel/helper-compilation-targets@^7.18.9", "@babel/helper-compilation-targets@^7.20.0": + version "7.20.0" + resolved "https://registry.yarnpkg.com/@babel/helper-compilation-targets/-/helper-compilation-targets-7.20.0.tgz#6bf5374d424e1b3922822f1d9bdaa43b1a139d0a" + integrity sha512-0jp//vDGp9e8hZzBc6N/KwA5ZK3Wsm/pfm4CrY7vzegkVxc65SgSn6wYOnwHe9Js9HRQ1YTCKLGPzDtaS3RoLQ== dependencies: - "@babel/compat-data" "^7.19.3" + "@babel/compat-data" "^7.20.0" "@babel/helper-validator-option" "^7.18.6" browserslist "^4.21.3" semver "^6.3.0" -"@babel/helper-create-class-features-plugin@^7.18.6", "@babel/helper-create-class-features-plugin@^7.19.0": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.19.0.tgz#bfd6904620df4e46470bae4850d66be1054c404b" - integrity sha512-NRz8DwF4jT3UfrmUoZjd0Uph9HQnP30t7Ash+weACcyNkiYTywpIjDBgReJMKgr+n86sn2nPVVmJ28Dm053Kqw== +"@babel/helper-create-class-features-plugin@^7.18.6", "@babel/helper-create-class-features-plugin@^7.20.2", "@babel/helper-create-class-features-plugin@^7.20.5": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.20.5.tgz#327154eedfb12e977baa4ecc72e5806720a85a06" + integrity sha512-3RCdA/EmEaikrhayahwToF0fpweU/8o2p8vhc1c/1kftHOdTKuC65kik/TLc+qfbS8JKw4qqJbne4ovICDhmww== dependencies: "@babel/helper-annotate-as-pure" "^7.18.6" "@babel/helper-environment-visitor" "^7.18.9" "@babel/helper-function-name" "^7.19.0" "@babel/helper-member-expression-to-functions" "^7.18.9" "@babel/helper-optimise-call-expression" "^7.18.6" - "@babel/helper-replace-supers" "^7.18.9" + "@babel/helper-replace-supers" "^7.19.1" "@babel/helper-split-export-declaration" "^7.18.6" -"@babel/helper-create-regexp-features-plugin@^7.18.6", "@babel/helper-create-regexp-features-plugin@^7.19.0": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.19.0.tgz#7976aca61c0984202baca73d84e2337a5424a41b" - integrity sha512-htnV+mHX32DF81amCDrwIDr8nrp1PTm+3wfBN9/v8QJOLEioOCOG7qNyq0nHeFiWbT3Eb7gsPwEmV64UCQ1jzw== +"@babel/helper-create-regexp-features-plugin@^7.18.6", "@babel/helper-create-regexp-features-plugin@^7.20.5": + version "7.20.5" + resolved "https://registry.yarnpkg.com/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.20.5.tgz#5ea79b59962a09ec2acf20a963a01ab4d076ccca" + integrity sha512-m68B1lkg3XDGX5yCvGO0kPx3v9WIYLnzjKfPcQiwntEQa5ZeRkPmo2X/ISJc8qxWGfwUr+kvZAeEzAwLec2r2w== dependencies: "@babel/helper-annotate-as-pure" "^7.18.6" - regexpu-core "^5.1.0" + regexpu-core "^5.2.1" "@babel/helper-define-polyfill-provider@^0.3.3": version "0.3.3" @@ -192,19 +192,19 @@ dependencies: "@babel/types" "^7.18.6" -"@babel/helper-module-transforms@^7.12.1", "@babel/helper-module-transforms@^7.18.6", "@babel/helper-module-transforms@^7.19.0": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-module-transforms/-/helper-module-transforms-7.19.0.tgz#309b230f04e22c58c6a2c0c0c7e50b216d350c30" - integrity sha512-3HBZ377Fe14RbLIA+ac3sY4PTgpxHVkFrESaWhoI5PuyXPBBX8+C34qblV9G89ZtycGJCmCI/Ut+VUDK4bltNQ== 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-213,10 +213,10 @@ dependencies: "@babel/types" "^7.18.6" -"@babel/helper-plugin-utils@^7.0.0", "@babel/helper-plugin-utils@^7.10.4", "@babel/helper-plugin-utils@^7.12.13", "@babel/helper-plugin-utils@^7.14.5", "@babel/helper-plugin-utils@^7.16.7", "@babel/helper-plugin-utils@^7.18.6", "@babel/helper-plugin-utils@^7.18.9", "@babel/helper-plugin-utils@^7.19.0", "@babel/helper-plugin-utils@^7.8.0", "@babel/helper-plugin-utils@^7.8.3": - version "7.19.0" - resolved "https://registry.yarnpkg.com/@babel/helper-plugin-utils/-/helper-plugin-utils-7.19.0.tgz#4796bb14961521f0f8715990bee2fb6e51ce21bf" - integrity sha512-40Ryx7I8mT+0gaNxm8JGTZFUITNqdLAgdg0hXzeVZxVD6nFsdhQvip6v8dqkRHzsz1VFpFAaOCHNn0vKBL7Czw== +"@babel/helper-plugin-utils@^7.0.0", "@babel/helper-plugin-utils@^7.10.4", "@babel/helper-plugin-utils@^7.12.13", "@babel/helper-plugin-utils@^7.14.5", "@babel/helper-plugin-utils@^7.16.7", "@babel/helper-plugin-utils@^7.18.6", "@babel/helper-plugin-utils@^7.18.9", 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- "@babel/types" "^7.19.4" + "@babel/types" "^7.20.2" babel-plugin-polyfill-corejs2 "^0.3.3" babel-plugin-polyfill-corejs3 "^0.6.0" babel-plugin-polyfill-regenerator "^0.4.1" @@ -1047,19 +1044,19 @@ "@babel/plugin-transform-typescript" "^7.18.6" "@babel/runtime-corejs3@^7.10.2": - version "7.19.4" - resolved "https://registry.yarnpkg.com/@babel/runtime-corejs3/-/runtime-corejs3-7.19.4.tgz#870dbfd9685b3dad5aeb2d00841bb8b6192e3095" - integrity sha512-HzjQ8+dzdx7dmZy4DQ8KV8aHi/74AjEbBGTFutBmg/pd3dY5/q1sfuOGPTFGEytlQhWoeVXqcK5BwMgIkRkNDQ== + version "7.20.6" + resolved "https://registry.yarnpkg.com/@babel/runtime-corejs3/-/runtime-corejs3-7.20.6.tgz#63dae945963539ab0ad578efbf3eff271e7067ae" + integrity sha512-tqeujPiuEfcH067mx+7otTQWROVMKHXEaOQcAeNV5dDdbPWvPcFA8/W9LXw2NfjNmOetqLl03dfnG2WALPlsRQ== dependencies: core-js-pure "^3.25.1" - regenerator-runtime "^0.13.4" + regenerator-runtime "^0.13.11" -"@babel/runtime@^7.0.0", "@babel/runtime@^7.10.2", "@babel/runtime@^7.11.0", 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material-ui-popup-state "^3.0.0" normalize-wheel "^1.0.1" + react-error-boundary "^3.0.0" react-popper "^2.0.0" -"@jbrowse/plugin-sequence@^2.1.7": - version "2.1.7" - resolved "https://registry.yarnpkg.com/@jbrowse/plugin-sequence/-/plugin-sequence-2.1.7.tgz#d5bb1b30a78ca8a990af448377acacda0424c5c4" - integrity sha512-F6GwLvC/tqKrKvhFxZIV2QehY0h2EzkVUDedn3YHojXu2OFB+/awdmWTqxzcdtPkROokQkPRIWTDsWvZKvhBJA== +"@jbrowse/plugin-sequence@^2.3.2": + version "2.3.2" + resolved "https://registry.yarnpkg.com/@jbrowse/plugin-sequence/-/plugin-sequence-2.3.2.tgz#a95514c6a69ffe202d93a062ed1ad3a0cce88c08" + integrity sha512-MqHpVGGZPg9Zq+SDsNzttAeo+Hc4WLOVXNqqudPGJfb1k6NRrqzB+RGNMTX+hSYoNr/s2cmirK3JNFGW4pJMXg== dependencies: "@gmod/indexedfasta" "^2.0.2" "@gmod/twobit" "^1.1.12" abortable-promise-cache "^1.5.0" -"@jbrowse/plugin-svg@^2.1.7": - version "2.1.7" - resolved "https://registry.yarnpkg.com/@jbrowse/plugin-svg/-/plugin-svg-2.1.7.tgz#ce4a8bcb343714f18842d167c0dd1d18ccdb3cc6" - integrity 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-"@jbrowse/plugin-variants@^2.1.7": - version "2.1.7" - resolved "https://registry.yarnpkg.com/@jbrowse/plugin-variants/-/plugin-variants-2.1.7.tgz#4db48178ce5a6e10b2ed7f5878b30dfcce883873" - integrity sha512-6l/L/u7usDqfew1VN6ln7tMVkfQH1O++jF3GrlfO0sxipyI0CWHtrYAx6czqF44nwkh1nr7YMU3gRvb+7O7B8A== +"@jbrowse/plugin-variants@^2.3.2": + version "2.3.2" + resolved "https://registry.yarnpkg.com/@jbrowse/plugin-variants/-/plugin-variants-2.3.2.tgz#71bb22f48a618c1f7604a05dfd62f2ebaba26997" + integrity sha512-gtIOzTDxacYKGj9RpvSN/M6tD7BIvV/oF1iEKARg2s5mmAc3pYKTv2KIHiY4djKX73pyf0GSA4WPQxYZtwk7rg== dependencies: "@flatten-js/interval-tree" "^1.0.15" "@gmod/bgzf-filehandle" "^1.4.3" "@gmod/tabix" "^1.5.2" - "@gmod/vcf" "^5.0.5" + "@gmod/vcf" "^5.0.9" "@mui/icons-material" "^5.0.2" "@mui/x-data-grid" "^5.0.1" generic-filehandle "^3.0.0" -"@jbrowse/plugin-wiggle@^2.1.7": - version "2.1.7" - resolved 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"@jbrowse/plugin-authentication" "^2.3.2" + "@jbrowse/plugin-bed" "^2.3.2" + "@jbrowse/plugin-circular-view" "^2.3.2" + "@jbrowse/plugin-config" "^2.3.2" + "@jbrowse/plugin-data-management" "^2.3.2" + "@jbrowse/plugin-gccontent" "^2.3.2" + "@jbrowse/plugin-gff3" "^2.3.2" + "@jbrowse/plugin-legacy-jbrowse" "^2.3.2" + "@jbrowse/plugin-linear-genome-view" "^2.3.2" + "@jbrowse/plugin-sequence" "^2.3.2" + "@jbrowse/plugin-svg" "^2.3.2" + "@jbrowse/plugin-trix" "^2.3.2" + "@jbrowse/plugin-variants" "^2.3.2" + "@jbrowse/plugin-wiggle" "^2.3.2" "@mui/icons-material" "^5.0.0" - "@mui/material" "^5.0.0" + "@mui/material" "^5.10.17" librpc-web-mod "^1.1.5" mobx "^6.6.0" mobx-react "^7.5.0" @@ -1646,7 +1662,7 @@ react-use-measure "^2.1.1" rxjs "^6.0.0" serialize-error "^8.0.0" - tss-react "^3.7.0" + tss-react "^4.4.1" "@jest/console@^26.6.2": version "26.6.2" @@ -1704,10 +1720,10 @@ "@types/node" "*" jest-mock "^26.6.2" -"@jest/expect-utils@^29.2.1": - version "29.2.1" - resolved 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+available-typed-arrays@^1.0.5: + version "1.0.5" + resolved "https://registry.yarnpkg.com/available-typed-arrays/-/available-typed-arrays-1.0.5.tgz#92f95616501069d07d10edb2fc37d3e1c65123b7" + integrity sha512-DMD0KiN46eipeziST1LPP/STfDU0sufISXmjSgvVsoU2tqxctQeASejWcfNtxYKqETM1UxQ8sp2OrSBWpHY6sw== + axe-core@^4.4.3: - version "4.4.3" - resolved "https://registry.yarnpkg.com/axe-core/-/axe-core-4.4.3.tgz#11c74d23d5013c0fa5d183796729bc3482bd2f6f" - integrity sha512-32+ub6kkdhhWick/UjvEwRchgoetXqTK14INLqbGm5U2TzBkBNF3nQtLYm8ovxSkQWArjEQvftCKryjZaATu3w== + version "4.6.1" + resolved "https://registry.yarnpkg.com/axe-core/-/axe-core-4.6.1.tgz#79cccdee3e3ab61a8f42c458d4123a6768e6fbce" + integrity sha512-lCZN5XRuOnpG4bpMq8v0khrWtUOn+i8lZSb6wHZH56ZfbIEv6XwJV84AAueh9/zi7qPVJ/E4yz6fmsiyOmXR4w== axobject-query@^2.2.0: version "2.2.0" @@ -3270,13 +3295,6 @@ babel-loader@8.1.0: pify "^4.0.1" schema-utils "^2.6.5" -babel-plugin-dynamic-import-node@^2.3.3: - version "2.3.3" - resolved 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which-typed-array "^1.1.8" + deep-is@^0.1.3, deep-is@~0.1.3: version "0.1.4" resolved "https://registry.yarnpkg.com/deep-is/-/deep-is-0.1.4.tgz#a6f2dce612fadd2ef1f519b73551f17e85199831" @@ -4867,10 +4906,10 @@ diff-sequences@^26.6.2: resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-26.6.2.tgz#48ba99157de1923412eed41db6b6d4aa9ca7c0b1" integrity sha512-Mv/TDa3nZ9sbc5soK+OoA74BsS3mL37yixCvUAQkiuA4Wz6YtwP/K47n2rv2ovzHZvoiQeA5FTQOschKkEwB0Q== -diff-sequences@^29.2.0: - version "29.2.0" - resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-29.2.0.tgz#4c55b5b40706c7b5d2c5c75999a50c56d214e8f6" - integrity sha512-413SY5JpYeSBZxmenGEmCVQ8mCgtFJF0w9PROdaS6z987XC2Pd2GOKqOITLtMftmyFZqgtCOb/QA7/Z3ZXfzIw== +diff-sequences@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-29.3.1.tgz#104b5b95fe725932421a9c6e5b4bef84c3f2249e" + integrity 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sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg== -emojis-list@^2.0.0: - version "2.1.0" - resolved "https://registry.yarnpkg.com/emojis-list/-/emojis-list-2.1.0.tgz#4daa4d9db00f9819880c79fa457ae5b09a1fd389" - integrity sha512-knHEZMgs8BB+MInokmNTg/OyPlAddghe1YBgNwJBc5zsJi/uyIcXoSDsL/W9ymOsBoBGdPIHXYJ9+qKFwRwDng== - emojis-list@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/emojis-list/-/emojis-list-3.0.0.tgz#5570662046ad29e2e916e71aae260abdff4f6a78" @@ -5162,10 +5196,10 @@ error-stack-parser@^2.0.6: dependencies: stackframe "^1.3.4" -es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19.2, es-abstract@^1.19.5, es-abstract@^1.20.1: - version "1.20.4" - resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.4.tgz#1d103f9f8d78d4cf0713edcd6d0ed1a46eed5861" - integrity sha512-0UtvRN79eMe2L+UNEF1BwRe364sj/DXhQ/k5FmivgoSdpM90b8Jc0mDzKMGo7QS0BVbOP/bTwBKNnDc9rNzaPA== +es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.20.4: + version "1.20.5" + resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.5.tgz#e6dc99177be37cacda5988e692c3fa8b218e95d2" + integrity sha512-7h8MM2EQhsCA7pU/Nv78qOXFpD8Rhqd12gYiSJVkrH9+e8VuA8JlPJK/hQjjlLv6pJvx/z1iRFKzYb0XT/RuAQ== dependencies: call-bind "^1.0.2" es-to-primitive "^1.2.1" @@ -5173,6 +5207,7 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 function.prototype.name "^1.1.5" get-intrinsic "^1.1.3" get-symbol-description "^1.0.0" + gopd "^1.0.1" has "^1.0.3" has-property-descriptors "^1.0.0" has-symbols "^1.0.3" @@ -5188,8 +5223,8 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 object.assign "^4.1.4" regexp.prototype.flags "^1.4.3" safe-regex-test "^1.0.0" - string.prototype.trimend "^1.0.5" - string.prototype.trimstart "^1.0.5" + string.prototype.trimend "^1.0.6" + string.prototype.trimstart "^1.0.6" unbox-primitive "^1.0.2" es-array-method-boxes-properly@^1.0.0: @@ -5197,6 +5232,20 @@ es-array-method-boxes-properly@^1.0.0: resolved "https://registry.yarnpkg.com/es-array-method-boxes-properly/-/es-array-method-boxes-properly-1.0.0.tgz#873f3e84418de4ee19c5be752990b2e44718d09e" integrity sha512-wd6JXUmyHmt8T5a2xreUwKcGPq6f1f+WwIJkijUqiGcJz1qqnZgP6XIK+QyIWU5lT7imeNxUll48bziG+TSYcA== +es-get-iterator@^1.1.2: + version "1.1.2" + resolved "https://registry.yarnpkg.com/es-get-iterator/-/es-get-iterator-1.1.2.tgz#9234c54aba713486d7ebde0220864af5e2b283f7" + integrity sha512-+DTO8GYwbMCwbywjimwZMHp8AuYXOS2JZFWoi2AlPOS3ebnII9w/NLpNZtA7A0YLaVDw+O7KFCeoIV7OPvM7hQ== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.0" + has-symbols "^1.0.1" + is-arguments "^1.1.0" + is-map "^2.0.2" + is-set "^2.0.2" + is-string "^1.0.5" + isarray "^2.0.5" + es-shim-unscopables@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/es-shim-unscopables/-/es-shim-unscopables-1.0.0.tgz#702e632193201e3edf8713635d083d378e510241" @@ -5231,7 +5280,7 @@ es6-iterator@2.0.3, es6-iterator@^2.0.3: es5-ext "^0.10.35" es6-symbol "^3.1.1" -es6-promisify@^6.0.1, es6-promisify@^6.1.1: +es6-promisify@^6.1.1: version "6.1.1" resolved "https://registry.yarnpkg.com/es6-promisify/-/es6-promisify-6.1.1.tgz#46837651b7b06bf6fff893d03f29393668d01621" integrity sha512-HBL8I3mIki5C1Cc9QjKUenHtnG0A5/xA8Q/AllRcfiwl2CZFXGK7ddBiCoRwAix4i2KxcQfjtIVcrVbB3vbmwg== @@ -5379,24 +5428,25 @@ eslint-plugin-react-hooks@^4.2.0: integrity sha512-oFc7Itz9Qxh2x4gNHStv3BqJq54ExXmfC+a1NjAta66IAN87Wu0R/QArgIS9qKzX3dXKPI9H5crl9QchNMY9+g== eslint-plugin-react@^7.21.5: - version "7.31.10" - resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.10.tgz#6782c2c7fe91c09e715d536067644bbb9491419a" - integrity sha512-e4N/nc6AAlg4UKW/mXeYWd3R++qUano5/o+t+wnWxIf+bLsOaH3a4q74kX3nDjYym3VBN4HyO9nEn1GcAqgQOA== + version "7.31.11" + resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.11.tgz#011521d2b16dcf95795df688a4770b4eaab364c8" + integrity sha512-TTvq5JsT5v56wPa9OYHzsrOlHzKZKjV+aLgS+55NJP/cuzdiQPC7PfYoUjMoxlffKtvijpk7vA/jmuqRb9nohw== dependencies: - array-includes "^3.1.5" - array.prototype.flatmap "^1.3.0" + array-includes "^3.1.6" + array.prototype.flatmap "^1.3.1" + array.prototype.tosorted "^1.1.1" doctrine "^2.1.0" estraverse "^5.3.0" jsx-ast-utils "^2.4.1 || ^3.0.0" minimatch "^3.1.2" - object.entries "^1.1.5" - object.fromentries "^2.0.5" - object.hasown "^1.1.1" - object.values "^1.1.5" + object.entries "^1.1.6" + object.fromentries "^2.0.6" + object.hasown "^1.1.2" + object.values "^1.1.6" prop-types "^15.8.1" resolve "^2.0.0-next.3" semver "^6.3.0" - string.prototype.matchall "^4.0.7" + string.prototype.matchall "^4.0.8" eslint-plugin-testing-library@^3.9.2: version "3.10.2" @@ -5648,15 +5698,15 @@ expect@^26.6.0, expect@^26.6.2: jest-regex-util 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es6-promisify "^6.1.1" @@ -6176,9 +6233,9 @@ globals@^11.1.0: integrity sha512-WOBp/EEGUiIsJSp7wcv/y6MO+lV9UoncWqxuFfm8eBwzWNgyfBd6Gz+IeKQ9jCmyhoH99g15M3T+QaVHFjizVA== globals@^13.6.0, globals@^13.9.0: - version "13.17.0" - resolved "https://registry.yarnpkg.com/globals/-/globals-13.17.0.tgz#902eb1e680a41da93945adbdcb5a9f361ba69bd4" - integrity sha512-1C+6nQRb1GwGMKm2dH/E7enFAMxGTmGI7/dEdhy/DNelv85w9B72t3uc5frtMNXIbzrarJJ/lTCjcaZwbLJmyw== + version "13.19.0" + resolved "https://registry.yarnpkg.com/globals/-/globals-13.19.0.tgz#7a42de8e6ad4f7242fbcca27ea5b23aca367b5c8" + integrity sha512-dkQ957uSRWHw7CFXLUtUHQI3g3aWApYhfNR2O6jn/907riyTYKVBmxYVROkBcY614FSSeSJh7Xm7SrUWCxvJMQ== dependencies: type-fest "^0.20.2" @@ -6217,6 +6274,13 @@ globby@^6.1.0: pify "^2.0.0" pinkie-promise "^2.0.0" +gopd@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/gopd/-/gopd-1.0.1.tgz#29ff76de69dac7489b7c0918a5788e56477c332c" + integrity 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+ version "1.0.4" + resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.4.tgz#8551e7baf74a7a6ba5f749cfb16aa60722f0d6f3" + integrity sha512-tA8URYccNzMo94s5MQZgH8NB/XTa6HsOo0MLfXTKKEnHVVdegzaQoFZ7Jp44bdvLvY2waT5dc+j5ICEswhi7UQ== dependencies: - get-intrinsic "^1.1.0" + get-intrinsic "^1.1.3" has "^1.0.3" side-channel "^1.0.4" @@ -6734,7 +6798,7 @@ is-accessor-descriptor@^1.0.0: dependencies: kind-of "^6.0.0" -is-arguments@^1.0.4: +is-arguments@^1.0.4, is-arguments@^1.1.0, is-arguments@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== @@ -6786,7 +6850,7 @@ is-buffer@^1.1.5, is-buffer@~1.1.6: resolved "https://registry.yarnpkg.com/is-buffer/-/is-buffer-1.1.6.tgz#efaa2ea9daa0d7ab2ea13a97b2b8ad51fefbe8be" integrity 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"2.0.2" + resolved "https://registry.yarnpkg.com/is-map/-/is-map-2.0.2.tgz#00922db8c9bf73e81b7a335827bc2a43f2b91127" + integrity sha512-cOZFQQozTha1f4MxLFzlgKYPTyj26picdZTx82hbc/Xf4K/tZOOXSCkMvU4pKioRXGDLJRn0GM7Upe7kR721yg== + is-module@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-module/-/is-module-1.0.0.tgz#3258fb69f78c14d5b815d664336b4cffb6441591" @@ -7020,6 +7089,11 @@ is-root@2.1.0: resolved "https://registry.yarnpkg.com/is-root/-/is-root-2.1.0.tgz#809e18129cf1129644302a4f8544035d51984a9c" integrity sha512-AGOriNp96vNBd3HtU+RzFEc75FfR5ymiYv8E553I71SCeXBiMsVDUtdio1OEFvrPyLIQ9tVR5RxXIFe5PUFjMg== +is-set@^2.0.1, is-set@^2.0.2: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-set/-/is-set-2.0.2.tgz#90755fa4c2562dc1c5d4024760d6119b94ca18ec" + integrity sha512-+2cnTEZeY5z/iXGbLhPrOAaK/Mau5k5eXq9j14CpRTftq0pAJu2MwVRSZhyZWBzx3o6X795Lz6Bpb6R0GKf37g== + is-shared-array-buffer@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-shared-array-buffer/-/is-shared-array-buffer-1.0.2.tgz#8f259c573b60b6a32d4058a1a07430c0a7344c79" @@ -7051,11 +7125,27 @@ is-symbol@^1.0.2, is-symbol@^1.0.3: dependencies: has-symbols "^1.0.2" +is-typed-array@^1.1.10: + version "1.1.10" + resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.10.tgz#36a5b5cb4189b575d1a3e4b08536bfb485801e3f" + integrity sha512-PJqgEHiWZvMpaFZ3uTc8kHPM4+4ADTlDniuQL7cU/UDA0Ql7F70yGfHph3cLNe+c9toaigv+DFzTJKhc2CtO6A== + dependencies: + available-typed-arrays "^1.0.5" + call-bind "^1.0.2" + for-each "^0.3.3" + gopd "^1.0.1" + has-tostringtag "^1.0.0" + is-typedarray@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-typedarray/-/is-typedarray-1.0.0.tgz#e479c80858df0c1b11ddda6940f96011fcda4a9a" integrity sha512-cyA56iCMHAh5CdzjJIa4aohJyeO1YbwLi3Jc35MmRU6poroFjIGZzUzupGiRPOjgHg9TLu43xbpwXk523fMxKA== +is-weakmap@^2.0.1: + version "2.0.1" + resolved "https://registry.yarnpkg.com/is-weakmap/-/is-weakmap-2.0.1.tgz#5008b59bdc43b698201d18f62b37b2ca243e8cf2" + integrity sha512-NSBR4kH5oVj1Uwvv970ruUkCV7O1mzgVFO4/rev2cLRda9Tm9HrL70ZPut4rOHgY0FNrUu9BCbXA2sdQ+x0chA== + is-weakref@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-weakref/-/is-weakref-1.0.2.tgz#9529f383a9338205e89765e0392efc2f100f06f2" @@ -7063,6 +7153,14 @@ is-weakref@^1.0.2: dependencies: call-bind "^1.0.2" +is-weakset@^2.0.1: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-weakset/-/is-weakset-2.0.2.tgz#4569d67a747a1ce5a994dfd4ef6dcea76e7c0a1d" + integrity sha512-t2yVvttHkQktwnNNmBQ98AhENLdPUTDTE21uPqAQ0ARwQfGeQKRVS0NNurH7bTf7RrvcVn1OOge45CnBeHCSmg== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.1" + is-windows@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-windows/-/is-windows-1.0.2.tgz#d1850eb9791ecd18e6182ce12a30f396634bb19d" @@ -7085,6 +7183,11 @@ isarray@1.0.0, isarray@^1.0.0, isarray@~1.0.0: resolved 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"https://registry.yarnpkg.com/typescript/-/typescript-4.8.4.tgz#c464abca159669597be5f96b8943500b238e60e6" - integrity sha512-QCh+85mCy+h0IGff8r5XWzOVSbBO+KfeYrMQh7NJ58QujwcE22u+NUSmUxqF+un70P9GXKxa2HCNiTTMJknyjQ== + version "4.9.4" + resolved "https://registry.yarnpkg.com/typescript/-/typescript-4.9.4.tgz#a2a3d2756c079abda241d75f149df9d561091e78" + integrity sha512-Uz+dTXYzxXXbsFpM86Wh3dKCxrQqUcVMxwU54orwlJjOpO3ao8L7j5lH+dWfTwgCwIuM9GQ2kvVotzYJMXTBZg== unbox-primitive@^1.0.2: version "1.0.2" @@ -11929,10 +12043,10 @@ unicode-match-property-ecmascript@^2.0.0: unicode-canonical-property-names-ecmascript "^2.0.0" unicode-property-aliases-ecmascript "^2.0.0" -unicode-match-property-value-ecmascript@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.0.0.tgz#1a01aa57247c14c568b89775a54938788189a714" - integrity sha512-7Yhkc0Ye+t4PNYzOGKedDhXbYIBe1XEQYQxOPyhcXNMJ0WCABqqj6ckydd6pWRZTHV4GuCPKdBAUiMc60tsKVw== +unicode-match-property-value-ecmascript@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.1.0.tgz#cb5fffdcd16a05124f5a4b0bf7c3770208acbbe0" + integrity sha512-qxkjQt6qjg/mYscYMC0XKRn3Rh0wFPlfxB0xkt9CfyTvpX1Ra0+rAmdX2QyAobptSEvuy4RtpPRui6XkV+8wjA== unicode-property-aliases-ecmascript@^2.0.0: version "2.1.0" @@ -12399,11 +12513,33 @@ which-boxed-primitive@^1.0.2: is-string "^1.0.5" is-symbol "^1.0.3" +which-collection@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/which-collection/-/which-collection-1.0.1.tgz#70eab71ebbbd2aefaf32f917082fc62cdcb70906" + integrity sha512-W8xeTUwaln8i3K/cY1nGXzdnVZlidBcagyNFtBdD5kxnb4TvGKR7FfSIS3mYpwWS1QUCutfKz8IY8RjftB0+1A== + dependencies: + is-map "^2.0.1" + is-set "^2.0.1" + is-weakmap "^2.0.1" + is-weakset "^2.0.1" + which-module@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/which-module/-/which-module-2.0.0.tgz#d9ef07dce77b9902b8a3a8fa4b31c3e3f7e6e87a" integrity sha512-B+enWhmw6cjfVC7kS8Pj9pCrKSc5txArRyaYGe088shv/FGWH+0Rjx/xPgtsWfsUtS27FkP697E4DDhgrgoc0Q== +which-typed-array@^1.1.8: + version "1.1.9" + resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.9.tgz#307cf898025848cf995e795e8423c7f337efbde6" + integrity sha512-w9c4xkx6mPidwp7180ckYWfMmvxpjlZuIudNtDf4N/tTAUB8VJbX25qZoAsrtGuYNnGw3pa0AXgbGKRB8/EceA== + dependencies: + available-typed-arrays "^1.0.5" + call-bind "^1.0.2" + for-each "^0.3.3" + gopd "^1.0.1" + has-tostringtag "^1.0.0" + is-typed-array "^1.1.10" + which@^1.2.9, which@^1.3.1: version "1.3.1" resolved "https://registry.yarnpkg.com/which/-/which-1.3.1.tgz#a45043d54f5805316da8d62f9f50918d3da70b0a" diff --git a/demos/update_demos.sh b/embedded_demos/update_demos.sh similarity index 100% rename from demos/update_demos.sh rename to embedded_demos/update_demos.sh diff --git a/lerna.json b/lerna.json index d717df801a..32e988a37c 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.1.7", + "version": "2.3.2", "npmClient": "yarn", "useWorkspaces": true } diff --git a/package.json b/package.json index f0f452f9c3..f56951df6b 100644 --- a/package.json +++ b/package.json @@ -17,9 +17,7 @@ "format": "prettier --write .", "check-format": "prettier --check .", "typecheck": "tsc --noEmit", - "pretest-jbimg": "cd products/jbrowse-react-linear-genome-view;yarn build;cd ../../", - "test-jbimg": "jest --env node --testMatch '**/*testmod.js'", - "test-ci": "cross-env NODE_OPTIONS='--max-old-space-size=7000' jest --ci --coverage && npm run test-jbimg", + "test-ci": "cross-env NODE_OPTIONS='--max-old-space-size=7000' jest --ci --coverage", "built-test-ci": "jest --ci integration.test.js", "test": "jest", "prepare": "husky install", @@ -37,41 +35,43 @@ "@babel/preset-env": "^7.16.4", "@babel/preset-react": "^7.0.0", "@babel/preset-typescript": "^7.3.3", - "@craco/craco": "^6.4.3", + "@craco/craco": "^7.0.0", + "@electron/notarize": "^1.2.3", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@mui/material": "^5.0.0", + "@mui/material": "^5.10.17", + "@mui/x-data-grid": "^5.0.0", "@oclif/dev-cli": "^1.26.9", "@oclif/test": "^1.2.7", - "@storybook/addon-actions": "^6.5.0", - "@storybook/addon-docs": "^6.5.0", - "@storybook/addon-links": "^6.5.0", - "@storybook/addons": "^6.5.0", - "@storybook/builder-webpack5": "^6.5.0", - "@storybook/manager-webpack5": "^6.5.0", - "@storybook/react": "^6.5.0", + "@storybook/addon-actions": "^6.5.13", + "@storybook/addon-docs": "^6.5.13", + "@storybook/addon-links": "^6.5.13", + "@storybook/addons": "^6.5.13", + "@storybook/builder-webpack5": "^6.5.13", + "@storybook/manager-webpack5": "^6.5.13", + "@storybook/react": "^6.5.13", "@testing-library/jest-dom": "^5.16.1", "@testing-library/react": "^12.0.0", "@types/base64-js": "^1.2.5", - "@types/buffer-crc32": "^0.2.0", + "@types/buffer-crc32": "^0.2.2", "@types/cli-progress": "^3.9.2", - "@types/clone": "^0.1.30", + "@types/clone": "^2.1.1", "@types/color": "^3.0.1", - "@types/cors": "^2.8.8", + "@types/cors": "^2.8.13", "@types/cross-spawn": "^6.0.2", "@types/crypto-js": "^4.0.1", "@types/d3-scale": "^3.0.0", "@types/deep-equal": "^1.0.1", "@types/detect-node": "^2.0.0", "@types/dompurify": "^2.0.2", - "@types/escape-html": "^0.0.20", + "@types/escape-html": "^1.0.2", "@types/express": "^4.17.8", "@types/file-saver": "^2.0.1", "@types/get-value": "^3.0.1", "@types/is-object": "^1.0.0", - "@types/jest": "^25.2.1", - "@types/jest-image-snapshot": "^2.12.0", + "@types/jest": "^29.2.4", + "@types/jest-image-snapshot": "^6.1.0", "@types/jexl": "^2.3.0", "@types/json-parse-better-errors": "^1.0.0", "@types/json-stable-stringify": "^1.0.32", @@ -80,13 +80,12 @@ "@types/node": "^14.14.0", "@types/node-fetch": "^2.5.7", "@types/normalize-wheel": "^1.0.0", - "@types/object.fromentries": "^2.0.1", "@types/offscreencanvas": "^2019.6.4", "@types/pako": "^1.0.1", "@types/pluralize": "^0.0.29", "@types/range-parser": "^1.2.3", "@types/rbush": "^3.0.0", - "@types/react": "^18.0.0", + "@types/react": "^18.0.26", "@types/react-color": "^3.0.4", "@types/react-dom": "^18.0.0", "@types/react-virtualized-auto-sizer": "^1.0.0", @@ -97,18 +96,18 @@ "@types/string-template": "^1.0.2", "@types/tmp": "^0.2.1", "@types/unzipper": "^0.10.3", - "@typescript-eslint/parser": "^5.8.0", - "babel-loader": "^8.2.5", + "@typescript-eslint/parser": "^5.45.1", + "babel-loader": "^9.1.0", "canvas": "^2.9.1", "chai": "^4.3.4", - "concurrently": "^7.2.1", "cross-env": "^7.0.2", "cross-spawn": "^7.0.1", + "crypto-js": "^3.0.0", "dependency-graph": "^0.11.0", - "electron": "20.1.4", + "electron": "22.0.0", "electron-builder": "^23.0.3", "electron-mock-ipc": "^0.3.8", - "electron-notarize": "^1.0.0", + "eslint": "^8.0.0", "eslint-config-prettier": "^8.5.0", "eslint-config-react-app": "^7.0.0", "eslint-plugin-cypress": "^2.12.1", @@ -118,23 +117,24 @@ "eslint-plugin-tsdoc": "^0.2.4", "file-loader": "^6.2.0", "find-yarn-workspace-root": "^2.0.0", - "get-yarn-workspaces": "^1.0.2", "husky": "^8.0.0", - "jest": "^28.1.1", - "jest-environment-jsdom": "^28.0.0", + "jest": "^29.3.1", + "jest-environment-jsdom": "^29.3.1", "jest-fetch-mock": "^3.0.3", - "jest-image-snapshot": "^5.1.0", + "jest-image-snapshot": "^6.1.0", "jest-localstorage-mock": "^2.4.3", "lerna": "^5.1.2", "lerna-changelog": "^2.2.0", "mobx": "^6.0.0", "mobx-react": "^7.0.0", - "mobx-state-tree": "^5.0.0", + "mobx-state-tree": "^5.1.7", "nock": "^13.2.1", - "node-polyfill-webpack-plugin": "^1.1.4", + "node-polyfill-webpack-plugin": "^2.0.1", "npm-run-all": "^4.1.5", "prettier": "^2.5.1", "prop-types": "^15.0.0", + "react": "^17.0.0", + "react-dom": "^17.0.0", "react-scripts": "^5.0.1", "requestidlecallback-polyfill": "^1.0.2", "rimraf": "^3.0.2", @@ -144,10 +144,12 @@ "ts-loader": "^9.3.0", "ts-node": "^10.4.0", "tslib": "^2.0.1", - "typescript": "^4.7.0", + "tss-react": "^4.0.0", + "typescript": "^4.9.3", "wait-on": "^6.0.0", "web-encoding": "^1.1.5", - "webpack-cli": "^4.9.1", + "webpack": "^5.0.0", + "webpack-cli": "^5.0.1", "webpack-dev-server": "^4.7.3" }, "version": "0.0.0", diff --git a/packages/__mocks__/@testing-library/react.js b/packages/__mocks__/@testing-library/react.js index c4cdfb6b36..8774907983 100644 --- a/packages/__mocks__/@testing-library/react.js +++ b/packages/__mocks__/@testing-library/react.js @@ -1,5 +1,5 @@ import { createTheme, ThemeProvider } from '@mui/material/styles' -// eslint-disable-next-line import/no-extraneous-dependencies + import React from 'react' const react = jest.requireActual('@testing-library/react') diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx index d52cd85210..bbef3f56f0 100644 --- a/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx +++ b/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx @@ -25,6 +25,8 @@ import { getSession, getUriLink, isUriLocation, + assembleLocString, + ParsedLocString, } from '../util' import { ErrorMessage, SanitizedHTML } from '../ui' import SequenceFeatureDetails from './SequenceFeatureDetails' @@ -249,15 +251,31 @@ const ArrayValue = ({ } const toLocale = (n: number) => n.toLocaleString('en-US') +function Position(props: BaseProps) { + const { feature } = props + const strand = feature.strand as number + const strandMap: Record = { + '-1': '-', + '0': '', + '1': '+', + } + const str = strandMap[strand] ? `(${strandMap[strand]})` : '' + // @ts-ignore + const loc = assembleLocString(feature as ParsedLocString) + return <>{`${loc} ${str}`} +} + function CoreDetails(props: BaseProps) { const { feature } = props const obj = feature as SimpleFeatureSerializedNoId & { start: number end: number + assemblyName?: string strand: number refName: string __jbrowsefmt: { start?: number + assemblyName?: string end?: number refName?: string name?: string @@ -266,33 +284,28 @@ function CoreDetails(props: BaseProps) { // eslint-disable-next-line no-underscore-dangle const formattedFeat = { ...obj, ...obj.__jbrowsefmt } - const { start, strand, end, refName } = formattedFeat + const { start, end } = formattedFeat - const strandMap: Record = { - '-1': '-', - '0': '', - '1': '+', - } - const str = strandMap[strand as number] ? `(${strandMap[strand]})` : '' const displayedDetails: Record = { ...formattedFeat, length: toLocale(end - start), - position: `${refName}:${toLocale(start + 1)}..${toLocale(end)} ${str}`, } const coreRenderedDetails = { - position: 'Position', description: 'Description', name: 'Name', length: 'Length', type: 'Type', - assemblyName: 'Assembly name', } return ( <> + } + /> {Object.entries(coreRenderedDetails) .map(([key, name]) => [name, displayedDetails[key]]) - .filter(([, value]) => value !== null && value !== undefined) + .filter(([, value]) => value != null) .map(([name, value]) => ( ))} @@ -311,6 +324,7 @@ export const BaseCoreDetails = (props: BaseProps) => { interface AttributeProps { attributes: Record omit?: string[] + omitSingleLevel?: string[] formatter?: (val: unknown, key: string) => React.ReactNode descriptions?: Record prefix?: string[] @@ -369,8 +383,10 @@ const DataGridDetails = ({ })) const rowHeight = 25 - const hideFooter = rows.length < 100 - const headerHeight = 80 + const hideFoot = rows.length < 100 + const headHeight = 80 + const height = + Math.min(rows.length, 100) * rowHeight + headHeight + (hideFoot ? 0 : 50) // disableSelection on click helps avoid // https://github.com/mui-org/material-ui-x/issues/1197 return ( @@ -378,10 +394,7 @@ const DataGridDetails = ({
@@ -389,10 +402,9 @@ const DataGridDetails = ({ disableSelectionOnClick rowHeight={rowHeight} rows={rows} - rowsPerPageOptions={[]} hideFooterSelectedRowCount columns={columns} - hideFooter={hideFooter} + hideFooter={hideFoot} />
@@ -401,7 +413,10 @@ const DataGridDetails = ({ return null } -// arr = ['a','b'], obj = {a:{b:'hello}}, returns hello (with special addition to grab description also) +// pick using a path from an object, similar to _.get from lodash with special logic +// for Descriptions from e.g. VCF headers +// @param arr example ['a','b'], obj = {a:{b:'hello}} +// @returns hello (with special addition to grab description also) function accessNested(arr: string[], obj: Record = {}) { arr.forEach(elt => { if (obj) { @@ -415,15 +430,13 @@ function accessNested(arr: string[], obj: Record = {}) { : undefined } -function generateMaxWidth(array: any, prefix: any) { - // @ts-ignore - const arr = [] - array.forEach((key: any, value: any) => { +function generateMaxWidth(array: unknown[][], prefix: any) { + const arr = [] as number[] + array.forEach(key => { const val = [...prefix, key[0]].join('.') arr.push(measureText(val, 12)) }) - // @ts-ignore return Math.ceil(Math.max(...arr)) + 10 } @@ -456,12 +469,14 @@ export function Attributes(props: AttributeProps) { const { attributes, omit = [], + omitSingleLevel = [], descriptions, formatter = val => val, hideUris, prefix = [], } = props - const omits = [...omit, ...globalOmit] + + const omits = [...omit, ...globalOmit, ...omitSingleLevel] const { __jbrowsefmt, ...rest } = attributes const formattedAttributes = { ...rest, ...__jbrowsefmt } @@ -498,6 +513,7 @@ export function Attributes(props: AttributeProps) { /> ) } else if (isObject(value)) { + const { omitSingleLevel, ...rest } = props return isUriLocation(value) ? ( hideUris ? null : ( +} + export const FeatureDetails = (props: { model: IAnyStateTreeNode feature: SimpleFeatureSerializedNoId @@ -569,18 +589,26 @@ export const FeatureDetails = (props: { }) => { const { omit = [], model, feature, depth = 0 } = props const { name = '', id = '', type = '', subfeatures } = feature - const { pluginManager } = getEnv(model) + const pm = getEnv(model).pluginManager const session = getSession(model) - const ExtraPanel = pluginManager?.evaluateExtensionPoint( - 'Core-extraFeaturePanel', - null, - { session, feature, model }, - ) as { name: string; Component: React.FC } | undefined + const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, { + session, + feature, + model, + }) as PanelDescriptor | undefined return ( Core details + {feature.mate ? ( + <> + + Mate details + {/* @ts-ignore */} + + + ) : null} Attributes @@ -588,7 +616,8 @@ export const FeatureDetails = (props: { a.start - b.start) - : exons + const chunks = ( + cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons + ).filter(f => f.start !== f.end) return ( <> {upstream ? ( {upstream} ) : null} - {chunks - .filter(f => f.start !== f.end) - .map((chunk, index) => { - const intron = sequence.slice(chunk.end, chunks[index + 1]?.start) - return ( - - - {sequence.slice(chunk.start, chunk.end)} + {chunks.map((chunk, idx) => { + const intron = sequence.slice(chunk.end, chunks[idx + 1]?.start) + + return ( + + + {sequence.slice(chunk.start, chunk.end)} + + {includeIntrons && idx < chunks.length - 1 ? ( + + {collapseIntron && intron.length > intronBp * 2 + ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}` + : intron} - {includeIntrons && index < chunks.length - 1 ? ( - - {collapseIntron && intron.length > intronBp * 2 - ? `${intron.slice(0, intronBp)}...${intron.slice( - -intronBp, - )}` - : intron} - - ) : null} - - ) - })} + ) : null} + + ) + })} {downstream ? ( {downstream} diff --git a/packages/core/BaseFeatureWidget/SequenceFeatureDetails.tsx b/packages/core/BaseFeatureWidget/SequenceFeatureDetails.tsx index f874903b43..f41ac04a33 100644 --- a/packages/core/BaseFeatureWidget/SequenceFeatureDetails.tsx +++ b/packages/core/BaseFeatureWidget/SequenceFeatureDetails.tsx @@ -20,6 +20,7 @@ import { BaseProps } from './types' import { getConf } from '../configuration' import { Feature, SimpleFeatureSerialized } from '../util/simpleFeature' import { ParentFeat, SeqState, ErrorState } from './util' +import { LoadingEllipses } from '../ui' // icons import SettingsIcon from '@mui/icons-material/Settings' @@ -106,6 +107,7 @@ export default function SequenceFeatureDetails({ model, feature }: BaseProps) { return (feat?.get('seq') as string) || '' } + // eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { try { setError(undefined) @@ -255,7 +257,7 @@ export default function SequenceFeatureDetails({ model, feature }: BaseProps) { {error ? ( {`${error}`} ) : loading ? ( - Loading gene sequence... + ) : sequence ? ( 'error' in sequence ? ( <> diff --git a/packages/core/BaseFeatureWidget/SequenceFeatureSettingsDialog.tsx b/packages/core/BaseFeatureWidget/SequenceFeatureSettingsDialog.tsx index 84dfcd84a3..1638ab54d3 100644 --- a/packages/core/BaseFeatureWidget/SequenceFeatureSettingsDialog.tsx +++ b/packages/core/BaseFeatureWidget/SequenceFeatureSettingsDialog.tsx @@ -1,30 +1,13 @@ import React, { useState } from 'react' -import { - Button, - Dialog, - DialogTitle, - DialogContent, - DialogActions, - Divider, - IconButton, - TextField, -} from '@mui/material' +import { Button, DialogContent, DialogActions, TextField } from '@mui/material' +import { Dialog } from '@jbrowse/core/ui' import { makeStyles } from 'tss-react/mui' -// icons -import CloseIcon from '@mui/icons-material/Close' - const useStyles = makeStyles()(theme => ({ formElt: { margin: theme.spacing(3), width: 400, }, - closeButton: { - position: 'absolute', - right: theme.spacing(1), - top: theme.spacing(1), - color: theme.palette.grey[500], - }, dialogContent: { width: '80em', }, @@ -45,20 +28,12 @@ export default function SequenceFeatureSettingsDialog({ const intronBpValid = !Number.isNaN(+intronBp) const upDownBpValid = !Number.isNaN(+upDownBp) return ( - handleClose()}> - - Feature sequence settings - {handleClose ? ( - handleClose()} - > - - - ) : null} - - - + handleClose()} + title={'Feature sequence settings'} + > ({ - closeButton: { - position: 'absolute', - right: theme.spacing(1), - top: theme.spacing(1), - color: theme.palette.grey[500], - }, - dialogContent: {}, -})) - export default function HelpDialog({ handleClose, }: { handleClose: () => void }) { - const { classes } = useStyles() return ( - handleClose()}> - - Feature sequence panel - {handleClose ? ( - handleClose()} - > - - - ) : null} - - - - + handleClose()} + title="Feature sequence panel help" + > + The "Feature sequence" panel shows the underlying genomic sequence for a given feature, fetched from the reference genome. diff --git a/packages/core/BaseFeatureWidget/__snapshots__/index.test.js.snap b/packages/core/BaseFeatureWidget/__snapshots__/index.test.js.snap index e9d88c7ceb..04a2bdd573 100644 --- a/packages/core/BaseFeatureWidget/__snapshots__/index.test.js.snap +++ b/packages/core/BaseFeatureWidget/__snapshots__/index.test.js.snap @@ -25,7 +25,7 @@ exports[`open up a widget 1`] = ` >

Position
-
- ctgA:3..102 (+) -
+ ctgA:3..102 (+)
Length
100 @@ -99,16 +97,16 @@ exports[`open up a widget 1`] = ` Attributes

score
37 @@ -116,7 +114,7 @@ exports[`open up a widget 1`] = `
- + session.removeView(view)} + onMinimize={() => view.setMinimized(!view.minimized)} + > + {!view.minimized ? ( + } + > + }> + + + + ) : ( + false + )} + ) }) -const ViewPanel = observer( - ({ view, session }: { view: AbstractViewModel; session: AppSession }) => { - const { pluginManager } = getEnv(session) - const viewType = pluginManager.getViewType(view.type) - if (!viewType) { - throw new Error(`unknown view type ${view.type}`) - } - const { ReactComponent } = viewType - return ( - session.removeView(view)}> - Loading...
}> - - - - ) - }, -) - -const App = observer( - (props: { - HeaderButtons?: React.ReactElement - session: SessionWithDrawerWidgets & { - savedSessionNames: string[] - menus: { label: string; menuItems: JBMenuItem[] }[] - renameCurrentSession: (arg: string) => void - snackbarMessages: SnackbarMessage[] - popSnackbarMessage: () => unknown - } - }) => { - const { session } = props - const { classes } = useStyles() - - const { - minimized, - visibleWidget, - drawerWidth, - activeWidgets, - views, - drawerPosition, - } = session - - const drawerVisible = visibleWidget && !minimized - - let grid - if (drawerPosition === 'right') { - grid = [ - `[main] 1fr`, - drawerVisible ? `[drawer] ${drawerWidth}px` : undefined, - ] - } else if (drawerPosition === 'left') { - grid = [ - drawerVisible ? `[drawer] ${drawerWidth}px` : undefined, - `[main] 1fr`, - ] - } - return ( -
!!f).join(' '), - }} - > - {drawerVisible && drawerPosition === 'left' ? ( - - ) : null} - - {session.DialogComponent ? ( - }> - - - ) : null} -
-
- - - -
-
- {views.length ? ( - views.map(view => ( - ( - - )} - > - - - )) - ) : ( - - )} +const App = observer(function (props: { + HeaderButtons?: React.ReactElement + session: SessionWithDrawerWidgets & { + savedSessionNames: string[] + menus: { label: string; menuItems: JBMenuItem[] }[] + renameCurrentSession: (arg: string) => void + snackbarMessages: SnackbarMessage[] + popSnackbarMessage: () => unknown + } +}) { + const { session } = props + const { classes } = useStyles() - {/* blank space at the bottom of screen allows scroll */} -
-
+ const { + minimized, + visibleWidget, + drawerWidth, + activeWidgets, + views, + drawerPosition, + } = session + + const drawerVisible = visibleWidget && !minimized + + let grid + if (drawerPosition === 'right') { + grid = [ + `[main] 1fr`, + drawerVisible ? `[drawer] ${drawerWidth}px` : undefined, + ] + } else if (drawerPosition === 'left') { + grid = [ + drawerVisible ? `[drawer] ${drawerWidth}px` : undefined, + `[main] 1fr`, + ] + } + return ( +
!!f).join(' '), + }} + > + {drawerVisible && drawerPosition === 'left' ? ( + + ) : null} + + {session.DialogComponent ? ( + }> + + + ) : null} +
+
+ + + +
+
+ {views.length ? ( + views.map(view => ( + + )) + ) : ( + + )} + + {/* blank space at the bottom of screen allows scroll */} +
+
- {activeWidgets.size > 0 && minimized ? ( - - session.showWidgetDrawer()} - > - - - - ) : null} + {activeWidgets.size > 0 && minimized ? ( + + session.showWidgetDrawer()} + > + + + + ) : null} - {drawerVisible && drawerPosition === 'right' ? ( - - ) : null} + {drawerVisible && drawerPosition === 'right' ? ( + + ) : null} - -
- ) - }, -) + +
+ ) +}) export default App diff --git a/packages/core/ui/AppLogo.tsx b/packages/core/ui/AppLogo.tsx new file mode 100644 index 0000000000..84a40be7fc --- /dev/null +++ b/packages/core/ui/AppLogo.tsx @@ -0,0 +1,24 @@ +import React from 'react' +import { observer } from 'mobx-react' + +// locals +import { readConfObject, AnyConfigurationModel } from '../configuration' + +// ui elements +import { LogoFull } from './Logo' + +const Logo = observer(function ({ + session, +}: { + session: { configuration: AnyConfigurationModel } +}) { + const { configuration } = session + const logoPath = readConfObject(configuration, 'logoPath') + if (!logoPath?.uri) { + return + } else { + return Custom logo + } +}) + +export default Logo diff --git a/packages/core/ui/AppToolbar.tsx b/packages/core/ui/AppToolbar.tsx new file mode 100644 index 0000000000..845431263e --- /dev/null +++ b/packages/core/ui/AppToolbar.tsx @@ -0,0 +1,99 @@ +import React from 'react' +import { Toolbar, Tooltip } from '@mui/material' +import { makeStyles } from 'tss-react/mui' +import { observer } from 'mobx-react' + +// locals +import { + NotificationLevel, + SessionWithDrawerWidgets, + SnackAction, +} from '../util' + +// ui elements +import DropDownMenu from './DropDownMenu' +import EditableTypography from './EditableTypography' +import AppLogo from './AppLogo' +import { MenuItem as JBMenuItem } from './Menu' + +const useStyles = makeStyles()(theme => ({ + grow: { + flexGrow: 1, + }, + inputBase: { + color: theme.palette.primary.contrastText, + }, + inputRoot: { + '&:hover': { + backgroundColor: theme.palette.primary.light, + }, + }, + inputFocused: { + borderColor: theme.palette.secondary.main, + backgroundColor: theme.palette.primary.light, + }, +})) + +type SnackbarMessage = [string, NotificationLevel, SnackAction] + +type AppSession = SessionWithDrawerWidgets & { + savedSessionNames: string[] + menus: { label: string; menuItems: JBMenuItem[] }[] + renameCurrentSession: (arg: string) => void + snackbarMessages: SnackbarMessage[] + popSnackbarMessage: () => unknown +} + +const AppToolbar = observer(function ({ + session, + HeaderButtons =
, +}: { + HeaderButtons?: React.ReactElement + session: AppSession +}) { + const { classes } = useStyles() + const { savedSessionNames, name, menus } = session + + function handleNameChange(newName: string) { + if (savedSessionNames?.includes(newName)) { + session.notify( + `Cannot rename session to "${newName}", a saved session with that name already exists`, + 'warning', + ) + } else { + session.renameCurrentSession(newName) + } + } + return ( + + {menus.map(menu => ( + + ))} +
+ + + + {HeaderButtons} +
+
+ +
+ + ) +}) + +export default AppToolbar diff --git a/packages/core/ui/AssemblySelector.tsx b/packages/core/ui/AssemblySelector.tsx index 52e3fda7f7..6fdd5aa2e0 100644 --- a/packages/core/ui/AssemblySelector.tsx +++ b/packages/core/ui/AssemblySelector.tsx @@ -1,18 +1,22 @@ -import React, { useEffect } from 'react' +import React, { useState, useEffect } from 'react' +import { + TextField, + MenuItem, + InputProps as IIP, + TextFieldProps as TFP, +} from '@mui/material' import { observer } from 'mobx-react' -import { TextField, MenuItem, InputProps as IIP } from '@mui/material' -import { useLocalStorage } from '@jbrowse/core/util' import { makeStyles } from 'tss-react/mui' // locals import { getConf } from '../configuration' -import { AbstractSessionModel } from '../util' +import { useLocalStorage, AbstractSessionModel } from '../util' -const useStyles = makeStyles()(() => ({ +const useStyles = makeStyles()({ importFormEntry: { minWidth: 180, }, -})) +}) const AssemblySelector = observer( ({ @@ -20,13 +24,17 @@ const AssemblySelector = observer( onChange, selected, InputProps, - extra = 0, + TextFieldProps, + localStorageKey, + helperText = 'Select assembly to view', }: { session: AbstractSessionModel + helperText?: string onChange: (arg: string) => void - selected: string | undefined + selected?: string + localStorageKey?: string InputProps?: IIP - extra?: unknown + TextFieldProps?: TFP }) => { const { classes } = useStyles() const { assemblyNames, assemblyManager } = session @@ -34,14 +42,17 @@ const AssemblySelector = observer( // constructs a localstorage key based on host/path/config to help // remember. non-config assists usage with e.g. embedded apps const config = new URLSearchParams(window.location.search).get('config') - const [lastSelected, setLastSelected] = useLocalStorage( - `lastAssembly-${[ - window.location.host + window.location.pathname, - config, - extra, - ].join('-')}`, - selected, - ) + const [lastSelected, setLastSelected] = + typeof jest === 'undefined' && localStorageKey + ? useLocalStorage( + `lastAssembly-${[ + window.location.host + window.location.pathname, + config, + localStorageKey, + ].join('-')}`, + selected, + ) + : useState(selected) const selection = assemblyNames.includes(lastSelected || '') ? lastSelected @@ -59,14 +70,15 @@ const AssemblySelector = observer( select label="Assembly" variant="outlined" - helperText={error || 'Select assembly to view'} - value={error ? '' : selection} + helperText={error || helperText} + value={selection || ''} inputProps={{ 'data-testid': 'assembly-selector' }} onChange={event => setLastSelected(event.target.value)} error={!!error} InputProps={InputProps} disabled={!!error} className={classes.importFormEntry} + {...TextFieldProps} > {assemblyNames.map(name => { const assembly = assemblyManager.get(name) diff --git a/packages/core/ui/Dialog.tsx b/packages/core/ui/Dialog.tsx new file mode 100644 index 0000000000..3e86d063c7 --- /dev/null +++ b/packages/core/ui/Dialog.tsx @@ -0,0 +1,52 @@ +import React from 'react' +import { + Dialog, + DialogTitle, + IconButton, + Divider, + DialogProps, + ScopedCssBaseline, +} from '@mui/material' +import { observer } from 'mobx-react' +import { makeStyles } from 'tss-react/mui' + +// icons +import CloseIcon from '@mui/icons-material/Close' + +const useStyles = makeStyles()(theme => ({ + closeButton: { + position: 'absolute', + right: theme.spacing(1), + top: theme.spacing(1), + color: theme.palette.grey[500], + }, +})) + +function JBrowseDialog(props: DialogProps & { title: string }) { + const { classes } = useStyles() + const { title, children, onClose } = props + + return ( + + + + {title} + {onClose ? ( + { + // @ts-ignore + onClose() + }} + > + + + ) : null} + + + {children} + + + ) +} +export default observer(JBrowseDialog) diff --git a/packages/core/ui/DrawerWidget.tsx b/packages/core/ui/DrawerWidget.tsx index 12294880a2..0a8d0f38cd 100644 --- a/packages/core/ui/DrawerWidget.tsx +++ b/packages/core/ui/DrawerWidget.tsx @@ -14,6 +14,7 @@ import { import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' import { getEnv } from '../util' +import LoadingEllipses from './LoadingEllipses' import { SessionWithDrawerWidgets } from '../util/types' // icons @@ -216,7 +217,7 @@ const DrawerWidget = observer( return ( - Loading...
}> + }> } > diff --git a/packages/core/ui/EditableTypography.tsx b/packages/core/ui/EditableTypography.tsx index f6a2a5ad2a..7ae296ceb6 100644 --- a/packages/core/ui/EditableTypography.tsx +++ b/packages/core/ui/EditableTypography.tsx @@ -29,7 +29,7 @@ const useStyles = makeStyles()(theme => ({ }, })) -interface EditableTypographyPropTypes { +interface Props { value: string setValue: (value: string) => void variant: Variant @@ -37,18 +37,17 @@ interface EditableTypographyPropTypes { } // using forwardRef so that MUI Tooltip can wrap this component -const EditableTypography = React.forwardRef( - (props: EditableTypographyPropTypes, ref: React.Ref) => { +const EditableTypography = React.forwardRef( + (props, ref) => { const { value, setValue, variant, ...other } = props const [editedValue, setEditedValue] = useState() - const [width, setWidth] = useState(0) const [sizerNode, setSizerNode] = useState(null) const [inputNode, setInputNode] = useState(null) const [blur, setBlur] = useState(false) useEffect(() => { if (blur) { - inputNode && inputNode.blur() + inputNode?.blur() setBlur(false) } }, [blur, inputNode]) @@ -60,9 +59,9 @@ const EditableTypography = React.forwardRef( const theme = useTheme() const clientWidth = sizerNode?.clientWidth - if (clientWidth && clientWidth !== width) { - setWidth(clientWidth) - } + const width = clientWidth || 0 + + const val = editedValue === undefined ? value : editedValue return (
@@ -73,7 +72,7 @@ const EditableTypography = React.forwardRef( variant={variant} className={classes.typography} > - {editedValue === undefined ? value : editedValue} + {val}
setEditedValue(event.target.value)} onKeyDown={event => { if (event.key === 'Enter') { - inputNode && inputNode.blur() + inputNode?.blur() } else if (event.key === 'Escape') { setEditedValue(undefined) setBlur(true) } }} onBlur={() => { - if (editedValue && editedValue !== value) { - setValue(editedValue) - } + setValue(editedValue || '') setEditedValue(undefined) }} /> diff --git a/packages/core/ui/FactoryResetDialog.tsx b/packages/core/ui/FactoryResetDialog.tsx index 9d6d62fdfb..19439913b8 100644 --- a/packages/core/ui/FactoryResetDialog.tsx +++ b/packages/core/ui/FactoryResetDialog.tsx @@ -1,10 +1,11 @@ -import Button from '@mui/material/Button' -import Dialog from '@mui/material/Dialog' -import DialogTitle from '@mui/material/DialogTitle' -import DialogContent from '@mui/material/DialogContent' -import DialogContentText from '@mui/material/DialogContentText' -import DialogActions from '@mui/material/DialogActions' import React from 'react' +import { + Button, + DialogContent, + DialogContentText, + DialogActions, +} from '@mui/material' +import Dialog from '@jbrowse/core/ui/Dialog' export default ({ onClose, @@ -23,10 +24,9 @@ export default ({ } return ( - handleDialogClose()}> - Reset + handleDialogClose()} open={open}> - + Are you sure you want to reset? This will restore the default configuration. diff --git a/packages/core/ui/LoadingEllipses.tsx b/packages/core/ui/LoadingEllipses.tsx new file mode 100644 index 0000000000..de876b978f --- /dev/null +++ b/packages/core/ui/LoadingEllipses.tsx @@ -0,0 +1,46 @@ +import React from 'react' +import { Typography, TypographyProps } from '@mui/material' +import { makeStyles } from 'tss-react/mui' +import { keyframes } from 'tss-react' + +const useStyles = makeStyles()({ + dots: { + '&::after': { + display: 'inline-block', + content: '""', + width: '1em', + textAlign: 'left', + animation: `${keyframes` + 0% { + content: ''; + } + 25% { + content: '.'; + } + 50% { + content: '..'; + } + 75% { + content: '...'; + } + `} 1.4s infinite ease-in-out`, + }, + }, +}) + +interface Props extends TypographyProps { + message?: string +} + +export default function LoadingEllipses({ + message = 'Loading', + variant = 'body2', + ...rest +}: Props) { + const { classes } = useStyles() + return ( + + {`${message || 'Loading'}`} + + ) +} diff --git a/packages/core/ui/PrerenderedCanvas.tsx b/packages/core/ui/PrerenderedCanvas.tsx index 3eac3940e1..e89891e174 100644 --- a/packages/core/ui/PrerenderedCanvas.tsx +++ b/packages/core/ui/PrerenderedCanvas.tsx @@ -1,22 +1,21 @@ /* eslint-disable @typescript-eslint/no-explicit-any */ -import ReactPropTypes from 'prop-types' import React, { useState, useRef, useEffect } from 'react' import { drawImageOntoCanvasContext } from '../util/offscreenCanvasPonyfill' function PrerenderedCanvas(props: { width: number height: number - highResolutionScaling: number - style: any - imageData: any + highResolutionScaling?: number + style?: any + imageData?: any showSoftClip?: boolean blockKey?: string }) { const { width, height, - highResolutionScaling, - style, + highResolutionScaling = 1, + style = {}, imageData, blockKey, showSoftClip, @@ -57,19 +56,4 @@ function PrerenderedCanvas(props: { ) } -PrerenderedCanvas.propTypes = { - height: ReactPropTypes.number.isRequired, - width: ReactPropTypes.number.isRequired, - highResolutionScaling: ReactPropTypes.number, - style: ReactPropTypes.objectOf(ReactPropTypes.any), - imageData: ReactPropTypes.any, - // config: ReactPropTypes.objectOf(ReactPropTypes.any), -} -PrerenderedCanvas.defaultProps = { - imageData: undefined, - highResolutionScaling: 1, - style: {}, - // config: {}, -} - export default PrerenderedCanvas diff --git a/packages/core/ui/ReturnToImportFormDialog.tsx b/packages/core/ui/ReturnToImportFormDialog.tsx index a54fcee3fa..5f40e043e0 100644 --- a/packages/core/ui/ReturnToImportFormDialog.tsx +++ b/packages/core/ui/ReturnToImportFormDialog.tsx @@ -1,26 +1,7 @@ import React from 'react' import { observer } from 'mobx-react' -import { - Button, - Dialog, - DialogActions, - DialogContent, - DialogTitle, - Divider, - IconButton, - Typography, -} from '@mui/material' -import { makeStyles } from 'tss-react/mui' -import CloseIcon from '@mui/icons-material/Close' - -const useStyles = makeStyles()(theme => ({ - closeButton: { - position: 'absolute', - right: theme.spacing(1), - top: theme.spacing(1), - color: theme.palette.grey[500], - }, -})) +import { Button, DialogActions, DialogContent, Typography } from '@mui/material' +import Dialog from './Dialog' function ReturnToImportFormDialog({ model, @@ -29,23 +10,8 @@ function ReturnToImportFormDialog({ model: { clearView: Function } handleClose: () => void }) { - const { classes } = useStyles() return ( - - - Reference sequence - {handleClose ? ( - handleClose()} - size="large" - > - - - ) : null} - - - + Are you sure you want to return to the import form? This will lose diff --git a/packages/core/ui/Snackbar.tsx b/packages/core/ui/Snackbar.tsx index c209be74ad..53cd664c53 100644 --- a/packages/core/ui/Snackbar.tsx +++ b/packages/core/ui/Snackbar.tsx @@ -1,8 +1,12 @@ -import React, { useEffect, useState } from 'react' +import React from 'react' import { Alert, Button, IconButton, Snackbar } from '@mui/material' -import CloseIcon from '@mui/icons-material/Close' import { observer } from 'mobx-react' import { IAnyStateTreeNode } from 'mobx-state-tree' + +// icons +import CloseIcon from '@mui/icons-material/Close' + +// locals import { AbstractSessionModel, NotificationLevel, SnackAction } from '../util' type SnackbarMessage = [string, NotificationLevel, SnackAction] @@ -17,49 +21,23 @@ function MessageSnackbar({ }: { session: SnackbarSession & IAnyStateTreeNode }) { - const [open, setOpen] = useState(false) - const [snackbarMessage, setSnackbarMessage] = useState() - const { popSnackbarMessage, snackbarMessages } = session const latestMessage = snackbarMessages.length ? snackbarMessages[snackbarMessages.length - 1] : null - useEffect(() => { - let timeoutId: ReturnType - - if (snackbarMessage) { - if (!latestMessage) { - setSnackbarMessage(undefined) - } else if (snackbarMessage[0] !== latestMessage[0]) { - setOpen(false) - timeoutId = setTimeout(() => { - setSnackbarMessage(latestMessage) - setOpen(true) - }, 100) - } - } else if (latestMessage) { - setSnackbarMessage(latestMessage) - setOpen(true) - } - - return () => { - clearTimeout(timeoutId) - } - }, [latestMessage, snackbarMessage]) - const handleClose = (_event: unknown, reason?: string) => { if (reason === 'clickaway') { return } popSnackbarMessage() - setOpen(false) } - const [message, level, action] = snackbarMessage || [] + const open = !!latestMessage + const [message, level, action] = latestMessage || [] return ( @@ -77,11 +55,7 @@ function MessageSnackbar({ > {action.name} - + diff --git a/packages/core/ui/SnackbarModel.ts b/packages/core/ui/SnackbarModel.ts index 6570d63f02..e7c6bf796b 100644 --- a/packages/core/ui/SnackbarModel.ts +++ b/packages/core/ui/SnackbarModel.ts @@ -2,15 +2,24 @@ import { IModelType, ModelProperties } from 'mobx-state-tree' import { IObservableArray, observable } from 'mobx' import { NotificationLevel, SnackAction } from '../util/types' +/** + * #stateModel SnackbarModel + */ // eslint-disable-next-line @typescript-eslint/no-explicit-any function makeExtension(snackbarMessages: IObservableArray) { return { views: { + /** + * #getter + */ get snackbarMessages() { return snackbarMessages }, }, actions: { + /** + * #action + */ notify(message: string, level?: NotificationLevel, action?: SnackAction) { this.pushSnackbarMessage(message, level, action) if (level === 'info' || level === 'success') { @@ -19,7 +28,9 @@ function makeExtension(snackbarMessages: IObservableArray) { }, 5000) } }, - + /** + * #action + */ pushSnackbarMessage( message: string, level?: NotificationLevel, @@ -27,11 +38,15 @@ function makeExtension(snackbarMessages: IObservableArray) { ) { return snackbarMessages.push([message, level, action]) }, - + /** + * #action + */ popSnackbarMessage() { return snackbarMessages.pop() }, - + /** + * #action + */ removeSnackbarMessage(message: string) { const element = snackbarMessages.find(f => f[0] === message) if (element) { diff --git a/packages/core/ui/Tooltip.tsx b/packages/core/ui/Tooltip.tsx index 63eba03fe9..64c9a23df6 100644 --- a/packages/core/ui/Tooltip.tsx +++ b/packages/core/ui/Tooltip.tsx @@ -1,7 +1,7 @@ import React, { useEffect, useState } from 'react' import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' -import { Feature } from '../util/simpleFeature' +import { Feature } from '../util' import { readConfObject, AnyConfigurationModel } from '../configuration' const useStyles = makeStyles()({ diff --git a/packages/core/ui/ViewContainer.tsx b/packages/core/ui/ViewContainer.tsx index baf0cfea85..ef217c7010 100644 --- a/packages/core/ui/ViewContainer.tsx +++ b/packages/core/ui/ViewContainer.tsx @@ -8,16 +8,20 @@ import { useTheme, } from '@mui/material' import { makeStyles } from 'tss-react/mui' -import { alpha } from '@mui/material/styles' import { observer } from 'mobx-react' import { isAlive } from 'mobx-state-tree' import useMeasure from 'react-use-measure' // icons import CloseIcon from '@mui/icons-material/Close' +import MinimizeIcon from '@mui/icons-material/Minimize' +import AddIcon from '@mui/icons-material/Add' import MenuIcon from '@mui/icons-material/Menu' +import ArrowDownward from '@mui/icons-material/ArrowDownward' +import ArrowUpward from '@mui/icons-material/ArrowUpward' // locals +import { getSession } from '../util' import { IBaseViewModel } from '../pluggableElementTypes/models' import EditableTypography from './EditableTypography' import Menu from './Menu' @@ -34,17 +38,6 @@ const useStyles = makeStyles()(theme => ({ grow: { flexGrow: 1, }, - iconRoot: { - '&:hover': { - backgroundColor: alpha( - theme.palette.secondary.contrastText, - theme.palette.action.hoverOpacity, - ), - '@media (hover: none)': { - backgroundColor: 'transparent', - }, - }, - }, input: { paddingBottom: 0, @@ -71,23 +64,39 @@ const ViewMenu = observer( IconProps, }: { model: IBaseViewModel - IconButtonProps: IconButtonPropsType + IconButtonProps?: IconButtonPropsType IconProps: SvgIconProps }) => { const [anchorEl, setAnchorEl] = useState() const { menuItems } = model + const session = getSession(model) + + const items = [ + ...(session.views.length > 1 + ? [ + { + label: 'Move view up', + icon: ArrowUpward, + onClick: () => session.moveViewUp(model.id), + }, + { + label: 'Move view down', + icon: ArrowDownward, + onClick: () => session.moveViewDown(model.id), + }, + ] + : []), - // <=1.3.3 didn't use a function - const items = typeof menuItems === 'function' ? menuItems() : menuItems + // <=1.3.3 didn't use a function, so check as value also + ...((typeof menuItems === 'function' ? menuItems() : menuItems) || []), + ] - return items?.length ? ( + return ( <> setAnchorEl(event.currentTarget)} data-testid="view_menu_icon" - size="small" > @@ -99,21 +108,23 @@ const ViewMenu = observer( setAnchorEl(undefined) }} onClose={() => setAnchorEl(undefined)} - menuItems={model.menuItems()} + menuItems={items} /> - ) : null + ) }, ) const ViewContainer = observer( ({ view, onClose, + onMinimize, style, children, }: { view: IBaseViewModel onClose: () => void + onMinimize: () => void style?: React.CSSProperties children: React.ReactNode }) => { @@ -145,22 +156,15 @@ const ViewContainer = observer( style={{ ...style, padding: `0px ${padWidth} ${padWidth}` }} >
- +
view.setDisplayName(val)} variant="body2" @@ -173,13 +177,14 @@ const ViewContainer = observer( />
- + + {view.minimized ? ( + + ) : ( + + )} + +
diff --git a/packages/core/ui/ViewLauncher.tsx b/packages/core/ui/ViewLauncher.tsx new file mode 100644 index 0000000000..a6fcb30353 --- /dev/null +++ b/packages/core/ui/ViewLauncher.tsx @@ -0,0 +1,69 @@ +import React, { useState } from 'react' +import { + Button, + FormControl, + MenuItem, + Paper, + Select, + Typography, +} from '@mui/material' +import { observer } from 'mobx-react' +import { makeStyles } from 'tss-react/mui' + +// locals +import { + getEnv, + NotificationLevel, + SnackAction, + SessionWithDrawerWidgets, +} from '../util' + +// ui elements +import { MenuItem as JBMenuItem } from './Menu' +type SnackbarMessage = [string, NotificationLevel, SnackAction] + +type AppSession = SessionWithDrawerWidgets & { + savedSessionNames: string[] + menus: { label: string; menuItems: JBMenuItem[] }[] + renameCurrentSession: (arg: string) => void + snackbarMessages: SnackbarMessage[] + popSnackbarMessage: () => unknown +} + +const useStyles = makeStyles()(theme => ({ + selectPaper: { + padding: theme.spacing(4), + }, +})) + +const ViewLauncher = observer(({ session }: { session: AppSession }) => { + const { classes } = useStyles() + const { pluginManager } = getEnv(session) + const viewTypes = pluginManager.getElementTypeRecord('view').all() + const [value, setValue] = useState(viewTypes[0]?.name) + return ( + + Select a view to launch + + + + + + + + ) +}) + +export default ViewLauncher diff --git a/packages/core/ui/index.ts b/packages/core/ui/index.ts index b9cd12a741..e3e626aa62 100644 --- a/packages/core/ui/index.ts +++ b/packages/core/ui/index.ts @@ -1,17 +1,19 @@ export * from './theme' export { LogoFull, Logomark } from './Logo' export { default as App } from './App' -export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog' -export { default as ErrorMessage } from './ErrorMessage' export { default as AssemblySelector } from './AssemblySelector' -export { default as FileSelector } from './FileSelector' -export { default as PrerenderedCanvas } from './PrerenderedCanvas' -export { default as ResizeHandle } from './ResizeHandle' +export { default as CascadingMenu } from './CascadingMenu' +export { default as Dialog } from './Dialog' export { default as EditableTypography } from './EditableTypography' +export { default as ErrorMessage } from './ErrorMessage' export { default as FactoryResetDialog } from './FactoryResetDialog' -export { default as Tooltip } from './Tooltip' export { default as FatalErrorDialog } from './FatalErrorDialog' +export { default as FileSelector } from './FileSelector' +export { default as LoadingEllipses } from './LoadingEllipses' export { default as Menu } from './Menu' -export { default as CascadingMenu } from './CascadingMenu' +export { default as PrerenderedCanvas } from './PrerenderedCanvas' +export { default as Tooltip } from './Tooltip' +export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog' +export { default as ResizeHandle } from './ResizeHandle' export { default as SanitizedHTML } from './SanitizedHTML' export * from './Menu' diff --git a/packages/core/ui/theme.ts b/packages/core/ui/theme.ts index 14010dd60d..bc77c520bc 100644 --- a/packages/core/ui/theme.ts +++ b/packages/core/ui/theme.ts @@ -1,6 +1,9 @@ import { blue, green, red, amber } from '@mui/material/colors' import { createTheme, ThemeOptions } from '@mui/material/styles' -import type { PaletteOptions } from '@mui/material/styles/createPalette' +import type { + PaletteAugmentColorOptions, + PaletteOptions, +} from '@mui/material/styles/createPalette' import deepmerge from 'deepmerge' declare module '@mui/material/styles/createPalette' { @@ -211,7 +214,7 @@ export function createJBrowseTheme(theme?: ThemeOptions) { palette: { tertiary: refTheme.palette.augmentColor( 'color' in theme.palette.tertiary - ? theme.palette.tertiary + ? (theme.palette.tertiary as PaletteAugmentColorOptions) : { color: theme.palette.tertiary }, ), }, @@ -222,7 +225,7 @@ export function createJBrowseTheme(theme?: ThemeOptions) { palette: { quaternary: refTheme.palette.augmentColor( 'color' in theme.palette.quaternary - ? theme.palette.quaternary + ? (theme.palette.quaternary as PaletteAugmentColorOptions) : { color: theme.palette.quaternary }, ), }, diff --git a/packages/core/util/Base1DUtils.ts b/packages/core/util/Base1DUtils.ts index 51651d2fa3..dbac1f1a26 100644 --- a/packages/core/util/Base1DUtils.ts +++ b/packages/core/util/Base1DUtils.ts @@ -40,11 +40,25 @@ export function moveTo( if (!start || !end) { return } - const { width, interRegionPaddingWidth } = self + const { + width, + interRegionPaddingWidth, + displayedRegions, + bpPerPx, + minimumBlockWidth, + } = self const len = lengthBetween(self, start, end) - const numBlocks = end.index - start.index - const targetBpPerPx = len / (width - interRegionPaddingWidth * numBlocks) + let numBlocksWideEnough = 0 + for (let i = start.index; i < end.index; i++) { + const r = displayedRegions[i] + if ((r.end - r.start) / bpPerPx > minimumBlockWidth) { + numBlocksWideEnough++ + } + } + + const targetBpPerPx = + len / (width - interRegionPaddingWidth * numBlocksWideEnough) const newBpPerPx = self.zoomTo(targetBpPerPx) // If our target bpPerPx was smaller than the allowed minBpPerPx, adjust @@ -141,7 +155,7 @@ export function pxToBp( } } - if (bp >= bpSoFar) { + if (bp >= bpSoFar && displayedRegions.length) { const region = displayedRegions[displayedRegions.length - 1] const len = region.end - region.start const offset = bp - bpSoFar + len diff --git a/packages/core/util/Base1DViewModel.ts b/packages/core/util/Base1DViewModel.ts index d1565eb418..19c2d34907 100644 --- a/packages/core/util/Base1DViewModel.ts +++ b/packages/core/util/Base1DViewModel.ts @@ -7,13 +7,38 @@ import calculateDynamicBlocks from './calculateDynamicBlocks' import calculateStaticBlocks from './calculateStaticBlocks' import { moveTo, pxToBp, bpToPx, BpOffset } from './Base1DUtils' +/** + * #stateModel Base1DView + * used in non-lgv view representations of a 1d view e.g. the two axes of the + * dotplot use this + */ +function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars + const Base1DView = types .model('Base1DView', { + /** + * #property + */ id: ElementId, + /** + * #property + */ displayedRegions: types.array(Region), + /** + * #property + */ bpPerPx: 0, + /** + * #property + */ offsetPx: 0, + /** + * #property + */ interRegionPaddingWidth: types.optional(types.number, 0), + /** + * #property + */ minimumBlockWidth: types.optional(types.number, 0), }) .volatile(() => ({ @@ -21,41 +46,68 @@ const Base1DView = types volatileWidth: 0, })) .actions(self => ({ + /** + * #action + */ setDisplayedRegions(regions: IRegion[]) { self.displayedRegions = cast(regions) }, + /** + * #action + */ setBpPerPx(val: number) { self.bpPerPx = val }, + /** + * #action + */ setVolatileWidth(width: number) { self.volatileWidth = width }, })) .views(self => ({ + /** + * #getter + */ get width() { return self.volatileWidth }, + /** + * #getter + */ get assemblyNames() { return [ ...new Set(self.displayedRegions.map(region => region.assemblyName)), ] }, - + /** + * #getter + */ get displayedRegionsTotalPx() { return this.totalBp / self.bpPerPx }, + /** + * #getter + */ get maxOffset() { // objectively determined to keep the linear genome on the main screen const leftPadding = 10 return this.displayedRegionsTotalPx - leftPadding }, + /** + * #getter + */ get minOffset() { // objectively determined to keep the linear genome on the main screen const rightPadding = 30 return -this.width + rightPadding }, + + /** + * #getter + */ get totalBp() { return self.displayedRegions .map(a => a.end - a.start) @@ -63,12 +115,23 @@ const Base1DView = types }, })) .views(self => ({ + /** + * #getter + */ get dynamicBlocks() { return calculateDynamicBlocks(self) }, + + /** + * #getter + */ get staticBlocks() { return calculateStaticBlocks(self) }, + + /** + * #getter + */ get currBp() { return this.dynamicBlocks .map(a => a.end - a.start) @@ -76,9 +139,16 @@ const Base1DView = types }, })) .views(self => ({ + /** + * #method + */ pxToBp(px: number) { return pxToBp(self, px) }, + + /** + * #method + */ bpToPx({ refName, coord, @@ -92,25 +162,40 @@ const Base1DView = types }, })) .actions(self => ({ + /** + * #action + */ setFeatures(features: Feature[]) { self.features = features }, - // this makes a zoomed out view that shows all displayedRegions - // that makes the overview bar square with the scale bar + /** + * #action + * this makes a zoomed out view that shows all displayedRegions that makes + * the overview bar square with the scale bar + */ showAllRegions() { self.bpPerPx = self.totalBp / self.width self.offsetPx = 0 }, + /** + * #action + */ zoomOut() { this.zoomTo(self.bpPerPx * 2) }, + /** + * #action + */ zoomIn() { this.zoomTo(self.bpPerPx / 2) }, + /** + * #action + */ zoomTo(newBpPerPx: number, offset = self.width / 2) { const bpPerPx = newBpPerPx if (bpPerPx === self.bpPerPx) { @@ -128,11 +213,17 @@ const Base1DView = types return self.bpPerPx }, + /** + * #action + */ scrollTo(offsetPx: number) { const newOffsetPx = clamp(offsetPx, self.minOffset, self.maxOffset) self.offsetPx = newOffsetPx return newOffsetPx }, + /** + * #action + */ centerAt(coord: number, refName: string | undefined, regionNumber: number) { if (!refName) { return @@ -147,9 +238,12 @@ const Base1DView = types } }, + /** + * #action + * note: the scroll is clamped to keep the view on the main screen + */ scroll(distance: number) { const oldOffsetPx = self.offsetPx - // the scroll is clamped to keep the linear genome on the main screen const newOffsetPx = clamp( self.offsetPx + distance, self.minOffset, @@ -161,6 +255,7 @@ const Base1DView = types })) .actions(self => ({ /** + * #action * offset is the base-pair-offset in the displayed region, index is the index of the * displayed region in the linear genome view * diff --git a/packages/core/util/__snapshots__/calculateDynamicBlocks.test.ts.snap b/packages/core/util/__snapshots__/calculateDynamicBlocks.test.ts.snap index 027fbfd29d..f814af2277 100644 --- a/packages/core/util/__snapshots__/calculateDynamicBlocks.test.ts.snap +++ b/packages/core/util/__snapshots__/calculateDynamicBlocks.test.ts.snap @@ -1,7 +1,7 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`five 1`] = ` -Array [ +[ ContentBlock { "assemblyName": "test", "end": 72.4, @@ -9,7 +9,7 @@ Array [ "isRightEndOfDisplayedRegion": false, "key": "{test}ctgA:27.05..72.4-0", "offsetPx": 521, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 50000, "refName": "ctgA", @@ -27,7 +27,7 @@ Array [ `; exports[`four 1`] = ` -Array [ +[ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -48,7 +48,7 @@ Array [ "isRightEndOfDisplayedRegion": false, "key": "{test}ctgA:1..250-0", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 50000, "refName": "ctgA", @@ -65,7 +65,7 @@ Array [ `; exports[`one 1`] = ` -Array [ +[ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -86,7 +86,7 @@ Array [ "isRightEndOfDisplayedRegion": false, "key": "{test}ctgA:1..200-0", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 50000, "refName": "ctgA", @@ -103,12 +103,12 @@ Array [ `; exports[`three 1`] = ` -Array [ +[ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, "isLeftEndOfDisplayedRegion": undefined, - "key": "{test}ctgA:49,901..50,000[rev]-0-reversed-beforeFirstRegion", + "key": "{test}ctgA:49901..50000[rev]-0-reversed-beforeFirstRegion", "offsetPx": -100, "refName": undefined, "regionNumber": undefined, @@ -122,9 +122,9 @@ Array [ "end": 50000, "isLeftEndOfDisplayedRegion": true, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:49,901..50,000[rev]-0-reversed", + "key": "{test}ctgA:49901..50000[rev]-0-reversed", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 50000, "refName": "ctgA", @@ -142,12 +142,12 @@ Array [ `; exports[`two 1`] = ` -Array [ +[ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, "isLeftEndOfDisplayedRegion": undefined, - "key": "{test}ctgA:49,801..50,000[rev]-0-reversed-beforeFirstRegion", + "key": "{test}ctgA:49801..50000[rev]-0-reversed-beforeFirstRegion", "offsetPx": 0, "refName": undefined, "regionNumber": undefined, @@ -161,9 +161,9 @@ Array [ "end": 50000, "isLeftEndOfDisplayedRegion": true, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:49,801..50,000[rev]-0-reversed", + "key": "{test}ctgA:49801..50000[rev]-0-reversed", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 50000, "refName": "ctgA", diff --git a/packages/core/util/__snapshots__/calculateStaticBlocks.test.ts.snap b/packages/core/util/__snapshots__/calculateStaticBlocks.test.ts.snap index 5901d8bbe9..faa18e4c8c 100644 --- a/packages/core/util/__snapshots__/calculateStaticBlocks.test.ts.snap +++ b/packages/core/util/__snapshots__/calculateStaticBlocks.test.ts.snap @@ -2,7 +2,7 @@ exports[`block calculation can calculate some blocks 1 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -23,7 +23,7 @@ BlockSet { "isRightEndOfDisplayedRegion": false, "key": "{test}ctgA:1..800-0", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -41,9 +41,9 @@ BlockSet { "end": 1600, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:801..1,600-0", + "key": "{test}ctgA:801..1600-0", "offsetPx": 800, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -62,7 +62,7 @@ BlockSet { exports[`block calculation can calculate some blocks 2 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -83,7 +83,7 @@ BlockSet { "isRightEndOfDisplayedRegion": true, "key": "{test}ctgA:1..100-0", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 100, "refName": "ctgA", @@ -116,7 +116,7 @@ BlockSet { "isRightEndOfDisplayedRegion": true, "key": "{test}ctgB:101..200-1", "offsetPx": 102, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 200, "refName": "ctgB", @@ -148,15 +148,15 @@ BlockSet { exports[`block calculation can calculate some blocks 5 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ ContentBlock { "assemblyName": "test", "end": 5600, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:4,801..5,600-0", + "key": "{test}ctgA:4801..5600-0", "offsetPx": 4800, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -174,9 +174,9 @@ BlockSet { "end": 6400, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:5,601..6,400-0", + "key": "{test}ctgA:5601..6400-0", "offsetPx": 5600, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -195,7 +195,7 @@ BlockSet { exports[`block calculation can calculate some blocks 6 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -216,7 +216,7 @@ BlockSet { "isRightEndOfDisplayedRegion": true, "key": "{test}ctgA:1..200-0", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 200, "refName": "ctgA", @@ -249,7 +249,7 @@ BlockSet { "isRightEndOfDisplayedRegion": false, "key": "{test}ctgB:1..800-1", "offsetPx": 202, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 1000, "refName": "ctgB", @@ -268,7 +268,7 @@ BlockSet { exports[`block calculation can calculate some blocks 7 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ ContentBlock { "assemblyName": "test", "end": 800, @@ -276,7 +276,7 @@ BlockSet { "isRightEndOfDisplayedRegion": false, "key": "{test}ctgB:1..800-1", "offsetPx": 200, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 1000, "refName": "ctgB", @@ -294,9 +294,9 @@ BlockSet { "end": 1000, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": true, - "key": "{test}ctgB:801..1,000-1", + "key": "{test}ctgB:801..1000-1", "offsetPx": 1000, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 1000, "refName": "ctgB", @@ -313,7 +313,7 @@ BlockSet { "assemblyName": undefined, "end": undefined, "isLeftEndOfDisplayedRegion": undefined, - "key": "{test}ctgB:801..1,000-1-afterLastRegion", + "key": "{test}ctgB:801..1000-1-afterLastRegion", "offsetPx": 1200, "refName": undefined, "regionNumber": undefined, @@ -328,15 +328,15 @@ BlockSet { exports[`block calculation can calculate some blocks 8 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ ContentBlock { "assemblyName": "test", "end": 1600, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgB:801..1,600-1", + "key": "{test}ctgB:801..1600-1", "offsetPx": 1000, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000000, "refName": "ctgB", @@ -354,9 +354,9 @@ BlockSet { "end": 2400, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgB:1,601..2,400-1", + "key": "{test}ctgB:1601..2400-1", "offsetPx": 1800, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000000, "refName": "ctgB", @@ -375,15 +375,15 @@ BlockSet { exports[`block calculation can calculate some blocks 9 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ ContentBlock { "assemblyName": "test", "end": 3200, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:1,601..3,200-0", + "key": "{test}ctgA:1601..3200-0", "offsetPx": 800, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 50000, "refName": "ctgA", @@ -401,9 +401,9 @@ BlockSet { "end": 4800, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:3,201..4,800-0", + "key": "{test}ctgA:3201..4800-0", "offsetPx": 1600, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 50000, "refName": "ctgA", @@ -421,7 +421,7 @@ BlockSet { `; exports[`block calculation can calculate some blocks 10 1`] = ` -Array [ +[ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -442,7 +442,7 @@ Array [ "isRightEndOfDisplayedRegion": false, "key": "{test}ctgA:101..140-0", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 200, "refName": "ctgA", @@ -462,7 +462,7 @@ Array [ "isRightEndOfDisplayedRegion": false, "key": "{test}ctgA:141..180-0", "offsetPx": 800, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 200, "refName": "ctgA", @@ -480,12 +480,12 @@ Array [ exports[`reverse block calculation 1 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, "isLeftEndOfDisplayedRegion": undefined, - "key": "{test}ctgA:9,201..10,000[rev]-0-reversed-beforeFirstRegion", + "key": "{test}ctgA:9201..10000[rev]-0-reversed-beforeFirstRegion", "offsetPx": -800, "refName": undefined, "regionNumber": undefined, @@ -499,9 +499,9 @@ BlockSet { "end": 10000, "isLeftEndOfDisplayedRegion": true, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:9,201..10,000[rev]-0-reversed", + "key": "{test}ctgA:9201..10000[rev]-0-reversed", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -520,9 +520,9 @@ BlockSet { "end": 9200, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:8,401..9,200[rev]-0-reversed", + "key": "{test}ctgA:8401..9200[rev]-0-reversed", "offsetPx": 800, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -542,7 +542,7 @@ BlockSet { exports[`reversed displayed regions with elided region 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -564,7 +564,7 @@ BlockSet { "isRightEndOfDisplayedRegion": true, "key": "{test}ctgA:1[rev]-0-reversed", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 1, "refName": "ctgA", @@ -583,9 +583,9 @@ BlockSet { "end": 10000, "isLeftEndOfDisplayedRegion": true, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:9,201..10,000[rev]-1-reversed", + "key": "{test}ctgA:9201..10000[rev]-1-reversed", "offsetPx": 1, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -604,9 +604,9 @@ BlockSet { "end": 9200, "isLeftEndOfDisplayedRegion": false, "isRightEndOfDisplayedRegion": false, - "key": "{test}ctgA:8,401..9,200[rev]-1-reversed", + "key": "{test}ctgA:8401..9200[rev]-1-reversed", "offsetPx": 801, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 10000, "refName": "ctgA", @@ -626,7 +626,7 @@ BlockSet { exports[`reversed displayed regions without elided region 1`] = ` BlockSet { - "blocks": Array [ + "blocks": [ InterRegionPaddingBlock { "assemblyName": undefined, "end": undefined, @@ -647,7 +647,7 @@ BlockSet { "isRightEndOfDisplayedRegion": true, "key": "{test}ctgA:101..200[rev]-0-reversed", "offsetPx": 0, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 200, "refName": "ctgA", @@ -681,7 +681,7 @@ BlockSet { "isRightEndOfDisplayedRegion": true, "key": "{test}ctgA:501..600[rev]-1-reversed", "offsetPx": 102, - "parentRegion": Object { + "parentRegion": { "assemblyName": "test", "end": 600, "refName": "ctgA", diff --git a/packages/core/util/analytics.ts b/packages/core/util/analytics.ts index e07df9e508..a244ecaff1 100644 --- a/packages/core/util/analytics.ts +++ b/packages/core/util/analytics.ts @@ -133,7 +133,10 @@ export function doAnalytics( rootModel && !readConfObject(rootModel.jbrowse.configuration, 'disableAnalytics') ) { + // ok if these are unhandled + // eslint-disable-next-line @typescript-eslint/no-floating-promises writeAWSAnalytics(rootModel, initialTimestamp, initialSessionQuery) + // eslint-disable-next-line @typescript-eslint/no-floating-promises writeGAAnalytics(rootModel, initialTimestamp) } } diff --git a/packages/core/util/calculateDynamicBlocks.ts b/packages/core/util/calculateDynamicBlocks.ts index b2c8e1cca7..002b926d1e 100644 --- a/packages/core/util/calculateDynamicBlocks.ts +++ b/packages/core/util/calculateDynamicBlocks.ts @@ -1,6 +1,6 @@ import { isStateTreeNode, getSnapshot } from 'mobx-state-tree' import { intersection2 } from './range' -import { assembleLocString } from '.' +import { assembleLocStringFast } from '.' import { BlockSet, ContentBlock, @@ -113,7 +113,7 @@ export default function calculateDynamicBlocks( isRightEndOfDisplayedRegion, key: '', } - blockData.key = `${assembleLocString(blockData)}-${regionNumber}${ + blockData.key = `${assembleLocStringFast(blockData)}-${regionNumber}${ reversed ? '-reversed' : '' }` diff --git a/packages/core/util/calculateStaticBlocks.ts b/packages/core/util/calculateStaticBlocks.ts index 5271cbbc06..6105107e46 100644 --- a/packages/core/util/calculateStaticBlocks.ts +++ b/packages/core/util/calculateStaticBlocks.ts @@ -1,5 +1,5 @@ import { isStateTreeNode, getSnapshot, Instance } from 'mobx-state-tree' -import { assembleLocString } from '.' +import { assembleLocStringFast } from '.' import { BlockSet, ContentBlock, @@ -103,7 +103,7 @@ export default function calculateStaticBlocks( isRightEndOfDisplayedRegion, key: '', } - blockData.key = `${assembleLocString(blockData)}-${regionNumber}${ + blockData.key = `${assembleLocStringFast(blockData)}-${regionNumber}${ reversed ? '-reversed' : '' }` diff --git a/packages/core/util/dedupe.ts b/packages/core/util/dedupe.ts new file mode 100644 index 0000000000..c436610961 --- /dev/null +++ b/packages/core/util/dedupe.ts @@ -0,0 +1,19 @@ +type Hasher = (input: T) => string + +// from https://github.com/seriousManual/dedupe/blob/master/LICENSE +export function dedupe(list: T[], hasher: Hasher = JSON.stringify) { + const clone: T[] = [] + const lookup = new Set() + + for (let i = 0; i < list.length; i++) { + const entry = list[i] + const hashed = hasher(entry) + + if (!lookup.has(hashed)) { + clone.push(entry) + lookup.add(hashed) + } + } + + return clone +} diff --git a/packages/core/util/formatFastaStrings.ts b/packages/core/util/formatFastaStrings.ts index 4bc2c592a0..0b948468d1 100644 --- a/packages/core/util/formatFastaStrings.ts +++ b/packages/core/util/formatFastaStrings.ts @@ -7,7 +7,7 @@ export interface SeqChunk { * ref https://stackoverflow.com/a/51506718/2129219 * * @param seqString - string - * @returns formated sequence string + * @returns formatted sequence string */ export function formatFastaLines(seqString: string) { return seqString.replace(/(.{1,80})/g, '$1\n').trimEnd() diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts index 43c4215882..1037a773a5 100644 --- a/packages/core/util/index.ts +++ b/packages/core/util/index.ts @@ -33,6 +33,7 @@ export * from './types' export * from './aborting' export * from './when' export * from './range' +export * from './dedupe' export { SimpleFeature, isFeature } export type { Feature } @@ -263,11 +264,21 @@ export function getContainingDisplay(node: IAnyStateTreeNode) { * ``` */ export function assembleLocString(region: ParsedLocString): string { + return assembleLocStringFast(region, toLocale) +} + +// same as assembleLocString above, but does not perform toLocaleString which +// can slow down the speed of block calculations which use assembleLocString +// for block.key +export function assembleLocStringFast( + region: ParsedLocString, + cb = (n: number): string | number => n, +): string { const { assemblyName, refName, start, end, reversed } = region const assemblyNameString = assemblyName ? `{${assemblyName}}` : '' let startString if (start !== undefined) { - startString = `:${(start + 1).toLocaleString('en-US')}` + startString = `:${cb(start + 1)}` } else if (end !== undefined) { startString = ':1' } else { @@ -275,10 +286,7 @@ export function assembleLocString(region: ParsedLocString): string { } let endString if (end !== undefined) { - endString = - start !== undefined && start + 1 === end - ? '' - : `..${end.toLocaleString('en-US')}` + endString = start !== undefined && start + 1 === end ? '' : `..${cb(end)}` } else { endString = start !== undefined ? '..' : '' } @@ -765,6 +773,12 @@ export function minmax(a: number, b: number) { return [Math.min(a, b), Math.max(a, b)] } +export function shorten(name: string, max = 70, short = 30) { + return name.length > max + ? name.slice(0, short) + '...' + name.slice(-short) + : name +} + export function stringify({ refName, coord, @@ -775,9 +789,7 @@ export function stringify({ oob?: boolean }) { return refName - ? `${refName}:${coord.toLocaleString('en-US')}${ - oob ? ' (out of bounds)' : '' - }` + ? `${shorten(refName)}:${toLocale(coord)}${oob ? ' (out of bounds)' : ''}` : '' } @@ -1180,3 +1192,9 @@ export function measureGridWidth(elements: string[]) { export function getEnv(obj: any) { return getEnvMST<{ pluginManager: PluginManager }>(obj) } + +export function localStorageGetItem(item: string) { + return typeof localStorage !== 'undefined' + ? localStorage.getItem(item) + : undefined +} diff --git a/packages/core/util/io/RemoteFileWithRangeCache.ts b/packages/core/util/io/RemoteFileWithRangeCache.ts index 02a4d01af7..b8a91f5551 100644 --- a/packages/core/util/io/RemoteFileWithRangeCache.ts +++ b/packages/core/util/io/RemoteFileWithRangeCache.ts @@ -72,9 +72,9 @@ export class RemoteFileWithRangeCache extends RemoteFile { const [, start, end] = rangeParse const s = parseInt(start, 10) const e = parseInt(end, 10) - const response = await (globalRangeCache.getRange(url, s, e - s + 1, { + const response = (await globalRangeCache.getRange(url, s, e - s + 1, { signal: init && init.signal, - }) as Promise) + })) as BinaryRangeResponse const { headers } = response return new Response(response.buffer, { status: 206, headers }) } diff --git a/packages/core/util/io/index.ts b/packages/core/util/io/index.ts index a257ea9f7e..4c5b1b8de1 100644 --- a/packages/core/util/io/index.ts +++ b/packages/core/util/io/index.ts @@ -12,7 +12,7 @@ import { FileLocation, LocalPathLocation, BlobLocation, - isAppRootModel, + isRootModelWithInternetAccounts, isUriLocation, AuthNeededError, UriLocation, @@ -109,7 +109,7 @@ function getInternetAccount( ): BaseInternetAccountModel | undefined { const { rootModel } = pluginManager // If there is an appRootModel, use it to find the internetAccount - if (rootModel && isAppRootModel(rootModel)) { + if (rootModel && isRootModelWithInternetAccounts(rootModel)) { return rootModel.findAppropriateInternetAccount(location) } // If there is no appRootModel, but there is pre-auth, create a temporary @@ -135,14 +135,10 @@ function getInternetAccount( // This fetch throws a special error if the response is "401" and includes a // "WWW-Authenticate: Basic" header. This is so downstream code can retry if // needed with HTTP Basic authentication included -async function checkAuthNeededFetch( - url: RequestInfo, - opts?: RequestInit, -): Promise { +async function checkAuthNeededFetch(url: RequestInfo, opts?: RequestInit) { const response = await fetch(url, opts) if (response.status === 401) { - const authHeaders = response.headers.get('WWW-Authenticate') - if (authHeaders && authHeaders.includes('Basic')) { + if (response.headers.get('WWW-Authenticate')?.includes('Basic')) { throw new AuthNeededError( 'Accessing HTTPBasic resource without authentication', url.toString(), diff --git a/packages/core/util/offscreenCanvasUtils.tsx b/packages/core/util/offscreenCanvasUtils.tsx index 3579b8c2cf..9d9830a30a 100644 --- a/packages/core/util/offscreenCanvasUtils.tsx +++ b/packages/core/util/offscreenCanvasUtils.tsx @@ -53,7 +53,7 @@ export async function renderToAbstractCanvas( type: 'image/png', }), ) - : canvas.toDataURL() + : canvas.toDataURL('image/png') } /> ), diff --git a/packages/core/util/stats.ts b/packages/core/util/stats.ts index 5c9412479a..a717901185 100644 --- a/packages/core/util/stats.ts +++ b/packages/core/util/stats.ts @@ -1,5 +1,7 @@ import { Observable } from 'rxjs' import { reduce } from 'rxjs/operators' + +// locals import { NoAssemblyRegion } from './types' import { Feature } from './simpleFeature' @@ -51,10 +53,12 @@ export function calcStdFromSums( } /** - * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered - * @returns - a summary stats object with scoreMean, scoreStdDev, and featureDensity added + * @param stats - a summary stats object with scoreSum, featureCount, + * scoreSumSquares, and basesCovered + * @returns - a summary stats object with + * scoreMean, scoreStdDev, and featureDensity added */ -export function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats { +export function rectifyStats(s: UnrectifiedFeatureStats) { return { ...s, scoreMean: (s.scoreSum || 0) / (s.featureCount || s.basesCovered || 1), @@ -64,11 +68,12 @@ export function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats { s.featureCount || s.basesCovered, ), featureDensity: (s.featureCount || 1) / s.basesCovered, - } + } as FeatureStats } /** * calculates per-base scores for variable width features over a region + * * @param region - object contains start, end * @param features - list of features with start, end, score * @returns array of numeric scores @@ -102,64 +107,59 @@ export function calcPerBaseStats( return scores } -interface Seed { - scoreMin: number - scoreMax: number - scoreSum: number - scoreSumSquares: number - featureCount: number -} - /** * transform a list of scores to summary statistics + * * @param region - object with start, end * @param features - array of features which are possibly summary features * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc */ export async function scoresToStats( region: NoAssemblyRegion, - features: Observable, + feats: Observable, ) { const { start, end } = region + const seed = { + scoreMin: Number.MAX_VALUE, + scoreMax: Number.MIN_VALUE, + scoreSum: 0, + scoreSumSquares: 0, + featureCount: 0, + } + let found = false const { scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount } = - await features + await feats .pipe( - reduce( - (seed: Seed, f: Feature) => { - const s = f.get('score') - const summary = f.get('summary') - const { scoreMax, scoreMin } = seed - seed.scoreMax = Math.max(scoreMax, summary ? f.get('maxScore') : s) - seed.scoreMin = Math.min(scoreMin, summary ? f.get('minScore') : s) - seed.scoreSum += s - seed.scoreSumSquares += s * s - seed.featureCount += 1 + reduce((acc, f) => { + const s = f.get('score') + const summary = f.get('summary') + const { scoreMax, scoreMin } = acc + acc.scoreMax = Math.max(scoreMax, summary ? f.get('maxScore') : s) + acc.scoreMin = Math.min(scoreMin, summary ? f.get('minScore') : s) + acc.scoreSum += s + acc.scoreSumSquares += s * s + acc.featureCount += 1 + found = true - return seed - }, - { - scoreMin: Number.MAX_VALUE, - scoreMax: Number.MIN_VALUE, - scoreSum: 0, - scoreSumSquares: 0, - featureCount: 0, - }, - ), + return acc + }, seed), ) .toPromise() - return rectifyStats({ - scoreMax, - scoreMin, - scoreSum, - scoreSumSquares, - featureCount, - basesCovered: end - start + 1, - }) + return found + ? rectifyStats({ + scoreMax, + scoreMin, + scoreSum, + scoreSumSquares, + featureCount, + basesCovered: end - start + 1, + }) + : blankStats() } -export function blankStats(): FeatureStats { +export function blankStats() { return { scoreMin: 0, scoreMax: 0, @@ -170,5 +170,5 @@ export function blankStats(): FeatureStats { featureCount: 0, featureDensity: 0, basesCovered: 0, - } + } as FeatureStats } diff --git a/packages/core/util/tracks.ts b/packages/core/util/tracks.ts index 116d93eae8..898d6558a8 100644 --- a/packages/core/util/tracks.ts +++ b/packages/core/util/tracks.ts @@ -105,7 +105,7 @@ export function storeBlobLocation(location: PreFileLocation) { * creates a new location from the provided location including the appropriate suffix and location type * @param location - the FileLocation * @param suffix - the file suffix (e.g. .bam) - * @returns the constructed location object from the provided prameters + * @returns the constructed location object from the provided parameters */ export function makeIndex(location: FileLocation, suffix: string) { if ('uri' in location) { diff --git a/packages/core/util/types/index.ts b/packages/core/util/types/index.ts index 72cd247300..473bf47da0 100644 --- a/packages/core/util/types/index.ts +++ b/packages/core/util/types/index.ts @@ -234,7 +234,9 @@ export interface AbstractViewModel { id: string type: string width: number + minimized: boolean setWidth(width: number): void + setMinimized(flag: boolean): void displayName: string | undefined setDisplayName: (arg: string) => void menuItems: () => MenuItem[] @@ -322,6 +324,24 @@ export function isAppRootModel(thing: unknown): thing is AppRootModel { ) } +export interface RootModelWithInternetAccounts extends AbstractRootModel { + internetAccounts: BaseInternetAccountModel[] + findAppropriateInternetAccount( + location: UriLocation, + ): BaseInternetAccountModel | undefined +} + +export function isRootModelWithInternetAccounts( + thing: unknown, +): thing is RootModelWithInternetAccounts { + return ( + typeof thing === 'object' && + thing !== null && + 'internetAccounts' in thing && + 'findAppropriateInternetAccount' in thing + ) +} + /** a root model that manages global menus */ export interface AbstractMenuManager { appendMenu(menuName: string): void @@ -365,7 +385,12 @@ export interface LocalPathLocation export interface UriLocation extends SnapshotIn {} export function isUriLocation(location: unknown): location is UriLocation { - return typeof location === 'object' && location !== null && 'uri' in location + return ( + typeof location === 'object' && + location !== null && + 'uri' in location && + !!location.uri + ) } export class AuthNeededError extends Error { constructor(public message: string, public url: string) { diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index 0541b50fbf..8561c5653b 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -36,21 +36,20 @@ "test": "cd ../..; jest packages/text-indexing", "clean": "rimraf dist esm *.tsbuildinfo", "prebuild": "yarn clean", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { "@babel/runtime": "^7.16.3", - "ixixx": "^1.0.19", + "ixixx": "^2.0.1", "node-fetch": "^2.6.0" }, "peerDependencies": { - "mobx": "^5.0.0", - "mobx-react": "^6.0.0", + "mobx": "^6.0.0", + "mobx-react": "^7.0.0", "mobx-state-tree": "^5.0.0", - "prop-types": "^15.0.0", "react": "^17.0.0", "react-dom": "^17.0.0", "rxjs": "^6.0.0" diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 1ca014c8cf..9cc2ec264d 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/alignments", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", @@ -40,6 +40,8 @@ "@gmod/bam": "^1.1.15", "@gmod/cram": "^1.7.1", "@mui/icons-material": "^5.0.1", + "canvas2svg": "^1.0.16", + "clone": "^2.1.2", "color": "^3.1.2", "copy-to-clipboard": "^3.3.1", "fast-deep-equal": "^3.1.3", @@ -53,10 +55,9 @@ "mobx": "^6.0.0", "mobx-react": "^7.0.0", "mobx-state-tree": "^5.0.0", - "prop-types": "^15.0.0", "react": ">=16.8.0", "rxjs": "^6.0.0", - "tss-react": "^3.0.0" + "tss-react": "^4.0.0" }, "publishConfig": { "access": "public" diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx b/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx index 69e36fa894..b7a3a3db1e 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +++ b/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx @@ -11,20 +11,21 @@ import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' import { getSession } from '@jbrowse/core/util' import copy from 'copy-to-clipboard' +import clone from 'clone' import { FeatureDetails, BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' -import { parseCigar } from '../BamAdapter/MismatchParser' +import { parseCigar } from '../MismatchParser' -const useStyles = makeStyles()(() => ({ +const useStyles = makeStyles()({ compact: { paddingRight: 0, paddingTop: 0, paddingBottom: 0, }, -})) +}) const omit = ['clipPos', 'flags'] @@ -144,12 +145,12 @@ function SupplementaryAlignments(props: { tag: string; model: any }) { return (
  • { + onClick={async event => { event.preventDefault() const { view } = model try { if (view) { - view.navToLocString(locString) + await view.navToLocString(locString) } else { throw new Error( 'No view associated with this view anymore', @@ -177,17 +178,15 @@ function PairLink({ locString, model }: { locString: string; model: any }) { const session = getSession(model) return ( { + onClick={async () => { const { view } = model + if (!view) { + throw new Error( + 'No view associated with this feature detail panel anymore', + ) + } try { - if (view) { - view.navToLocString(locString) - } else { - session.notify( - 'No view associated with this feature detail panel anymore', - 'warning', - ) - } + await view.navToLocString(locString) } catch (e) { console.error(e) session.notify(`${e}`) @@ -203,7 +202,7 @@ function PairLink({ locString, model }: { locString: string; model: any }) { // eslint-disable-next-line @typescript-eslint/no-explicit-any function AlignmentFeatureDetails(props: { model: any }) { const { model } = props - const feat = JSON.parse(JSON.stringify(model.featureData)) + const feat = clone(model.featureData) const SA = (feat.tags && feat.tags.SA) || feat.SA return ( @@ -211,7 +210,7 @@ function AlignmentFeatureDetails(props: { model: any }) { {...props} omit={omit} feature={feat} - formatter={(value: unknown, key: string) => { + formatter={(value, key) => { return key === 'next_segment_position' ? ( ) : ( @@ -220,7 +219,9 @@ function AlignmentFeatureDetails(props: { model: any }) { }} /> {SA ? : null} - + {feat.flags !== undefined ? ( + + ) : null} ) } diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap b/plugins/alignments/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap index 67ffe79c66..7aebda6938 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +++ b/plugins/alignments/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap @@ -29,7 +29,7 @@ exports[`open up a widget 1`] = ` >

    Position
    -
    - ctgA:3..102 (+) -
    + ctgA:3..102 (+)
    Name
    ctgA_3_555_0:0:0_2:0:0_102d @@ -95,15 +93,15 @@ exports[`open up a widget 1`] = `
    Length
    100 @@ -111,15 +109,15 @@ exports[`open up a widget 1`] = `
    Type
    match @@ -135,16 +133,16 @@ exports[`open up a widget 1`] = ` Attributes

    seq
    TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG @@ -152,16 +150,16 @@ exports[`open up a widget 1`] = `
    score
    37 @@ -169,16 +167,16 @@ exports[`open up a widget 1`] = `
    qual
    MQ
    37 @@ -213,16 +211,16 @@ exports[`open up a widget 1`] = `
    CIGAR
    100M @@ -230,16 +228,16 @@ exports[`open up a widget 1`] = `
    length_on_ref
    100 @@ -247,16 +245,16 @@ exports[`open up a widget 1`] = `
    template_length
    0 @@ -264,16 +262,16 @@ exports[`open up a widget 1`] = `
    seq_length
    100 @@ -281,7 +279,7 @@ exports[`open up a widget 1`] = `
    -
    -
    -
    - - - Flags - -
    -
    - -
    -
    -
    -
    -
    -
    -
    -
    - - - - - - - - - - - - -
    -
    -
    -
    -
    -
    -
    `; diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/index.test.js b/plugins/alignments/src/AlignmentsFeatureDetail/index.test.js index 504ca41018..0a039c0cc3 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/index.test.js +++ b/plugins/alignments/src/AlignmentsFeatureDetail/index.test.js @@ -11,14 +11,16 @@ test('open up a widget', () => { const pluginManager = new PluginManager([]) const Session = types.model({ - pluginManager: types.optional(types.frozen(), {}), rpcManager: types.optional(types.frozen(), {}), configuration: ConfigurationSchema('test', {}), widget: stateModelFactory(pluginManager), }) - const session = Session.create({ - widget: { type: 'AlignmentsFeatureWidget' }, - }) + const session = Session.create( + { + widget: { type: 'AlignmentsFeatureWidget' }, + }, + { pluginManager }, + ) session.widget.setFeatureData({ seq: 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG', start: 2, diff --git a/plugins/alignments/src/AlignmentsTrack/index.ts b/plugins/alignments/src/AlignmentsTrack/index.ts index 75b0ef6657..3e0cb2f397 100644 --- a/plugins/alignments/src/AlignmentsTrack/index.ts +++ b/plugins/alignments/src/AlignmentsTrack/index.ts @@ -29,6 +29,7 @@ export default function register(pm: PluginManager) { const configSchema = configSchemaFactory(pm) const track = new TrackType({ name: 'AlignmentsTrack', + displayName: 'Alignments track', configSchema, stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema), }) diff --git a/plugins/alignments/src/BamAdapter/BamAdapter.ts b/plugins/alignments/src/BamAdapter/BamAdapter.ts index d35c2107d0..8a97a6beff 100644 --- a/plugins/alignments/src/BamAdapter/BamAdapter.ts +++ b/plugins/alignments/src/BamAdapter/BamAdapter.ts @@ -4,11 +4,12 @@ import { BaseOptions, } from '@jbrowse/core/data_adapters/BaseAdapter' import { Region } from '@jbrowse/core/util/types' -import { bytesForRegions, updateStatus } from '@jbrowse/core/util' +import { bytesForRegions, updateStatus, Feature } from '@jbrowse/core/util' import { openLocation } from '@jbrowse/core/util/io' import { ObservableCreate } from '@jbrowse/core/util/rxjs' -import { Feature } from '@jbrowse/core/util/simpleFeature' import { toArray } from 'rxjs/operators' + +// locals import BamSlightlyLazyFeature from './BamSlightlyLazyFeature' interface Header { diff --git a/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts b/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts index b97a405b01..52c6f252b1 100644 --- a/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts +++ b/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts @@ -4,8 +4,9 @@ import { SimpleFeatureSerialized, } from '@jbrowse/core/util/simpleFeature' import { BamRecord } from '@gmod/bam' -import { getMismatches } from './MismatchParser' +// locals +import { getClip, getMismatches } from '../MismatchParser' import BamAdapter from './BamAdapter' export default class BamSlightlyLazyFeature implements Feature { @@ -41,23 +42,21 @@ export default class BamSlightlyLazyFeature implements Feature { return this.record.isPaired() ? this.record.getPairOrientation() : undefined } - _get_next_seq_id() { - return this.record._next_refid() - } - - _get_seq_id() { - // @ts-ignore - return this.record._refID + _get_next_ref() { + return this.record.isPaired() + ? this.adapter.refIdToName(this.record._next_refid()) + : undefined } - _get_next_refName() { - return this.adapter.refIdToName(this.record._next_refid()) + _get_next_pos() { + return this.record.isPaired() ? this.record._next_pos() : undefined } _get_next_segment_position() { - const { record, adapter } = this - return record.isPaired() - ? `${adapter.refIdToName(record._next_refid())}:${record._next_pos() + 1}` + return this.record.isPaired() + ? `${this.adapter.refIdToName(this.record._next_refid())}:${ + this.record._next_pos() + 1 + }` : undefined } @@ -83,9 +82,7 @@ export default class BamSlightlyLazyFeature implements Feature { prop => prop.startsWith('_get_') && prop !== '_get_mismatches' && - prop !== '_get_tags' && - prop !== '_get_next_seq_id' && - prop !== '_get_seq_id', + prop !== '_get_tags', ) .map(methodName => methodName.replace('_get_', '')) .concat(this.record._tags()), @@ -147,8 +144,6 @@ export default class BamSlightlyLazyFeature implements Feature { _get_clipPos() { const cigar = this.get('CIGAR') || '' - return this.get('strand') === -1 - ? +(cigar.match(/(\d+)[SH]$/) || [])[1] || 0 - : +(cigar.match(/^(\d+)([SH])/) || [])[1] || 0 + return getClip(cigar, this.get('strand')) } } diff --git a/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap b/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap index b5d0d43c87..1529ea1f7d 100644 --- a/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap +++ b/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap @@ -1,8 +1,8 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`adapter can fetch features from volvox.bam 1`] = ` -Array [ - Object { +[ + { "CIGAR": "100M", "MD": "22A32C15T12A15", "MQ": 37, @@ -29,7 +29,7 @@ Array [ "type": "match", "uniqueId": "test-10158054", }, - Object { + { "CIGAR": "100M", "MD": "66G33", "MQ": 37, @@ -56,7 +56,7 @@ Array [ "type": "match", "uniqueId": "test-10158322", }, - Object { + { "CIGAR": "100M", "MD": "25G23C1C24A23", "MQ": 37, @@ -83,7 +83,7 @@ Array [ "type": "match", "uniqueId": "test-10158581", }, - Object { + { "CIGAR": "100M", "MD": "42C57", "MQ": 37, @@ -110,7 +110,7 @@ Array [ "type": "match", "uniqueId": "test-10158847", }, - Object { + { "CIGAR": "100M", "MD": "49G11G38", "MQ": 37, @@ -137,7 +137,7 @@ Array [ "type": "match", "uniqueId": "test-12607066", }, - Object { + { "CIGAR": "100M", "MD": "22T13C63", "MQ": 37, @@ -164,7 +164,7 @@ Array [ "type": "match", "uniqueId": "test-12607328", }, - Object { + { "CIGAR": "100M", "MD": "35C3G60", "MQ": 37, @@ -191,7 +191,7 @@ Array [ "type": "match", "uniqueId": "test-12607590", }, - Object { + { "CIGAR": "100M", "MD": "100", "MQ": 37, @@ -218,7 +218,7 @@ Array [ "type": "match", "uniqueId": "test-12607851", }, - Object { + { "CIGAR": "100M", "MD": "52G43A3", "MQ": 37, @@ -245,7 +245,7 @@ Array [ "type": "match", "uniqueId": "test-12608107", }, - Object { + { "CIGAR": "100M", "MD": "92C7", "MQ": 37, @@ -276,825 +276,825 @@ Array [ `; exports[`test usage of BamSlightlyLazyFeature for extended CIGAR 1`] = ` -Array [ - Object { +[ + { "base": "S2666", "cliplen": 2666, "length": 1, "start": 0, "type": "softclip", }, - Object { + { "base": "*", "length": 1, "start": 33, "type": "deletion", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 40, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 75, "type": "deletion", }, - Object { + { "base": "*", "length": 1, "start": 90, "type": "deletion", }, - Object { + { "base": "1", "length": 0, "start": 108, "type": "insertion", }, - Object { + { "base": "*", "length": 1, "start": 132, "type": "deletion", }, - Object { + { "base": "*", "length": 1, "start": 146, "type": "deletion", }, - Object { + { "base": "3", "length": 0, "start": 177, "type": "insertion", }, - Object { + { "base": "1", "length": 0, "start": 209, "type": "insertion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 216, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 222, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 228, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 230, "type": "deletion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 235, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 241, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 247, "type": "deletion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 248, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 254, "type": "deletion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 255, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 263, "type": "deletion", }, - Object { + { "base": "1", "length": 0, "start": 284, "type": "insertion", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 289, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 290, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 293, "type": "deletion", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 294, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 296, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 302, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 308, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 314, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 320, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 326, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 329, "type": "deletion", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 333, "type": "mismatch", }, - Object { + { "base": "1", "length": 0, "start": 339, "type": "insertion", }, - Object { + { "base": "1", "length": 0, "start": 345, "type": "insertion", }, - Object { + { "base": "2", "length": 0, "start": 352, "type": "insertion", }, - Object { + { "base": "*", "length": 1, "start": 375, "type": "deletion", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 384, "type": "mismatch", }, - Object { + { "base": "67", "length": 0, "start": 403, "type": "insertion", }, - Object { + { "base": "1", "length": 0, "start": 427, "type": "insertion", }, - Object { + { "base": "1", "length": 0, "start": 433, "type": "insertion", }, - Object { + { "base": "*", "length": 1, "start": 439, "type": "deletion", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 491, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 621, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 622, "type": "mismatch", }, - Object { + { "base": "7", "length": 0, "start": 626, "type": "insertion", }, - Object { + { "base": "1", "length": 0, "start": 627, "type": "insertion", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 800, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 802, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 803, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 804, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 807, "type": "deletion", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 808, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 809, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 814, "type": "mismatch", }, - Object { + { "base": "4", "length": 0, "start": 818, "type": "insertion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 820, "type": "mismatch", }, - Object { + { "base": "4", "length": 0, "start": 822, "type": "insertion", }, - Object { + { "base": "8", "length": 0, "start": 828, "type": "insertion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 828, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 883, "type": "mismatch", }, - Object { + { "base": "47", "length": 0, "start": 889, "type": "insertion", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 896, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 926, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 930, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 933, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 935, "type": "mismatch", }, - Object { + { "base": "1", "length": 0, "start": 968, "type": "insertion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 1001, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 1016, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 39, "start": 1018, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 1034, "type": "mismatch", }, - Object { + { "base": "1", "length": 0, "start": 1063, "type": "insertion", }, - Object { + { "base": "2", "length": 0, "start": 1068, "type": "insertion", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 1074, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 1078, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 1112, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 1133, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 1153, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 1166, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 1390, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 1408, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 1456, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 1507, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 1541, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 1564, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 1771, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 2197, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 2382, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 2782, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 3115, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 3117, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 3301, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 3326, "type": "mismatch", }, - Object { + { "base": "*", "length": 2, "start": 3656, "type": "deletion", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 3895, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 3957, "type": "deletion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 3979, "type": "mismatch", }, - Object { + { "base": "5", "length": 0, "start": 4455, "type": "insertion", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 4672, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 4698, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 4906, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 4929, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 5117, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 5210, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 5273, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 5816, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 5819, "type": "mismatch", }, - Object { + { "base": "1", "length": 0, "start": 5903, "type": "insertion", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 5905, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 5921, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 5955, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 6067, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 6102, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 6297, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 6377, "type": "mismatch", }, - Object { + { "base": "T", "length": 1, "qual": 93, "start": 6533, "type": "mismatch", }, - Object { + { "base": "A", "length": 1, "qual": 93, "start": 6570, "type": "mismatch", }, - Object { + { "base": "C", "length": 1, "qual": 93, "start": 6806, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 6808, "type": "mismatch", }, - Object { + { "base": "G", "length": 1, "qual": 93, "start": 6855, "type": "mismatch", }, - Object { + { "base": "S1", "cliplen": 1, "length": 1, diff --git a/plugins/alignments/src/BamAdapter/configSchema.ts b/plugins/alignments/src/BamAdapter/configSchema.ts index daf8895dc1..376506f1f7 100644 --- a/plugins/alignments/src/BamAdapter/configSchema.ts +++ b/plugins/alignments/src/BamAdapter/configSchema.ts @@ -44,7 +44,7 @@ const configSchema = ConfigurationSchema( fetchSizeLimit: { type: 'number', description: - 'used to determine when to display a warning to the user that too much data will be fetched', + 'size to fetch in bytes over which to display a warning to the user that too much data will be fetched', defaultValue: 5_000_000, }, /** diff --git a/plugins/alignments/src/BamAdapter/index.ts b/plugins/alignments/src/BamAdapter/index.ts index 2ddd04e95c..dd797972b2 100644 --- a/plugins/alignments/src/BamAdapter/index.ts +++ b/plugins/alignments/src/BamAdapter/index.ts @@ -3,12 +3,12 @@ import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' import configSchema from './configSchema' export default (pluginManager: PluginManager) => { - pluginManager.addAdapterType( - () => - new AdapterType({ - name: 'BamAdapter', - configSchema, - getAdapterClass: () => import('./BamAdapter').then(r => r.default), - }), - ) + pluginManager.addAdapterType(() => { + return new AdapterType({ + name: 'BamAdapter', + displayName: 'BAM adapter', + configSchema, + getAdapterClass: () => import('./BamAdapter').then(r => r.default), + }) + }) } diff --git a/plugins/alignments/src/CombinationTest.test.ts b/plugins/alignments/src/CombinationTest.test.ts new file mode 100644 index 0000000000..e0c225fe27 --- /dev/null +++ b/plugins/alignments/src/CombinationTest.test.ts @@ -0,0 +1,107 @@ +import PluginManager from '@jbrowse/core/PluginManager' +import { toArray } from 'rxjs/operators' +import { LocalFile } from 'generic-filehandle' +import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache' + +import CramAdapter from './CramAdapter/CramAdapter' +import BamAdapter from './BamAdapter/BamAdapter' +import { SequenceAdapter } from './CramAdapter/CramTestAdapters' + +import cramConfigSchema from './CramAdapter/configSchema' +import bamConfigSchema from './BamAdapter/configSchema' + +const pluginManager = new PluginManager() + +const getVolvoxSequenceSubAdapter: getSubAdapterType = async () => { + return { + dataAdapter: new SequenceAdapter( + new LocalFile(require.resolve('../test_data/volvox.fa')), + ), + sessionIds: new Set(), + } +} + +async function getFeats(f1: string, f2: string) { + const cramAdapter = new CramAdapter( + cramConfigSchema.create({ + cramLocation: { + localPath: require.resolve(f1), + }, + craiLocation: { + localPath: require.resolve(f1 + '.crai'), + }, + }), + getVolvoxSequenceSubAdapter, + pluginManager, + ) + + const bamAdapter = new BamAdapter( + bamConfigSchema.create({ + bamLocation: { + localPath: require.resolve(f2), + }, + index: { + location: { + localPath: require.resolve(f2 + '.bai'), + }, + }, + }), + ) + const query = { + assemblyName: 'volvox', + refName: 'ctgA', + start: 1, + end: 10200, + } + const bamFeatures = bamAdapter.getFeatures(query) + const cramFeatures = cramAdapter.getFeatures(query) + const bamFeaturesArray = await bamFeatures.pipe(toArray()).toPromise() + const cramFeaturesArray = await cramFeatures.pipe(toArray()).toPromise() + return { bamFeaturesArray, cramFeaturesArray } +} + +type M = { start: number } + +async function cigarCheck(f: string) { + const { cramFeaturesArray, bamFeaturesArray } = await getFeats( + `../test_data/${f}.cram`, + `../test_data/${f}.bam`, + ) + const cramMap = Object.fromEntries( + cramFeaturesArray.map(f => [f.get('name'), f.get('CIGAR')]), + ) + const bamMap = Object.fromEntries( + bamFeaturesArray.map(f => [f.get('name'), f.get('CIGAR')]), + ) + expect(bamMap).toEqual(cramMap) +} + +async function mismatchesCheck(f: string) { + const { cramFeaturesArray, bamFeaturesArray } = await getFeats( + `../test_data/${f}.cram`, + `../test_data/${f}.bam`, + ) + const cramMap = Object.fromEntries( + cramFeaturesArray.map(f => [ + f.get('name'), + f.get('mismatches').sort((a: M, b: M) => b.start - a.start), + ]), + ) + const bamMap = Object.fromEntries( + bamFeaturesArray.map(f => [ + f.get('name'), + f.get('mismatches').sort((a: M, b: M) => b.start - a.start), + ]), + ) + expect(bamMap).toEqual(cramMap) +} + +test('match CIGAR across file types', async () => { + await cigarCheck('volvox-sorted') + await cigarCheck('volvox-long-reads.fastq.sorted') +}) + +test('mismatches same across file types', async () => { + await mismatchesCheck('volvox-sorted') + await mismatchesCheck('volvox-long-reads.fastq.sorted') +}) diff --git a/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts b/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts index a0b9a6f7fd..c711a23787 100644 --- a/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts +++ b/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts @@ -4,23 +4,14 @@ import { SimpleFeatureSerialized, } from '@jbrowse/core/util/simpleFeature' import { CramRecord } from '@gmod/cram' -import CramAdapter from './CramAdapter' -export interface Mismatch { - qual?: number - start: number - length: number - type: string - base: string - altbase?: string - seq?: string - cliplen?: number -} +// locals +import CramAdapter from './CramAdapter' +import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util' export default class CramSlightlyLazyFeature implements Feature { // uses parameter properties to automatically create fields on the class // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties - constructor(private record: CramRecord, private _store: CramAdapter) {} _get_name() { @@ -68,12 +59,8 @@ export default class CramSlightlyLazyFeature implements Feature { return this.record.qualityScores } - _get_seq_id() { - return this._store.refIdToName(this.record.sequenceId) - } - _get_refName() { - return this._get_seq_id() + return this._store.refIdToName(this.record.sequenceId) } _get_is_paired() { @@ -88,16 +75,12 @@ export default class CramSlightlyLazyFeature implements Feature { return this.record.templateLength || this.record.templateSize } - _get_next_seq_id() { + _get_next_ref() { return this.record.mate ? this._store.refIdToName(this.record.mate.sequenceId) : undefined } - _get_next_pos() { - return this.record.mate ? this.record.mate.alignmentStart : undefined - } - _get_next_segment_position() { return this.record.mate ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${ @@ -106,6 +89,10 @@ export default class CramSlightlyLazyFeature implements Feature { : undefined } + _get_next_pos() { + return this.record.mate?.alignmentStart + } + _get_tags() { const RG = this._read_group_id() const { tags } = this.record @@ -119,122 +106,16 @@ export default class CramSlightlyLazyFeature implements Feature { // generate a CIGAR, based on code from jkbonfield _get_CIGAR() { - let seq = '' - let cigar = '' - let op = 'M' - let oplen = 0 - if (!this.record._refRegion) { - return '' - } - - // not sure I should access these, but... - const ref = this.record._refRegion.seq - const refStart = this.record._refRegion.start - let last_pos = this.record.alignmentStart - let sublen = 0 - if (typeof this.record.readFeatures !== 'undefined') { - let insLen = 0 - // @ts-ignore - for (let i = 0; i < this.record.readFeatures.length; i++) { - const { code, refPos, sub, data } = this.record.readFeatures[i] - sublen = refPos - last_pos - seq += ref.substring(last_pos - refStart, refPos - refStart) - last_pos = refPos - - if (oplen && op !== 'M') { - cigar += oplen + op - oplen = 0 - } - if (sublen) { - op = 'M' - oplen += sublen - } - if (insLen > 0 && code !== 'i') { - cigar += `${insLen}I` - insLen = 0 - } - - if (code === 'b') { - // An array of bases stored verbatim - const ret = data.split(',') - const added = String.fromCharCode(...ret) - seq += added - last_pos += added.length - oplen += added.length - } else if (code === 'B') { - // Single base (+ qual score) - seq += sub - last_pos++ - oplen++ - } else if (code === 'X') { - // Substitution - seq += sub - last_pos++ - oplen++ - } else if (code === 'D' || code === 'N') { - // Deletion or Ref Skip - last_pos += data - if (oplen) { - cigar += oplen + op - } - cigar += data + code - oplen = 0 - } else if (code === 'I' || code === 'S') { - // Insertion or soft-clip - seq += data - if (oplen) { - cigar += oplen + op - } - cigar += data.length + code - oplen = 0 - } else if (code === 'i') { - // Single base insertion - // seq += data - if (oplen) { - cigar += oplen + op - } - insLen++ - oplen = 0 - } else if (code === 'P') { - // Padding - if (oplen) { - cigar += oplen + op - } - cigar += `${data}P` - } else if (code === 'H') { - // Hard clip - if (oplen) { - cigar += oplen + op - } - cigar += `${data}H` - oplen = 0 - } // else q or Q - } - } else { - sublen = this.record.readLength - seq.length - } - if (seq.length !== this.record.readLength) { - sublen = this.record.readLength - seq.length - seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen) - - if (oplen && op !== 'M') { - cigar += oplen + op - oplen = 0 - } - op = 'M' - oplen += sublen - } - if (oplen) { - cigar += oplen + op - } - return cigar + return readFeaturesToCIGAR( + this.record.readFeatures, + this.record.alignmentStart, + this.record.readLength, + this.record._refRegion, + ) } tags() { - const properties = Object.getOwnPropertyNames( - CramSlightlyLazyFeature.prototype, - ) - return properties + return Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype) .filter( prop => prop.startsWith('_get_') && @@ -258,15 +139,15 @@ export default class CramSlightlyLazyFeature implements Feature { return undefined } - parent(): undefined | Feature { + parent() { return undefined } - children(): undefined | Feature[] { + children() { return undefined } - set(): void {} + set() {} pairedFeature() { return false @@ -298,102 +179,10 @@ export default class CramSlightlyLazyFeature implements Feature { } } - _get_mismatches(): Mismatch[] { - const readFeatures = this.get('cram_read_features') + _get_mismatches() { + const readFeatures = this.record.readFeatures const qual = this.qualRaw() - if (!readFeatures) { - return [] - } const start = this.get('start') - const mismatches: Mismatch[] = new Array(readFeatures.length) - let j = 0 - let insLen = 0 - - let refPos = 0 - for (let i = 0; i < readFeatures.length; i++) { - const f = readFeatures[i] - const { code, pos, data, sub, ref } = f - if (insLen > 0 && code !== 'i') { - mismatches[j++] = { - start: refPos, - type: 'insertion', - base: `${insLen}`, - length: 0, - } - insLen = 0 - } - refPos = f.refPos - 1 - start - - if (code === 'X') { - // substitution - mismatches[j++] = { - start: refPos, - length: 1, - base: sub, - qual: qual?.[pos], - altbase: ref, - type: 'mismatch', - } - } else if (code === 'I') { - // insertion - mismatches[j++] = { - start: refPos, - type: 'insertion', - base: `${data.length}`, - length: 0, - } - } else if (code === 'N') { - // reference skip - mismatches[j++] = { - type: 'skip', - length: data, - start: refPos, - base: 'N', - } - } else if (code === 'S') { - // soft clip - const len = data.length - mismatches[j++] = { - start: refPos, - type: 'softclip', - base: `S${len}`, - cliplen: len, - length: 1, - } - } else if (code === 'P') { - // padding - } else if (code === 'H') { - // hard clip - const len = data - mismatches[j++] = { - start: refPos, - type: 'hardclip', - base: `H${len}`, - cliplen: len, - length: 1, - } - } else if (code === 'D') { - // deletion - mismatches[j++] = { - type: 'deletion', - length: data, - start: refPos, - base: '*', - } - } else if (code === 'b') { - // stretch of bases - } else if (code === 'q') { - // stretch of qual scores - } else if (code === 'B') { - // a pair of [base, qual] - } else if (code === 'i') { - // single-base insertion - // insertion - insLen++ - } else if (code === 'Q') { - // single quality value - } - } - return mismatches.slice(0, j) + return readFeaturesToMismatches(readFeatures, start, qual) } } diff --git a/plugins/alignments/src/CramAdapter/CramTestAdapters.ts b/plugins/alignments/src/CramAdapter/CramTestAdapters.ts index 1ed29083d9..2e1796c175 100644 --- a/plugins/alignments/src/CramAdapter/CramTestAdapters.ts +++ b/plugins/alignments/src/CramAdapter/CramTestAdapters.ts @@ -37,7 +37,7 @@ export class FetchableSmallFasta { if (!entry) { throw new Error(`no sequence with id ${id} exists`) } - return entry.sequence.substr(start - 1, length) + return entry.sequence.slice(start, start + length) } async getSequenceList() { @@ -89,6 +89,7 @@ export class SequenceAdapter extends BaseFeatureDataAdapter { ) observer.complete() }) + .catch(e => observer.error(e)) return { unsubscribe: () => {} } }) } diff --git a/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap b/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap index 7630307da2..732da67d5a 100644 --- a/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +++ b/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap @@ -1,8 +1,8 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`adapter can fetch features from volvox-sorted.cram 1`] = ` -Array [ - Object { +[ + { "CIGAR": "100M", "clipPos": 0, "end": 5540, @@ -12,11 +12,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "ATACACTGGTTCGGAGACGGTTGATGACGAGCGCGCTATATGTCGGCATCTGCGCGCCATGAGCGGCCGCTATCCGGCGGCACGCATAATATAGTGCAAG", - "seq_id": "ctgA", + "seq": "TACACTGGTTCGGAGACGGTTCGTGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGACCGGCGGCACGACTAATATAGTGCAAGA", "start": 5440, "strand": -1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -28,7 +27,7 @@ Array [ "type": "match", "uniqueId": "test-1618", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5541, @@ -38,11 +37,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "TACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCGGCTGTCCGGCGGCACGAATAATATAGTGCAAGA", - "seq_id": "ctgA", + "seq": "ACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCCCTGTCCGGCGGCACGAATAATATAGTGCAAGAA", "start": 5441, "strand": -1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -54,7 +52,7 @@ Array [ "type": "match", "uniqueId": "test-1619", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5544, @@ -64,11 +62,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "ACTGGTTCGGAGACGGTTCATGACGGGCGCGCTATATGTCGGCATCTGCTCGCCATGAGCGGCCGCTGTCCGGCGGTACGAATAATATAGTGCAAGAAAA", - "seq_id": "ctgA", + "seq": "CTGGTTCGGAGACGGTTCATGACGACCGCGCTATATGTCGGCATCTGCGTCGCATGAGCGGCCGCTGTCCGGCGGCTCGAATAATATAGTGCAAGAAAAA", "start": 5444, "strand": 1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -80,7 +77,7 @@ Array [ "type": "match", "uniqueId": "test-1620", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5553, @@ -90,11 +87,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "GAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCGCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGAC", - "seq_id": "ctgA", + "seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT", "start": 5453, "strand": 1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -106,7 +102,7 @@ Array [ "type": "match", "uniqueId": "test-1621", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5554, @@ -116,11 +112,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGGGGCCGCTGTCCAGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT", - "seq_id": "ctgA", + "seq": "GACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCCGCCGCTGTCCGACGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTA", "start": 5454, "strand": 1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -132,7 +127,7 @@ Array [ "type": "match", "uniqueId": "test-1622", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5559, @@ -142,11 +137,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "GTTCATGACGAGCGCGCTATATATCGGCATCTGCGCGCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGT", - "seq_id": "ctgA", + "seq": "TTCATGACGAGCGCGCTATATGACGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT", "start": 5459, "strand": -1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -158,7 +152,7 @@ Array [ "type": "match", "uniqueId": "test-1623", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5560, @@ -168,11 +162,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "TTCATGACGAGCGCGCTATATGTCGGCATCTGCGCGCCACGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT", - "seq_id": "ctgA", + "seq": "TCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATCAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTA", "start": 5460, "strand": 1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -184,7 +177,7 @@ Array [ "type": "match", "uniqueId": "test-1624", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5568, @@ -194,11 +187,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "GAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGA", - "seq_id": "ctgA", + "seq": "AGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGAT", "start": 5468, "strand": 1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -210,7 +202,7 @@ Array [ "type": "match", "uniqueId": "test-1625", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5594, @@ -220,11 +212,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "CCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACTGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCAAAC", - "seq_id": "ctgA", + "seq": "CCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCTAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCTCACA", "start": 5494, "strand": -1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, @@ -236,7 +227,7 @@ Array [ "type": "match", "uniqueId": "test-1626", }, - Object { + { "CIGAR": "100M", "clipPos": 0, "end": 5596, @@ -246,11 +237,10 @@ Array [ "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17", "refName": "ctgA", "score": 37, - "seq": "CCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATCCTAACAG", - "seq_id": "ctgA", + "seq": "CATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTGTAACAGG", "start": 5496, "strand": 1, - "tags": Object { + "tags": { "X0": 1, "X1": 0, "XG": 0, diff --git a/plugins/alignments/src/CramAdapter/__snapshots__/util.test.ts.snap b/plugins/alignments/src/CramAdapter/__snapshots__/util.test.ts.snap new file mode 100644 index 0000000000..ba5c9636c5 --- /dev/null +++ b/plugins/alignments/src/CramAdapter/__snapshots__/util.test.ts.snap @@ -0,0 +1,14 @@ +// Jest Snapshot v1, https://goo.gl/fbAQLP + +exports[`cram read features mismatches 1`] = ` +[ + { + "base": "1", + "length": 0, + "start": 24, + "type": "insertion", + }, +] +`; + +exports[`cram read features to CIGAR 1`] = `"24M1I75M"`; diff --git a/plugins/alignments/src/CramAdapter/configSchema.ts b/plugins/alignments/src/CramAdapter/configSchema.ts index e430aa1aab..b1fe36c2d4 100644 --- a/plugins/alignments/src/CramAdapter/configSchema.ts +++ b/plugins/alignments/src/CramAdapter/configSchema.ts @@ -15,7 +15,7 @@ const configSchema = ConfigurationSchema( fetchSizeLimit: { type: 'number', description: - 'used to determine when to display a warning to the user that too much data will be fetched', + 'size in bytes over which to display a warning to the user that too much data will be fetched', defaultValue: 3_000_000, }, @@ -48,8 +48,7 @@ const configSchema = ConfigurationSchema( */ sequenceAdapter: { type: 'frozen', - description: - 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags', + description: 'sequence data adapter', defaultValue: null, }, }, diff --git a/plugins/alignments/src/CramAdapter/index.ts b/plugins/alignments/src/CramAdapter/index.ts index 840e9bb385..5fcb6cd433 100644 --- a/plugins/alignments/src/CramAdapter/index.ts +++ b/plugins/alignments/src/CramAdapter/index.ts @@ -5,12 +5,12 @@ import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' import configSchema from './configSchema' export default (pluginManager: PluginManager) => { - pluginManager.addAdapterType( - () => - new AdapterType({ - name: 'CramAdapter', - configSchema, - getAdapterClass: () => import('./CramAdapter').then(r => r.default), - }), - ) + pluginManager.addAdapterType(() => { + return new AdapterType({ + name: 'CramAdapter', + displayName: 'CRAM adapter', + configSchema, + getAdapterClass: () => import('./CramAdapter').then(r => r.default), + }) + }) } diff --git a/plugins/alignments/src/CramAdapter/util.test.ts b/plugins/alignments/src/CramAdapter/util.test.ts new file mode 100644 index 0000000000..45a89195e2 --- /dev/null +++ b/plugins/alignments/src/CramAdapter/util.test.ts @@ -0,0 +1,26 @@ +import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util' + +test('cram read features mismatches', () => { + expect( + // from ctgA_15140_15565_0:0:1_1:0:0_2e8 in volvox-sorted.cram + readFeaturesToMismatches( + [{ code: 'i', data: 'C', pos: 25, refPos: 15164 }], + 15139, + ), + ).toMatchSnapshot() +}) + +test('cram read features to CIGAR', () => { + expect( + // from ctgA_15140_15565_0:0:1_1:0:0_2e8 in volvox-sorted.cram + readFeaturesToCIGAR( + [{ code: 'i', data: 'C', pos: 25, refPos: 15164 }], + 15140, + 100, + { + start: 14998, + seq: 'agaccacattcagctctcggtaacatgggaggcttgtggttgcaccgtaaaagggggatagcccatccatcctgtaaacctacaatcgcgcgtagcttaatacgctcacattagacattcgatcgagagacctggtttcaagagccttcccttttgctttagtgggccaaatcgcaaccctgctcccctcccttacgccttatacacttcagtgcaaattcatgcgttcagcgaacaactggacttctgttgtacgtagtccacgggggcttattcattatagaaagccccctactgtcaccgttatatggttcacacatgagctgatcacctagagagtcgtcatgcacattcgcctaacaaggacatatgagtaaccg', + }, + ), + ).toMatchSnapshot() +}) diff --git a/plugins/alignments/src/CramAdapter/util.ts b/plugins/alignments/src/CramAdapter/util.ts new file mode 100644 index 0000000000..3021bad07a --- /dev/null +++ b/plugins/alignments/src/CramAdapter/util.ts @@ -0,0 +1,251 @@ +import { CramRecord } from '@gmod/cram' + +type ReadFeatures = CramRecord['readFeatures'] + +export interface Mismatch { + qual?: number + start: number + length: number + type: string + base: string | undefined + altbase?: string + seq?: string + cliplen?: number +} + +export function readFeaturesToMismatches( + readFeatures: ReadFeatures, + start: number, + qual?: number[] | null, +) { + if (!readFeatures) { + return [] + } + const mismatches: Mismatch[] = new Array(readFeatures.length) + let j = 0 + let insLen = 0 + let refPos = 0 + let sublen = 0 + let lastPos = start + + for (let i = 0; i < readFeatures.length; i++) { + const f = readFeatures[i] + const { code, pos, data, sub, ref } = f + sublen = refPos - lastPos + lastPos = refPos + + if (sublen && insLen > 0) { + mismatches[j++] = { + start: refPos, + type: 'insertion', + base: `${insLen}`, + length: 0, + } + insLen = 0 + } + refPos = f.refPos - 1 - start + + if (code === 'X') { + // substitution + mismatches[j++] = { + start: refPos, + length: 1, + base: sub, + qual: qual?.[pos - 1], + altbase: ref?.toUpperCase(), + type: 'mismatch', + } + } else if (code === 'I') { + // insertion + mismatches[j++] = { + start: refPos, + type: 'insertion', + base: `${data.length}`, + length: 0, + } + } else if (code === 'N') { + // reference skip + mismatches[j++] = { + type: 'skip', + length: data, + start: refPos, + base: 'N', + } + } else if (code === 'S') { + // soft clip + const len = data.length + mismatches[j++] = { + start: refPos, + type: 'softclip', + base: `S${len}`, + cliplen: len, + length: 1, + } + } else if (code === 'P') { + // padding + } else if (code === 'H') { + // hard clip + const len = data + mismatches[j++] = { + start: refPos, + type: 'hardclip', + base: `H${len}`, + cliplen: len, + length: 1, + } + } else if (code === 'D') { + // deletion + mismatches[j++] = { + type: 'deletion', + length: data, + start: refPos, + base: '*', + } + } else if (code === 'b') { + // stretch of bases + } else if (code === 'q') { + // stretch of qual scores + } else if (code === 'B') { + // a pair of [base, qual] + } else if (code === 'i') { + // single-base insertion, we collect these if there are multiple in a row + // into a single insertion entry + insLen++ + } else if (code === 'Q') { + // single quality value + } + } + + if (sublen && insLen > 0) { + mismatches[j++] = { + start: refPos, + type: 'insertion', + base: `${insLen}`, + length: 0, + } + insLen = 0 + } + + return mismatches.slice(0, j) +} + +export function readFeaturesToCIGAR( + readFeatures: ReadFeatures, + alignmentStart: number, + readLen: number, + refRegion?: { seq: string; start: number }, +) { + let seq = '' + let cigar = '' + let op = 'M' + let oplen = 0 + if (!refRegion) { + return '' + } + + // not sure I should access these, but... + const ref = refRegion.seq + const refStart = refRegion.start + let lastPos = alignmentStart + let sublen = 0 + let insLen = 0 + if (readFeatures !== undefined) { + for (let i = 0; i < readFeatures.length; i++) { + const { code, refPos, sub, data } = readFeatures[i] + sublen = refPos - lastPos + seq += ref.substring(lastPos - refStart, refPos - refStart) + lastPos = refPos + + if (insLen > 0 && sublen) { + cigar += `${insLen}I` + insLen = 0 + } + if (oplen && op !== 'M') { + cigar += oplen + op + oplen = 0 + } + if (sublen) { + op = 'M' + oplen += sublen + } + + if (code === 'b') { + // An array of bases stored verbatim + const ret = data.split(',') + const added = String.fromCharCode(...ret) + seq += added + lastPos += added.length + oplen += added.length + } else if (code === 'B') { + // Single base (+ qual score) + seq += sub + lastPos++ + oplen++ + } else if (code === 'X') { + // Substitution + seq += sub + lastPos++ + oplen++ + } else if (code === 'D' || code === 'N') { + // Deletion or Ref Skip + lastPos += data + if (oplen) { + cigar += oplen + op + } + cigar += data + code + oplen = 0 + } else if (code === 'I' || code === 'S') { + // Insertion or soft-clip + seq += data + if (oplen) { + cigar += oplen + op + } + cigar += data.length + code + oplen = 0 + } else if (code === 'i') { + // Single base insertion + // seq += data + if (oplen) { + cigar += oplen + op + } + insLen++ + seq += data + oplen = 0 + } else if (code === 'P') { + // Padding + if (oplen) { + cigar += oplen + op + } + cigar += `${data}P` + } else if (code === 'H') { + // Hard clip + if (oplen) { + cigar += oplen + op + } + cigar += `${data}H` + oplen = 0 + } // else q or Q + } + } else { + sublen = readLen - seq.length + } + if (seq.length !== readLen) { + sublen = readLen - seq.length + seq += ref.substring(lastPos - refStart, lastPos - refStart + sublen) + + if (oplen && op !== 'M') { + cigar += oplen + op + oplen = 0 + } + op = 'M' + oplen += sublen + } + if (sublen && insLen > 0) { + cigar += `${insLen}I` + } + if (oplen) { + cigar += oplen + op + } + + return cigar +} diff --git a/plugins/alignments/src/GuessAlignmentsTypes/index.ts b/plugins/alignments/src/GuessAlignmentsTypes/index.ts new file mode 100644 index 0000000000..a0c2089ab0 --- /dev/null +++ b/plugins/alignments/src/GuessAlignmentsTypes/index.ts @@ -0,0 +1,79 @@ +import PluginManager from '@jbrowse/core/PluginManager' +import { FileLocation } from '@jbrowse/core/util/types' +import { + makeIndex, + makeIndexType, + getFileName, + AdapterGuesser, + TrackTypeGuesser, +} from '@jbrowse/core/util/tracks' + +export default (pluginManager: PluginManager) => { + pluginManager.addToExtensionPoint( + 'Core-guessAdapterForLocation', + (adapterGuesser: AdapterGuesser) => { + return ( + file: FileLocation, + index?: FileLocation, + adapterHint?: string, + ) => { + const regexGuess = /\.cram$/i + const adapterName = 'CramAdapter' + const fileName = getFileName(file) + const obj = { + type: adapterName, + cramLocation: file, + craiLocation: index || makeIndex(file, '.crai'), + } + if (regexGuess.test(fileName) && !adapterHint) { + return obj + } else if (adapterHint === adapterName) { + return obj + } + return adapterGuesser(file, index, adapterHint) + } + }, + ) + + pluginManager.addToExtensionPoint( + 'Core-guessAdapterForLocation', + (adapterGuesser: AdapterGuesser) => { + return ( + file: FileLocation, + index?: FileLocation, + adapterHint?: string, + ) => { + const regexGuess = /\.bam$/i + const adapterName = 'BamAdapter' + const fileName = getFileName(file) + const indexName = index && getFileName(index) + + const obj = { + type: adapterName, + bamLocation: file, + index: { + location: index || makeIndex(file, '.bai'), + indexType: makeIndexType(indexName, 'CSI', 'BAI'), + }, + } + if (regexGuess.test(fileName) && !adapterHint) { + return obj + } else if (adapterHint === adapterName) { + return obj + } + return adapterGuesser(file, index, adapterHint) + } + }, + ) + pluginManager.addToExtensionPoint( + 'Core-guessTrackTypeForLocation', + (trackTypeGuesser: TrackTypeGuesser) => { + return (adapterName: string) => { + if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') { + return 'AlignmentsTrack' + } + return trackTypeGuesser(adapterName) + } + }, + ) +} diff --git a/plugins/alignments/src/HtsgetBamAdapter/index.ts b/plugins/alignments/src/HtsgetBamAdapter/index.ts index a3f923d6bd..036743a0cd 100644 --- a/plugins/alignments/src/HtsgetBamAdapter/index.ts +++ b/plugins/alignments/src/HtsgetBamAdapter/index.ts @@ -3,19 +3,15 @@ import PluginManager from '@jbrowse/core/PluginManager' import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' export default (pluginManager: PluginManager) => { - pluginManager.addAdapterType( - () => - new AdapterType({ - name: 'HtsgetBamAdapter', - adapterMetadata: { - category: null, - hiddenFromGUI: true, - displayName: null, - description: null, - }, - configSchema, - getAdapterClass: () => - import('./HtsgetBamAdapter').then(r => r.default), - }), - ) + pluginManager.addAdapterType(() => { + return new AdapterType({ + name: 'HtsgetBamAdapter', + displayName: 'Htsget BAM adapter', + adapterMetadata: { + hiddenFromGUI: true, + }, + configSchema, + getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default), + }) + }) } diff --git a/plugins/alignments/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx b/plugins/alignments/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx index 33665e5545..ff7524e213 100644 --- a/plugins/alignments/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +++ b/plugins/alignments/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx @@ -1,8 +1,10 @@ import React from 'react' import { observer } from 'mobx-react' +import { makeStyles } from 'tss-react/mui' import { getConf } from '@jbrowse/core/configuration' import { ResizeHandle } from '@jbrowse/core/ui' -import { makeStyles } from 'tss-react/mui' + +// locals import { AlignmentsDisplayModel } from '../models/model' const useStyles = makeStyles()(() => ({ @@ -14,7 +16,7 @@ const useStyles = makeStyles()(() => ({ })) function AlignmentsDisplay({ model }: { model: AlignmentsDisplayModel }) { - const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model + const { PileupDisplay, SNPCoverageDisplay } = model const { classes } = useStyles() const top = SNPCoverageDisplay.height return ( @@ -22,35 +24,27 @@ function AlignmentsDisplay({ model }: { model: AlignmentsDisplayModel }) { data-testid={`display-${getConf(model, 'displayId')}`} style={{ position: 'relative' }} > - {showCoverage ? ( - <> -
    - -
    - { - SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta) - return delta - }} - className={classes.resizeHandle} - style={{ - top, - }} - /> - - ) : null} +
    + +
    + { + SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta) + return delta + }} + className={classes.resizeHandle} + style={{ top }} + /> - {showPileup ? ( -
    - -
    - ) : null} +
    + +
    ) } diff --git a/plugins/alignments/src/LinearAlignmentsDisplay/index.ts b/plugins/alignments/src/LinearAlignmentsDisplay/index.ts index bdc37d983b..4676aeb336 100644 --- a/plugins/alignments/src/LinearAlignmentsDisplay/index.ts +++ b/plugins/alignments/src/LinearAlignmentsDisplay/index.ts @@ -10,6 +10,7 @@ export default function (pluginManager: PluginManager) { const configSchema = configSchemaFactory(pluginManager) return new DisplayType({ name: 'LinearAlignmentsDisplay', + displayName: 'Alignments display (combination)', configSchema, stateModel: modelFactory(pluginManager, configSchema), trackType: 'AlignmentsTrack', diff --git a/plugins/alignments/src/LinearAlignmentsDisplay/models/configSchema.ts b/plugins/alignments/src/LinearAlignmentsDisplay/models/configSchema.ts index 63be0d3b3b..29c7bf54fc 100644 --- a/plugins/alignments/src/LinearAlignmentsDisplay/models/configSchema.ts +++ b/plugins/alignments/src/LinearAlignmentsDisplay/models/configSchema.ts @@ -7,9 +7,7 @@ import PluginManager from '@jbrowse/core/PluginManager' * has a "pileup" sub-display, where you can see individual reads and a * quantitative "snpcoverage" sub-display track showing SNP frequencies */ -function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars - -const configModelFactory = (pm: PluginManager) => { +export default function configModelFactory(pm: PluginManager) { return ConfigurationSchema( 'LinearAlignmentsDisplay', { @@ -17,6 +15,7 @@ const configModelFactory = (pm: PluginManager) => { * #slot */ pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema, + /** * #slot */ @@ -32,6 +31,3 @@ const configModelFactory = (pm: PluginManager) => { }, ) } - -export type AlignmentsConfigModel = ReturnType -export default configModelFactory diff --git a/plugins/alignments/src/LinearAlignmentsDisplay/models/model.tsx b/plugins/alignments/src/LinearAlignmentsDisplay/models/model.tsx index a53ef0a86a..182dc77c35 100644 --- a/plugins/alignments/src/LinearAlignmentsDisplay/models/model.tsx +++ b/plugins/alignments/src/LinearAlignmentsDisplay/models/model.tsx @@ -1,4 +1,16 @@ import React from 'react' +import { autorun, when } from 'mobx' +import { + addDisposer, + getSnapshot, + isAlive, + types, + Instance, + IStateTreeNode, +} from 'mobx-state-tree' +import deepEqual from 'fast-deep-equal' + +// jbrowse import { ConfigurationReference, AnyConfigurationModel, @@ -8,13 +20,109 @@ import { import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models' import PluginManager from '@jbrowse/core/PluginManager' import { MenuItem } from '@jbrowse/core/ui' -import { autorun, when } from 'mobx' -import { addDisposer, getSnapshot, Instance, types } from 'mobx-state-tree' -import { getContainingTrack } from '@jbrowse/core/util' -import deepEqual from 'fast-deep-equal' const minDisplayHeight = 20 +function getLowerPanelDisplays(pluginManager: PluginManager) { + return ( + pluginManager + .getDisplayElements() + // @ts-ignore + .filter(f => f.subDisplay?.type === 'LinearAlignmentsDisplay') + // @ts-ignore + .filter(f => f.subDisplay?.lowerPanel) + ) +} + +function deepSnap( + x1: T, + x2: U, +) { + return deepEqual( + x1 ? getSnapshot(x1) : undefined, + x2 ? getSnapshot(x2) : undefined, + ) +} + +function preCheck(self: AlignmentsDisplayModel) { + const { PileupDisplay, SNPCoverageDisplay } = self + return ( + PileupDisplay || + isAlive(PileupDisplay) || + SNPCoverageDisplay || + isAlive(SNPCoverageDisplay) + ) +} + +function propagateColorBy(self: AlignmentsDisplayModel) { + const { PileupDisplay, SNPCoverageDisplay } = self + if (!preCheck(self) || !PileupDisplay.colorBy) { + return + } + if (!deepSnap(PileupDisplay.colorBy, SNPCoverageDisplay.colorBy)) { + SNPCoverageDisplay.setColorBy(getSnapshot(PileupDisplay.colorBy)) + } +} + +function propagateFilterBy(self: AlignmentsDisplayModel) { + const { PileupDisplay, SNPCoverageDisplay } = self + if (!preCheck(self) || !PileupDisplay.filterBy) { + return + } + if (!deepSnap(PileupDisplay.filterBy, SNPCoverageDisplay.filterBy)) { + SNPCoverageDisplay.setFilterBy(getSnapshot(PileupDisplay.filterBy)) + } +} + +function AlignmentsModel( + pluginManager: PluginManager, + configSchema: AnyConfigurationSchemaType, +) { + const lowerPanelDisplays = getLowerPanelDisplays(pluginManager).map( + f => f.stateModel, + ) + + return types.model({ + /** + * #property + * refers to LinearPileupDisplay sub-display model + */ + // @ts-ignore + PileupDisplay: types.maybe(types.union(...lowerPanelDisplays)), + /** + * #property + * refers to LinearSNPCoverageDisplay sub-display model + */ + SNPCoverageDisplay: types.maybe( + pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel, + ), + /** + * #property + */ + snpCovHeight: 45, + /** + * #property + */ + type: types.literal('LinearAlignmentsDisplay'), + /** + * #property + */ + configuration: ConfigurationReference(configSchema), + /** + * #property + */ + height: 250, + /** + * #property + */ + userFeatureScreenDensity: types.maybe(types.number), + /** + * #property + */ + lowerPanelType: 'LinearPileupDisplay', + }) +} + /** * #stateModel LinearAlignmentsDisplay * extends `BaseDisplay` @@ -27,67 +135,12 @@ function stateModelFactory( .compose( 'LinearAlignmentsDisplay', BaseDisplay, - types.model({ - /** - * #property - * refers to LinearPileupDisplay sub-display model - */ - PileupDisplay: types.maybe( - pluginManager.getDisplayType('LinearPileupDisplay').stateModel, - ), - /** - * #property - * refers to LinearSNPCoverageDisplay sub-display model - */ - SNPCoverageDisplay: types.maybe( - pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel, - ), - /** - * #property - */ - snpCovHeight: 45, - /** - * #property - */ - type: types.literal('LinearAlignmentsDisplay'), - /** - * #property - */ - configuration: ConfigurationReference(configSchema), - /** - * #property - */ - height: 250, - /** - * #property - */ - showCoverage: true, - /** - * #property - */ - showPileup: true, - /** - * #property - */ - userFeatureScreenDensity: types.maybe(types.number), - }), + AlignmentsModel(pluginManager, configSchema), ) .volatile(() => ({ scrollTop: 0, })) .actions(self => ({ - /** - * #action - */ - toggleCoverage() { - self.showCoverage = !self.showCoverage - }, - /** - * #action - */ - togglePileup() { - self.showPileup = !self.showPileup - }, /** * #action */ @@ -102,141 +155,105 @@ function stateModelFactory( self.snpCovHeight = n }, })) - .views(self => { - const { trackMenuItems: superTrackMenuItems } = self - return { - /** - * #getter - */ - get pileupDisplayConfig() { - const conf = getConf(self, 'pileupDisplay') - const track = getContainingTrack(self) - return { - ...conf, - type: 'LinearPileupDisplay', - name: `${getConf(track, 'name')} pileup`, - displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this - } - }, - - /** - * #method - */ - getFeatureByID(blockKey: string, id: string) { - return self.PileupDisplay.getFeatureByID(blockKey, id) - }, - /** - * #method - */ - searchFeatureByID(id: string) { - return self.PileupDisplay.searchFeatureByID(id) - }, + .views(self => ({ + /** + * #getter + */ + get pileupConf() { + const conf = getConf(self, 'pileupDisplay') + return { + ...conf, + type: self.lowerPanelType, + displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this + } + }, - /** - * #getter - */ - get features() { - return self.PileupDisplay.features - }, + /** + * #method + */ + getFeatureByID(blockKey: string, id: string) { + return self.PileupDisplay.getFeatureByID(blockKey, id) + }, + /** + * #method + */ + searchFeatureByID(id: string) { + return self.PileupDisplay.searchFeatureByID(id) + }, - /** - * #getter - */ - get DisplayBlurb() { - return self.PileupDisplay?.DisplayBlurb - }, + /** + * #getter + */ + get features() { + return self.PileupDisplay.features + }, - /** - * #getter - */ - get sortedBy() { - return self.PileupDisplay.sortedBy - }, - /** - * #getter - */ - get sortedByPosition() { - return self.PileupDisplay.sortedByPosition - }, - /** - * #getter - */ - get sortedByRefName() { - return self.PileupDisplay.sortedByRefName - }, + /** + * #getter + */ + get DisplayBlurb() { + return self.PileupDisplay?.DisplayBlurb + }, - /** - * #getter - */ - get snpCoverageDisplayConfig() { - const conf = getConf(self, 'snpCoverageDisplay') - const track = getContainingTrack(self) - return { - ...conf, - type: 'LinearSNPCoverageDisplay', - name: `${getConf(track, 'name')} snp coverage`, - displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this - } - }, + /** + * #getter + */ + get sortedBy() { + return self.PileupDisplay.sortedBy + }, - /** - * #method - */ - trackMenuItems(): MenuItem[] { - return [ - ...superTrackMenuItems(), - { - type: 'subMenu', - label: 'Pileup settings', - subMenu: self.PileupDisplay.trackMenuItems(), - }, - { - type: 'subMenu', - label: 'SNPCoverage settings', - subMenu: self.SNPCoverageDisplay.trackMenuItems(), - }, - ] - }, - } - }) + /** + * #getter + */ + get coverageConf() { + const conf = getConf(self, 'snpCoverageDisplay') + return { + ...conf, + displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this + } + }, + })) .actions(self => ({ /** * #action */ - setSNPCoverageDisplay(displayConfig: AnyConfigurationModel) { + setSNPCoverageDisplay(configuration: AnyConfigurationModel) { self.SNPCoverageDisplay = { type: 'LinearSNPCoverageDisplay', - configuration: displayConfig, + configuration, height: self.snpCovHeight, } }, /** * #action */ - setUserFeatureScreenDensity(limit: number) { - self.PileupDisplay.setUserFeatureScreenDensity(limit) - self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit) + updateStatsLimit(stats: unknown) { + self.PileupDisplay.updateStatsLimit(stats) + self.SNPCoverageDisplay.updateStatsLimit(stats) }, + /** * #action */ - setPileupDisplay(displayConfig: AnyConfigurationModel) { + setPileupDisplay(configuration: AnyConfigurationModel) { self.PileupDisplay = { - type: 'LinearPileupDisplay', - configuration: displayConfig, + type: configuration.type || 'LinearPileupDisplay', + configuration, } }, /** * #action */ - setHeight(displayHeight: number) { - if (displayHeight > minDisplayHeight) { - self.height = displayHeight - } else { - self.height = minDisplayHeight - } + setHeight(n: number) { + self.height = Math.max(n, minDisplayHeight) return self.height }, + /** + * #action + */ + setLowerPanelType(type: string) { + self.lowerPanelType = type + }, /** * #action */ @@ -251,64 +268,53 @@ function stateModelFactory( addDisposer( self, autorun(() => { - if (!self.SNPCoverageDisplay) { - self.setSNPCoverageDisplay(self.snpCoverageDisplayConfig) + const { + SNPCoverageDisplay, + PileupDisplay, + coverageConf, + pileupConf, + } = self + + if (!SNPCoverageDisplay) { + self.setSNPCoverageDisplay(coverageConf) } else if ( !deepEqual( - self.snpCoverageDisplayConfig, - getSnapshot(self.SNPCoverageDisplay.configuration), + coverageConf, + getSnapshot(SNPCoverageDisplay.configuration), ) ) { - self.SNPCoverageDisplay.setHeight(self.snpCovHeight) - self.SNPCoverageDisplay.setConfig(self.snpCoverageDisplayConfig) + SNPCoverageDisplay.setHeight(self.snpCovHeight) + SNPCoverageDisplay.setConfig(self.coverageConf) } - if (!self.PileupDisplay) { - self.setPileupDisplay(self.pileupDisplayConfig) + if (!PileupDisplay || self.lowerPanelType !== PileupDisplay.type) { + self.setPileupDisplay(pileupConf) } else if ( - !deepEqual( - self.pileupDisplayConfig, - getSnapshot(self.PileupDisplay.configuration), - ) + !deepEqual(pileupConf, getSnapshot(PileupDisplay.configuration)) ) { - self.PileupDisplay.setConfig(self.pileupDisplayConfig) + PileupDisplay.setConfig(self.pileupConf) } - // propagate the filterBy setting from pileupdisplay to snpcoverage - // note: the snpcoverage display is not able to control filterBy - // itself - if ( - self.PileupDisplay.filterBy && - !deepEqual( - getSnapshot(self.PileupDisplay.filterBy), - getSnapshot(self.SNPCoverageDisplay.filterBy), - ) - ) { - self.SNPCoverageDisplay.setFilterBy( - getSnapshot(self.PileupDisplay.filterBy), - ) - } - if ( - self.PileupDisplay.colorBy && - !deepEqual( - getSnapshot(self.PileupDisplay.colorBy), - self.SNPCoverageDisplay.colorBy - ? getSnapshot(self.SNPCoverageDisplay.colorBy) - : {}, - ) - ) { - self.SNPCoverageDisplay.setColorBy( - getSnapshot(self.PileupDisplay.colorBy), - ) - } + propagateColorBy(self as AlignmentsDisplayModel) + propagateFilterBy(self as AlignmentsDisplayModel) }), ) + addDisposer( self, autorun(() => { self.setSNPCoverageHeight(self.SNPCoverageDisplay.height) }), ) + + addDisposer( + self, + autorun(() => { + self.PileupDisplay.setHeight( + self.height - self.SNPCoverageDisplay.height, + ) + }), + ) }, /** * #action @@ -329,6 +335,40 @@ function stateModelFactory( ) }, })) + .views(self => { + const { trackMenuItems: superTrackMenuItems } = self + return { + /** + * #method + */ + trackMenuItems(): MenuItem[] { + const extra = getLowerPanelDisplays(pluginManager).map(d => ({ + type: 'radio', + label: d.displayName, + checked: d.name === self.PileupDisplay.type, + onClick: () => self.setLowerPanelType(d.name), + })) + return [ + ...superTrackMenuItems(), + { + type: 'subMenu', + label: 'Pileup settings', + subMenu: self.PileupDisplay.trackMenuItems(), + }, + { + type: 'subMenu', + label: 'SNPCoverage settings', + subMenu: self.SNPCoverageDisplay.trackMenuItems(), + }, + { + type: 'subMenu', + label: `Replace lower panel with...`, + subMenu: extra, + }, + ] + }, + } + }) } export default stateModelFactory diff --git a/plugins/alignments/src/LinearPileupDisplay/components/ColorByModifications.tsx b/plugins/alignments/src/LinearPileupDisplay/components/ColorByModifications.tsx index ce37a5c322..b220097bc9 100644 --- a/plugins/alignments/src/LinearPileupDisplay/components/ColorByModifications.tsx +++ b/plugins/alignments/src/LinearPileupDisplay/components/ColorByModifications.tsx @@ -4,23 +4,14 @@ import { ObservableMap } from 'mobx' import { Button, CircularProgress, - Dialog, DialogActions, DialogContent, - DialogTitle, - IconButton, Typography, } from '@mui/material' +import { Dialog } from '@jbrowse/core/ui' import { makeStyles } from 'tss-react/mui' -import CloseIcon from '@mui/icons-material/Close' const useStyles = makeStyles()(theme => ({ - closeButton: { - position: 'absolute', - right: theme.spacing(1), - top: theme.spacing(1), - color: theme.palette.grey[500], - }, table: { border: '1px solid #888', margin: theme.spacing(4), @@ -58,30 +49,19 @@ function ModificationTable({ function ColorByTagDlg(props: { model: { - setColorScheme: Function + setColorScheme: (arg: { type: string }) => void modificationTagMap: ObservableMap colorBy?: { type: string } } handleClose: () => void }) { - const { classes } = useStyles() const { model, handleClose } = props const { colorBy, modificationTagMap } = model const modifications = [...modificationTagMap.entries()] return ( - - - Color by modifications - - - - + You can choose to color the modifications in the BAM/CRAM MM/ML @@ -126,12 +106,8 @@ function ColorByTagDlg(props: {
    + ) +}) type Coord = [number, number] diff --git a/plugins/alignments/src/LinearSNPCoverageDisplay/index.ts b/plugins/alignments/src/LinearSNPCoverageDisplay/index.ts index ad63efd85e..9a8f50e9e9 100644 --- a/plugins/alignments/src/LinearSNPCoverageDisplay/index.ts +++ b/plugins/alignments/src/LinearSNPCoverageDisplay/index.ts @@ -9,6 +9,7 @@ export default function register(pluginManager: PluginManager) { const configSchema = configSchemaFactory(pluginManager) return new DisplayType({ name: 'LinearSNPCoverageDisplay', + displayName: 'SNPCoverage display', configSchema, stateModel: modelFactory(pluginManager, configSchema), trackType: 'AlignmentsTrack', diff --git a/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts b/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts index 9257ecb6b6..d68116bedd 100644 --- a/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts +++ b/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts @@ -1,5 +1,9 @@ import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree' -import { observable, autorun } from 'mobx' +import clone from 'clone' +import { autorun } from 'mobx' + +// jbrowse +import PluginManager from '@jbrowse/core/PluginManager' import { getConf, readConfObject, @@ -7,13 +11,12 @@ import { AnyConfigurationModel, } from '@jbrowse/core/configuration' import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle' -import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' -import PluginManager from '@jbrowse/core/PluginManager' import { getContainingView } from '@jbrowse/core/util' +import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' // locals import Tooltip from '../components/Tooltip' -import { getUniqueModificationValues } from '../../shared' +import { FilterModel, getUniqueModificationValues } from '../../shared' // using a map because it preserves order const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]) @@ -52,17 +55,7 @@ function stateModelFactory( /** * #property */ - filterBy: types.optional( - types.model({ - flagInclude: types.optional(types.number, 0), - flagExclude: types.optional(types.number, 1540), - readName: types.maybe(types.string), - tagFilter: types.maybe( - types.model({ tag: types.string, value: types.string }), - ), - }), - {}, - ), + filterBy: types.optional(FilterModel, {}), /** * #property */ @@ -75,7 +68,7 @@ function stateModelFactory( }), ) .volatile(() => ({ - modificationTagMap: observable.map({}), + modificationTagMap: undefined as Record | undefined, })) .actions(self => ({ /** @@ -109,12 +102,14 @@ function stateModelFactory( const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'] let i = 0 + const newMap = clone(self.modificationTagMap) || {} uniqueModifications.forEach(value => { - if (!self.modificationTagMap.has(value)) { + if (!newMap[value]) { const newColor = colorPalette[i++] - self.modificationTagMap.set(value, newColor) + newMap[value] = newColor } }) + self.modificationTagMap = newMap }, })) .views(self => { @@ -170,8 +165,7 @@ function stateModelFactory( */ get modificationsReady() { return self.colorBy?.type === 'modifications' - ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap))) - .length > 0 + ? self.modificationTagMap !== undefined : true }, @@ -184,7 +178,7 @@ function stateModelFactory( return { ...superProps, notReady: superProps.notReady || !this.modificationsReady, - modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()), + modificationTagMap: modificationTagMap, // must use getSnapshot because otherwise changes to e.g. just the // colorBy.type are not read diff --git a/plugins/alignments/src/BamAdapter/MismatchParser.test.ts b/plugins/alignments/src/MismatchParser/index.test.ts similarity index 95% rename from plugins/alignments/src/BamAdapter/MismatchParser.test.ts rename to plugins/alignments/src/MismatchParser/index.test.ts index 2d1f829811..4dc42e0d10 100644 --- a/plugins/alignments/src/BamAdapter/MismatchParser.test.ts +++ b/plugins/alignments/src/MismatchParser/index.test.ts @@ -5,7 +5,7 @@ import { parseCigar, getNextRefPos, getModificationPositions, -} from './MismatchParser' +} from './index' const seq = 'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTT' @@ -139,79 +139,88 @@ test('more skip', () => { (a, b) => a.start - b.start, ), ).toMatchInlineSnapshot(` - Array [ - Object { + [ + { "altbase": "G", "base": "A", "length": 1, + "qual": undefined, "start": 6, "type": "mismatch", }, - Object { + { "altbase": "C", "base": "A", "length": 1, + "qual": undefined, "start": 11, "type": "mismatch", }, - Object { + { "base": "1", "length": 0, "start": 31, "type": "insertion", }, - Object { + { "altbase": "G", "base": "C", "length": 1, + "qual": undefined, "start": 32, "type": "mismatch", }, - Object { + { "altbase": "A", "base": "C", "length": 1, + "qual": undefined, "start": 34, "type": "mismatch", }, - Object { + { "altbase": "C", "base": "C", "length": 1, + "qual": undefined, "start": 40, "type": "mismatch", }, - Object { + { "altbase": "A", "base": "C", "length": 1, + "qual": undefined, "start": 46, "type": "mismatch", }, - Object { + { "base": "*", "length": 1, "start": 48, "type": "deletion", }, - Object { + { "altbase": "A", "base": "G", "length": 1, + "qual": undefined, "start": 52, "type": "mismatch", }, - Object { + { "altbase": "G", "base": "G", "length": 1, + "qual": undefined, "start": 68, "type": "mismatch", }, - Object { + { "altbase": "G", "base": "G", "length": 1, + "qual": undefined, "start": 70, "type": "mismatch", }, diff --git a/plugins/alignments/src/BamAdapter/MismatchParser.ts b/plugins/alignments/src/MismatchParser/index.ts similarity index 70% rename from plugins/alignments/src/BamAdapter/MismatchParser.ts rename to plugins/alignments/src/MismatchParser/index.ts index a1e5a0383d..8c926a31f6 100644 --- a/plugins/alignments/src/BamAdapter/MismatchParser.ts +++ b/plugins/alignments/src/MismatchParser/index.ts @@ -1,4 +1,5 @@ -import { revcom } from '@jbrowse/core/util' +import { revcom, Feature } from '@jbrowse/core/util' + export interface Mismatch { qual?: number start: number @@ -11,12 +12,17 @@ export interface Mismatch { } const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi) const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/) +const cigarRegex = new RegExp(/([MIDNSHPX=])/) +const startClip = new RegExp(/(\d+)[SH]$/) +const endClip = new RegExp(/^(\d+)([SH])/) + export function parseCigar(cigar = '') { - return cigar.split(/([MIDNSHPX=])/).slice(0, -1) + return cigar.split(cigarRegex).slice(0, -1) } + export function cigarToMismatches( ops: string[], - seq: string, + seq?: string, ref?: string, qual?: Buffer, ): Mismatch[] { @@ -70,7 +76,7 @@ export function cigarToMismatches( length: len, }) } else if (op === 'X') { - const r = seq.slice(soffset, soffset + len) + const r = seq?.slice(soffset, soffset + len) || [] const q = qual?.slice(soffset, soffset + len) || [] for (let j = 0; j < len; j++) { @@ -195,10 +201,7 @@ export function mdToMismatches( } const s = getTemplateCoordLocal(curr.start) curr.base = seq[s] || 'X' - const qualScore = qual?.[s] - if (qualScore) { - curr.qual = qualScore - } + curr.qual = qual?.[s] curr.altbase = token nextRecord() } @@ -209,8 +212,8 @@ export function mdToMismatches( export function getMismatches( cigar: string, - md: string, - seq: string, + md?: string, + seq?: string, ref?: string, qual?: Buffer, ): Mismatch[] { @@ -223,7 +226,7 @@ export function getMismatches( } // now let's look for CRAM or MD mismatches - if (md) { + if (md && seq) { mismatches = mismatches.concat( mdToMismatches(md, ops, mismatches, seq, qual), ) @@ -332,7 +335,7 @@ export function getModificationTypes(mm: string) { const matches = basemod.match(modificationRegex) if (!matches) { - throw new Error('bad format for MM tag') + throw new Error(`bad format for MM tag: ${mm}`) } const [, , , typestr] = matches @@ -342,3 +345,124 @@ export function getModificationTypes(mm: string) { }) .flat() } + +export function getOrientedCigar(flip: boolean, cigar: string[]) { + if (flip) { + const ret = [] + for (let i = 0; i < cigar.length; i += 2) { + const len = cigar[i] + let op = cigar[i + 1] + if (op === 'D') { + op = 'I' + } else if (op === 'I') { + op = 'D' + } + ret.push(len) + ret.push(op) + } + return ret + } else { + return cigar + } +} + +export function getOrientedMismatches(flip: boolean, cigar: string) { + const p = parseCigar(cigar) + return cigarToMismatches(flip ? getOrientedCigar(flip, p) : p) +} + +export function getLengthOnRef(cigar: string) { + const cigarOps = parseCigar(cigar) + let lengthOnRef = 0 + for (let i = 0; i < cigarOps.length; i += 2) { + const len = +cigarOps[i] + const op = cigarOps[i + 1] + if (op !== 'H' && op !== 'S' && op !== 'I') { + lengthOnRef += len + } + } + return lengthOnRef +} + +export function getLength(cigar: string) { + const cigarOps = parseCigar(cigar) + let length = 0 + for (let i = 0; i < cigarOps.length; i += 2) { + const len = +cigarOps[i] + const op = cigarOps[i + 1] + if (op !== 'D' && op !== 'N') { + length += len + } + } + return length +} + +export function getLengthSansClipping(cigar: string) { + const cigarOps = parseCigar(cigar) + let length = 0 + for (let i = 0; i < cigarOps.length; i += 2) { + const len = +cigarOps[i] + const op = cigarOps[i + 1] + if (op !== 'H' && op !== 'S' && op !== 'D' && op !== 'N') { + length += len + } + } + return length +} + +export function getClip(cigar: string, strand: number) { + return strand === -1 + ? +(cigar.match(startClip) || [])[1] || 0 + : +(cigar.match(endClip) || [])[1] || 0 +} + +export function getTag(f: Feature, tag: string) { + const tags = f.get('tags') + return tags ? tags[tag] : f.get(tag) +} + +// produces a list of "feature-like" object from parsing supplementary +// alignments in the SA tag +// +// @param normalize - used specifically in the linear-read-vs-ref context, it +// flips features around relative to the original feature. other contexts of +// usage can keep this false +export function featurizeSA( + SA: string | undefined, + id: string, + strand: number, + readName: string, + normalize?: boolean, +) { + return ( + SA?.split(';') + .filter(aln => !!aln) + .map((aln, index) => { + const [saRef, saStart, saStrand, saCigar] = aln.split(',') + const saLengthOnRef = getLengthOnRef(saCigar) + const saLength = getLength(saCigar) + const saLengthSansClipping = getLengthSansClipping(saCigar) + const saStrandNormalized = saStrand === '-' ? -1 : 1 + const saClipPos = getClip( + saCigar, + (normalize ? strand : 1) * saStrandNormalized, + ) + const saRealStart = +saStart - 1 + return { + refName: saRef, + start: saRealStart, + end: saRealStart + saLengthOnRef, + seqLength: saLength, + clipPos: saClipPos, + CIGAR: saCigar, + strand: (normalize ? strand : 1) * saStrandNormalized, + uniqueId: `${id}_SA${index}`, + mate: { + start: saClipPos, + end: saClipPos + saLengthSansClipping, + refName: readName, + }, + } + }) || [] + ) +} diff --git a/plugins/alignments/src/PileupRPC/base.ts b/plugins/alignments/src/PileupRPC/base.ts new file mode 100644 index 0000000000..a9a9fbe082 --- /dev/null +++ b/plugins/alignments/src/PileupRPC/base.ts @@ -0,0 +1,24 @@ +import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType' +import { renameRegionsIfNeeded } from '@jbrowse/core/util' +import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods' + +// specialized get features to return limited data about alignments +export default abstract class PileupBaseRPC extends RpcMethodType { + async serializeArguments( + args: RenderArgs & { + signal?: AbortSignal + statusCallback?: (arg: string) => void + }, + rpcDriver: string, + ) { + const { rootModel } = this.pluginManager + const assemblyManager = rootModel?.session?.assemblyManager + if (!assemblyManager) { + throw new Error('no assembly manager available') + } + + const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args) + + return super.serializeArguments(renamedArgs, rpcDriver) + } +} diff --git a/plugins/alignments/src/PileupRPC/index.ts b/plugins/alignments/src/PileupRPC/index.ts new file mode 100644 index 0000000000..4af626b985 --- /dev/null +++ b/plugins/alignments/src/PileupRPC/index.ts @@ -0,0 +1,12 @@ +import PluginManager from '@jbrowse/core/PluginManager' +import { + PileupGetGlobalValueForTag, + PileupGetVisibleModifications, + PileupGetReducedFeatures, +} from './rpcMethods' + +export default (pm: PluginManager) => { + pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm)) + pm.addRpcMethod(() => new PileupGetVisibleModifications(pm)) + pm.addRpcMethod(() => new PileupGetReducedFeatures(pm)) +} diff --git a/plugins/alignments/src/PileupRPC/methods/GetGlobalValueForTag.ts b/plugins/alignments/src/PileupRPC/methods/GetGlobalValueForTag.ts new file mode 100644 index 0000000000..62c493c168 --- /dev/null +++ b/plugins/alignments/src/PileupRPC/methods/GetGlobalValueForTag.ts @@ -0,0 +1,41 @@ +import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache' +import { Region } from '@jbrowse/core/util' +import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals' +import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter' +import { toArray } from 'rxjs/operators' +import PileupBaseRPC from '../base' +import { getTag } from '../../util' + +export default class PileupGetGlobalValueForTag extends PileupBaseRPC { + name = 'PileupGetGlobalValueForTag' + + async execute( + args: { + adapterConfig: {} + signal?: RemoteAbortSignal + headers?: Record + regions: Region[] + sessionId: string + tag: string + }, + rpcDriver: string, + ) { + const { adapterConfig, sessionId, regions, tag } = + await this.deserializeArguments(args, rpcDriver) + + const dataAdapter = ( + await getAdapter(this.pluginManager, sessionId, adapterConfig) + ).dataAdapter as BaseFeatureDataAdapter + + const features = dataAdapter.getFeaturesInMultipleRegions(regions) + const featuresArray = await features.pipe(toArray()).toPromise() + return [ + ...new Set( + featuresArray + .map(feature => getTag(feature, tag)) + .filter(f => f !== undefined) + .map(f => `${f}`), + ), + ] + } +} diff --git a/plugins/alignments/src/PileupRPC/methods/GetReducedFeatures.ts b/plugins/alignments/src/PileupRPC/methods/GetReducedFeatures.ts new file mode 100644 index 0000000000..de0e1c1a1b --- /dev/null +++ b/plugins/alignments/src/PileupRPC/methods/GetReducedFeatures.ts @@ -0,0 +1,76 @@ +import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache' +import { Region, dedupe } from '@jbrowse/core/util' +import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals' +import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter' +import { toArray } from 'rxjs/operators' + +// locals +import { filterForPairs, getInsertSizeStats } from '../util' +import { ReducedFeature } from '../../shared/fetchChains' +import PileupBaseRPC from '../base' +import { getTag } from '../../util' + +// specialized get features to return limited data about alignments +export default class PileupGetReducedFeatures extends PileupBaseRPC { + name = 'PileupGetReducedFeatures' + + async execute( + args: { + adapterConfig: {} + signal?: RemoteAbortSignal + headers?: Record + regions: Region[] + sessionId: string + tag: string + }, + rpcDriver: string, + ) { + const des = await this.deserializeArguments(args, rpcDriver) + const { adapterConfig, sessionId, regions } = des + const dataAdapter = ( + await getAdapter(this.pluginManager, sessionId, adapterConfig) + ).dataAdapter as BaseFeatureDataAdapter + + const featuresArray = await dataAdapter + .getFeaturesInMultipleRegions(regions, des) + .pipe(toArray()) + .toPromise() + + const reduced = dedupe( + featuresArray.map(f => ({ + id: f.id(), + refName: f.get('refName'), + name: f.get('name'), + start: f.get('start'), + strand: f.get('strand'), + end: f.get('end'), + flags: f.get('flags'), + tlen: f.get('template_length'), + pair_orientation: f.get('pair_orientation'), + next_ref: f.get('next_ref'), + next_pos: f.get('next_pos'), + clipPos: f.get('clipPos'), + SA: getTag(f, 'SA'), + })), + f => f.id, + ) + + const filtered = filterForPairs(reduced) + const stats = filtered.length ? getInsertSizeStats(filtered) : undefined + const chains = {} as { [key: string]: ReducedFeature[] } + + // pair features + reduced.forEach(f => { + if (!chains[f.name]) { + chains[f.name] = [] + } + chains[f.name].push(f) + }) + return { + chains: Object.values(chains), + stats, + hasPaired: !!stats, + containsNoTransferables: true, + } + } +} diff --git a/plugins/alignments/src/PileupRPC/methods/GetVisibleModifications.ts b/plugins/alignments/src/PileupRPC/methods/GetVisibleModifications.ts new file mode 100644 index 0000000000..17d898c612 --- /dev/null +++ b/plugins/alignments/src/PileupRPC/methods/GetVisibleModifications.ts @@ -0,0 +1,45 @@ +import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache' +import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals' +import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter' +import { Region } from '@jbrowse/core/util' +import { toArray } from 'rxjs/operators' + +// locals +import { getModificationTypes } from '../../MismatchParser' +import PileupBaseRPC from '../base' +import { getTagAlt } from '../../util' + +export default class PileupGetVisibleModifications extends PileupBaseRPC { + name = 'PileupGetVisibleModifications' + + async execute( + args: { + adapterConfig: {} + signal?: RemoteAbortSignal + headers?: Record + regions: Region[] + sessionId: string + tag: string + }, + rpcDriver: string, + ) { + const { adapterConfig, sessionId, regions } = + await this.deserializeArguments(args, rpcDriver) + const dataAdapter = ( + await getAdapter(this.pluginManager, sessionId, adapterConfig) + ).dataAdapter as BaseFeatureDataAdapter + + const featuresArray = await dataAdapter + .getFeaturesInMultipleRegions(regions) + .pipe(toArray()) + .toPromise() + + const uniqueValues = new Set() + featuresArray.forEach(f => { + getModificationTypes(getTagAlt(f, 'MM', 'Mm') || '').forEach(t => + uniqueValues.add(t), + ) + }) + return [...uniqueValues] + } +} diff --git a/plugins/alignments/src/PileupRPC/rpcMethods.ts b/plugins/alignments/src/PileupRPC/rpcMethods.ts index 5a081d3eaf..566138c9e0 100644 --- a/plugins/alignments/src/PileupRPC/rpcMethods.ts +++ b/plugins/alignments/src/PileupRPC/rpcMethods.ts @@ -1,119 +1,9 @@ -import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache' -import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType' -import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods' -import { renameRegionsIfNeeded } from '@jbrowse/core/util' -import { Region } from '@jbrowse/core/util/types' -import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals' -import { toArray } from 'rxjs/operators' -import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter' -import { getTagAlt } from '../util' -import { getModificationTypes } from '../BamAdapter/MismatchParser' - -export class PileupGetGlobalValueForTag extends RpcMethodType { - name = 'PileupGetGlobalValueForTag' - - async serializeArguments( - args: RenderArgs & { - signal?: AbortSignal - statusCallback?: (arg: string) => void - }, - rpcDriverClassName: string, - ) { - const { rootModel } = this.pluginManager - const assemblyManager = rootModel?.session?.assemblyManager - if (!assemblyManager) { - throw new Error('no assembly manager available') - } - - const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args) - - return super.serializeArguments(renamedArgs, rpcDriverClassName) - } - - async execute( - args: { - adapterConfig: {} - signal?: RemoteAbortSignal - headers?: Record - regions: Region[] - sessionId: string - tag: string - }, - rpcDriverClassName: string, - ) { - const deserializedArgs = await this.deserializeArguments( - args, - rpcDriverClassName, - ) - const { adapterConfig, sessionId, regions, tag } = deserializedArgs - const dataAdapter = ( - await getAdapter(this.pluginManager, sessionId, adapterConfig) - ).dataAdapter as BaseFeatureDataAdapter - - const features = dataAdapter.getFeaturesInMultipleRegions(regions) - const featuresArray = await features.pipe(toArray()).toPromise() - const uniqueValues = new Set() - featuresArray.forEach(feature => { - const tags = feature.get('tags') - const val = tags ? tags[tag] : feature.get(tag) - if (val !== undefined) { - uniqueValues.add(`${val}`) - } - }) - return [...uniqueValues] - } -} - -export class PileupGetVisibleModifications extends RpcMethodType { - name = 'PileupGetVisibleModifications' - - async serializeArguments( - args: RenderArgs & { - signal?: AbortSignal - statusCallback?: (arg: string) => void - }, - rpcDriverClassName: string, - ) { - const { rootModel } = this.pluginManager - const assemblyManager = rootModel?.session?.assemblyManager - if (!assemblyManager) { - throw new Error('no assembly manager available') - } - - const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args) - - return super.serializeArguments(renamedArgs, rpcDriverClassName) - } - - async execute( - args: { - adapterConfig: {} - signal?: RemoteAbortSignal - headers?: Record - regions: Region[] - sessionId: string - tag: string - }, - rpcDriverClassName: string, - ) { - const deserializedArgs = await this.deserializeArguments( - args, - rpcDriverClassName, - ) - const { adapterConfig, sessionId, regions } = deserializedArgs - const dataAdapter = ( - await getAdapter(this.pluginManager, sessionId, adapterConfig) - ).dataAdapter as BaseFeatureDataAdapter - - const features = dataAdapter.getFeaturesInMultipleRegions(regions) - const featuresArray = await features.pipe(toArray()).toPromise() - const uniqueValues = new Set() - featuresArray.forEach(feature => { - const val = (getTagAlt(feature, 'MM', 'Mm') as string) || '' - if (val !== undefined) { - getModificationTypes(val).forEach(t => uniqueValues.add(t)) - } - }) - return [...uniqueValues] - } +import PileupGetReducedFeatures from './methods/GetReducedFeatures' +import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag' +import PileupGetVisibleModifications from './methods/GetVisibleModifications' + +export { + PileupGetReducedFeatures, + PileupGetVisibleModifications, + PileupGetGlobalValueForTag, } diff --git a/plugins/alignments/src/PileupRPC/util.ts b/plugins/alignments/src/PileupRPC/util.ts new file mode 100644 index 0000000000..1a50e80601 --- /dev/null +++ b/plugins/alignments/src/PileupRPC/util.ts @@ -0,0 +1,19 @@ +import { ReducedFeature } from '../shared/fetchChains' + +export function getInsertSizeStats(features: ReducedFeature[]) { + const filtered = features.map(f => Math.abs(f.tlen)) + const sum = filtered.reduce((a, b) => a + b, 0) + const sum2 = filtered.map(a => a * a).reduce((a, b) => a + b, 0) + const total = filtered.length + const avg = sum / total + const sd = Math.sqrt((total * sum2 - sum * sum) / (total * total)) + const upper = avg + 4 * sd + const lower = avg - 3 * sd + return { upper, lower, avg, sd } +} + +export function filterForPairs(features: ReducedFeature[]) { + return features.filter( + f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048), + ) +} diff --git a/plugins/alignments/src/PileupRenderer/PileupRenderer.tsx b/plugins/alignments/src/PileupRenderer/PileupRenderer.ts similarity index 94% rename from plugins/alignments/src/PileupRenderer/PileupRenderer.tsx rename to plugins/alignments/src/PileupRenderer/PileupRenderer.ts index bf70107fd4..3c50438d6b 100644 --- a/plugins/alignments/src/PileupRenderer/PileupRenderer.tsx +++ b/plugins/alignments/src/PileupRenderer/PileupRenderer.ts @@ -29,7 +29,7 @@ import { parseCigar, getModificationPositions, getNextRefPos, -} from '../BamAdapter/MismatchParser' +} from '../MismatchParser' import { sortFeature } from './sortUtil' import { getTagAlt, @@ -178,9 +178,9 @@ export default class PileupRenderer extends BoxRendererType { // Expand the start and end of feature when softclipping enabled if (showSoftClip) { - const mismatches = feature.get('mismatches') as Mismatch[] + const mismatches = feature.get('mismatches') as Mismatch[] | undefined const seq = feature.get('seq') as string - if (seq) { + if (seq && mismatches) { for (let i = 0; i < mismatches.length; i += 1) { const { type, start, cliplen = 0 } = mismatches[i] if (type === 'softclip') { @@ -271,7 +271,7 @@ export default class PileupRenderer extends BoxRendererType { colorByInsertSize(feature: Feature, _config: AnyConfigurationModel) { return feature.get('is_paired') && - feature.get('seq_id') !== feature.get('next_seq_id') + feature.get('refName') !== feature.get('next_ref') ? '#555' : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)` } @@ -292,7 +292,7 @@ export default class PileupRenderer extends BoxRendererType { ? 'color_rev_missing_mate' : 'color_fwd_missing_mate' } - if (feature.get('seq_id') === feature.get('next_seq_id')) { + if (feature.get('refName') === feature.get('next_refName')) { return strand * flipper === 1 ? 'color_rev_strand_not_proper' : 'color_fwd_strand_not_proper' @@ -849,7 +849,7 @@ export default class PileupRenderer extends BoxRendererType { const pxPerBp = Math.min(1 / bpPerPx, 2) const w = Math.max(minSubfeatureWidth, pxPerBp) - const mismatches: Mismatch[] = feature.get('mismatches') + const mismatches = feature.get('mismatches') as Mismatch[] | undefined const heightLim = charHeight - 2 // extraHorizontallyFlippedOffset is used to draw interbase items, which @@ -858,6 +858,10 @@ export default class PileupRenderer extends BoxRendererType { ? 1 / bpPerPx + 1 : -1 + if (!mismatches) { + return + } + // two pass rendering: first pass, draw all the mismatches except wide // insertion markers for (let i = 0; i < mismatches.length; i += 1) { @@ -915,7 +919,7 @@ export default class PileupRenderer extends BoxRendererType { ctx, leftPx, topPx, - widthPx, + Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorForBase.deletion, @@ -934,10 +938,7 @@ export default class PileupRenderer extends BoxRendererType { ctx.fillStyle = 'purple' const pos = leftPx + extraHorizontallyFlippedOffset const len = +mismatch.base || mismatch.length - const insW = Math.max( - minSubfeatureWidth / 2, - Math.min(1.2, 1 / bpPerPx), - ) + const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx)) if (len < 10) { fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple') if (1 / bpPerPx >= charWidth && heightPx >= heightLim) { @@ -1052,7 +1053,7 @@ export default class PileupRenderer extends BoxRendererType { const { regions, bpPerPx } = renderArgs const [region] = regions const minFeatWidth = readConfObject(config, 'minSubfeatureWidth') - const mismatches: Mismatch[] = feature.get('mismatches') + const mismatches = feature.get('mismatches') as Mismatch[] | undefined const seq = feature.get('seq') const { charWidth, charHeight } = this.getCharWidthHeight() const { bases } = theme.palette @@ -1065,59 +1066,49 @@ export default class PileupRenderer extends BoxRendererType { } // Display all bases softclipped off in lightened colors - if (seq) { - mismatches - .filter(mismatch => mismatch.type === 'softclip') - .forEach(mismatch => { - const softClipLength = mismatch.cliplen || 0 - const s = feature.get('start') - const softClipStart = - mismatch.start === 0 ? s - softClipLength : s + mismatch.start - - for (let k = 0; k < softClipLength; k += 1) { - const base = seq.charAt(k + mismatch.start) - - // If softclip length+start is longer than sequence, no need to - // continue showing base - if (!base) { - return - } - - const [softClipLeftPx, softClipRightPx] = bpSpanPx( - softClipStart + k, - softClipStart + k + 1, - region, - bpPerPx, - ) - const softClipWidthPx = Math.max( - minFeatWidth, - Math.abs(softClipLeftPx - softClipRightPx), - ) + if (!(seq && mismatches)) { + return + } + mismatches + .filter(mismatch => mismatch.type === 'softclip') + .forEach(mismatch => { + const len = mismatch.cliplen || 0 + const s = feature.get('start') + const start = mismatch.start === 0 ? s - len : s + mismatch.start + + for (let k = 0; k < len; k += 1) { + const base = seq.charAt(k + mismatch.start) + + // If softclip length+start is longer than sequence, no need to + // continue showing base + if (!base) { + return + } - // Black accounts for IUPAC ambiguity code bases such as N that - // show in soft clipping - const baseColor = colorForBase[base] || '#000000' - ctx.fillStyle = baseColor - fillRect( - ctx, - softClipLeftPx, - topPx, - softClipWidthPx, - heightPx, - canvasWidth, - ) + const [leftPx, rightPx] = bpSpanPx( + start + k, + start + k + 1, + region, + bpPerPx, + ) + const widthPx = Math.max(minFeatWidth, rightPx - leftPx) + + // Black accounts for IUPAC ambiguity code bases such as N that + // show in soft clipping + const baseColor = colorForBase[base] || '#000000' + ctx.fillStyle = baseColor + fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth) - if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) { - ctx.fillStyle = theme.palette.getContrastText(baseColor) - ctx.fillText( - base, - softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1, - topPx + heightPx, - ) - } + if (widthPx >= charWidth && heightPx >= charHeight - 5) { + ctx.fillStyle = theme.palette.getContrastText(baseColor) + ctx.fillText( + base, + leftPx + (widthPx - charWidth) / 2 + 1, + topPx + heightPx, + ) } - }) - } + } + }) } makeImageData({ diff --git a/plugins/alignments/src/PileupRenderer/configSchema.ts b/plugins/alignments/src/PileupRenderer/configSchema.ts index a8d86fc71b..38258d0d29 100644 --- a/plugins/alignments/src/PileupRenderer/configSchema.ts +++ b/plugins/alignments/src/PileupRenderer/configSchema.ts @@ -28,7 +28,7 @@ const PileupRenderer = ConfigurationSchema( model: types.enumeration('orientationType', ['fr', 'rf', 'ff']), defaultValue: 'fr', description: - 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options', + 'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options', }, /** * #slot diff --git a/plugins/alignments/src/PileupRenderer/index.ts b/plugins/alignments/src/PileupRenderer/index.ts index 5417ce41c6..25a0744985 100644 --- a/plugins/alignments/src/PileupRenderer/index.ts +++ b/plugins/alignments/src/PileupRenderer/index.ts @@ -4,13 +4,13 @@ import ReactComponent from './components/PileupRendering' import configSchema from './configSchema' export default function register(pluginManager: PluginManager) { - pluginManager.addRendererType( - () => - new PileupRenderer({ - name: 'PileupRenderer', - ReactComponent, - configSchema, - pluginManager, - }), - ) + pluginManager.addRendererType(() => { + return new PileupRenderer({ + name: 'PileupRenderer', + displayName: 'Pileup renderer', + ReactComponent, + configSchema, + pluginManager, + }) + }) } diff --git a/plugins/alignments/src/PileupRenderer/sortUtil.ts b/plugins/alignments/src/PileupRenderer/sortUtil.ts index bd467893e0..3186196ade 100644 --- a/plugins/alignments/src/PileupRenderer/sortUtil.ts +++ b/plugins/alignments/src/PileupRenderer/sortUtil.ts @@ -1,6 +1,5 @@ -import { Feature } from '@jbrowse/core/util/simpleFeature' -import { doesIntersect2 } from '@jbrowse/core/util/range' -import { Mismatch } from '../BamAdapter/MismatchParser' +import { doesIntersect2, Feature } from '@jbrowse/core/util' +import { Mismatch } from '../MismatchParser' interface SortObject { pos: number diff --git a/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts b/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts index 49ffb495e4..99739216cc 100644 --- a/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +++ b/plugins/alignments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts @@ -6,46 +6,13 @@ import { AugmentedRegion as Region } from '@jbrowse/core/util/types' import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature' import { ObservableCreate } from '@jbrowse/core/util/rxjs' import { toArray } from 'rxjs/operators' -import { - getTag, - getTagAlt, - fetchSequence, - shouldFetchReferenceSequence, -} from '../util' -import { - parseCigar, - getNextRefPos, - getModificationPositions, - Mismatch, -} from '../BamAdapter/MismatchParser' - -function mismatchLen(mismatch: Mismatch) { - return !isInterbase(mismatch.type) ? mismatch.length : 1 -} - -function isInterbase(type: string) { - return type === 'softclip' || type === 'hardclip' || type === 'insertion' -} - -// eslint-disable-next-line @typescript-eslint/no-explicit-any -function inc(bin: any, strand: number, type: string, field: string) { - let thisBin = bin[type][field] - if (thisBin === undefined) { - thisBin = bin[type][field] = { - total: 0, - '-1': 0, - '0': 0, - '1': 0, - } - } - thisBin.total++ - thisBin[strand]++ -} +import generateCoverageBins from './generateCoverageBins' +import { fetchSequence } from '../util' export default class SNPCoverageAdapter extends BaseFeatureDataAdapter { protected async configure() { const subadapterConfig = this.getConf('subadapter') - const sequenceConf = this.getConf(['subadapter', 'sequenceAdapter']) + const sequenceConf = subadapterConfig.sequenceAdapter const dataAdapter = await this.getSubAdapter?.(subadapterConfig) const sequenceAdapter = sequenceConf @@ -81,10 +48,11 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter { .pipe(toArray()) .toPromise() - const { bins, skipmap } = await this.generateCoverageBins( + const { bins, skipmap } = await generateCoverageBins( feats, region, opts, + arg => this.fetchSequence(arg), ) bins.forEach((bin, index) => { @@ -135,218 +103,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter { } freeResources(/* { region } */): void {} - - async generateCoverageBins( - features: Feature[], - region: Region, - opts: { bpPerPx?: number; colorBy?: { type: string; tag?: string } }, - ) { - const { colorBy } = opts - const binMax = Math.ceil(region.end - region.start) - - const skipmap = {} as { - [key: string]: { - score: number - feature: unknown - start: number - end: number - strand: number - xs: string - } - } - - // bins contain: - // - cov feature if they contribute to coverage - // - noncov are insertions/clip features that don't contribute to coverage - // - delskips deletions or introns that don't contribute to coverage - type BinType = { total: number; strands: { [key: string]: number } } - - const regionSeq = - features.length && shouldFetchReferenceSequence(opts.colorBy?.type) - ? await this.fetchSequence(region) - : undefined - - const bins = [] as { - refbase?: string - total: number - all: number - ref: number - '-1': 0 - '0': 0 - '1': 0 - lowqual: BinType - cov: BinType - delskips: BinType - noncov: BinType - }[] - - for (let i = 0; i < features.length; i++) { - const feature = features[i] - const fstart = feature.get('start') - const fend = feature.get('end') - const fstrand = feature.get('strand') as -1 | 0 | 1 - - for (let j = fstart; j < fend + 1; j++) { - const i = j - region.start - if (i >= 0 && i < binMax) { - if (bins[i] === undefined) { - bins[i] = { - total: 0, - all: 0, - ref: 0, - '-1': 0, - '0': 0, - '1': 0, - lowqual: {} as BinType, - cov: {} as BinType, - delskips: {} as BinType, - noncov: {} as BinType, - } - } - if (j !== fend) { - bins[i].total++ - bins[i].all++ - bins[i].ref++ - bins[i][fstrand]++ - } - } - } - - if (colorBy?.type === 'modifications') { - const seq = feature.get('seq') as string - const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || '' - const ops = parseCigar(feature.get('CIGAR')) - const fend = feature.get('end') - - getModificationPositions(mm, seq, fstrand).forEach( - ({ type, positions }) => { - const mod = `mod_${type}` - for (const pos of getNextRefPos(ops, positions)) { - const epos = pos + fstart - region.start - if (epos >= 0 && epos < bins.length && pos + fstart < fend) { - const bin = bins[epos] - if (bin) { - inc(bin, fstrand, 'cov', mod) - } else { - console.warn( - 'Undefined position in modifications snpcoverage encountered', - ) - } - } - } - }, - ) - } - - // methylation based coloring takes into account both reference - // sequence CpG detection and reads - else if (colorBy?.type === 'methylation') { - if (!regionSeq) { - throw new Error( - 'no region sequence detected, need sequenceAdapter configuration', - ) - } - const seq = feature.get('seq') - const mm = getTagAlt(feature, 'MM', 'Mm') || '' - const methBins = new Array(region.end - region.start).fill(0) - const ops = parseCigar(feature.get('CIGAR')) - - getModificationPositions(mm, seq, fstrand).forEach( - ({ type, positions }) => { - // we are processing methylation - if (type === 'm') { - for (const pos of getNextRefPos(ops, positions)) { - const epos = pos + fstart - region.start - if (epos >= 0 && epos < methBins.length) { - methBins[epos] = 1 - } - } - } - }, - ) - - for (let j = fstart; j < fend; j++) { - const i = j - region.start - if (i >= 0 && i < bins.length - 1) { - const l1 = regionSeq[i].toLowerCase() - const l2 = regionSeq[i + 1].toLowerCase() - const bin = bins[i] - const bin1 = bins[i + 1] - - // color - if (l1 === 'c' && l2 === 'g') { - if (methBins[i] || methBins[i + 1]) { - inc(bin, fstrand, 'cov', 'meth') - inc(bin1, fstrand, 'cov', 'meth') - bins[i].ref-- - bins[i][fstrand]-- - bins[i + 1].ref-- - bins[i + 1][fstrand]-- - } else { - inc(bin, fstrand, 'cov', 'unmeth') - inc(bin1, fstrand, 'cov', 'unmeth') - bins[i].ref-- - bins[i][fstrand]-- - bins[i + 1].ref-- - bins[i + 1][fstrand]-- - } - } - } - } - } - - // normal SNP based coloring - const mismatches = (feature.get('mismatches') as Mismatch[]) || [] - const colorSNPs = - colorBy?.type !== 'modifications' && colorBy?.type !== 'methylation' - - for (let i = 0; i < mismatches.length; i++) { - const mismatch = mismatches[i] - const mstart = fstart + mismatch.start - const mlen = mismatchLen(mismatch) - const mend = mstart + mlen - for (let j = mstart; j < mstart + mlen; j++) { - const epos = j - region.start - if (epos >= 0 && epos < bins.length) { - const bin = bins[epos] - const { base, type } = mismatch - const interbase = isInterbase(type) - if (!interbase) { - bin.ref-- - bin[fstrand]-- - } else { - inc(bin, fstrand, 'noncov', type) - } - - if (type === 'deletion' || type === 'skip') { - inc(bin, fstrand, 'delskips', type) - bin.total-- - } else if (!interbase && colorSNPs) { - inc(bin, fstrand, 'cov', base) - bin.refbase = mismatch.altbase - } - } - } - - if (mismatch.type === 'skip') { - const hash = `${mstart}_${mend}_${fstrand}` - if (skipmap[hash] === undefined) { - skipmap[hash] = { - feature: feature, - start: mstart, - end: mend, - strand: fstrand, - xs: getTag(feature, 'XS') || getTag(feature, 'TS'), - score: 0, - } - } - skipmap[hash].score++ - } - } - } - - return { bins, skipmap } - } } const { capabilities } = SNPCoverageAdapter diff --git a/plugins/alignments/src/SNPCoverageAdapter/configSchema.ts b/plugins/alignments/src/SNPCoverageAdapter/configSchema.ts index c815a99a7f..521db955ce 100644 --- a/plugins/alignments/src/SNPCoverageAdapter/configSchema.ts +++ b/plugins/alignments/src/SNPCoverageAdapter/configSchema.ts @@ -1,22 +1,23 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration' -import PluginManager from '@jbrowse/core/PluginManager' /** * #config SNPCoverageAdapter */ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars -const SNPCoverageAdapter = (pluginManager: PluginManager) => - ConfigurationSchema( - 'SNPCoverageAdapter', - { - /** - * #slot - * normally refers to a BAM or CRAM adapter - */ - subadapter: pluginManager.pluggableConfigSchemaType('adapter'), +const configSchema = ConfigurationSchema( + 'SNPCoverageAdapter', + { + /** + * #slot + * normally refers to a BAM or CRAM adapter + */ + subadapter: { + type: 'frozen', + defaultValue: null, }, - { explicitlyTyped: true }, - ) + }, + { explicitlyTyped: true }, +) -export default SNPCoverageAdapter +export default configSchema diff --git a/plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts b/plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts new file mode 100644 index 0000000000..06e50bcb98 --- /dev/null +++ b/plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts @@ -0,0 +1,245 @@ +import { AugmentedRegion as Region } from '@jbrowse/core/util/types' +import { Feature } from '@jbrowse/core/util/simpleFeature' +import { getTag, getTagAlt, shouldFetchReferenceSequence } from '../util' +import { + parseCigar, + getNextRefPos, + getModificationPositions, + Mismatch, +} from '../MismatchParser' + +function mismatchLen(mismatch: Mismatch) { + return !isInterbase(mismatch.type) ? mismatch.length : 1 +} + +function isInterbase(type: string) { + return type === 'softclip' || type === 'hardclip' || type === 'insertion' +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any +function inc(bin: any, strand: number, type: string, field: string) { + let thisBin = bin[type][field] + if (thisBin === undefined) { + thisBin = bin[type][field] = { + total: 0, + '-1': 0, + '0': 0, + '1': 0, + } + } + thisBin.total++ + thisBin[strand]++ +} + +export default async function generateCoverageBins( + features: Feature[], + region: Region, + opts: { bpPerPx?: number; colorBy?: { type: string; tag?: string } }, + fetchSequence: (arg: Region) => Promise, +) { + const { colorBy } = opts + const binMax = Math.ceil(region.end - region.start) + + const skipmap = {} as { + [key: string]: { + score: number + feature: unknown + start: number + end: number + strand: number + xs: string + } + } + + // bins contain: + // - cov feature if they contribute to coverage + // - noncov are insertions/clip features that don't contribute to coverage + // - delskips deletions or introns that don't contribute to coverage + type BinType = { total: number; strands: { [key: string]: number } } + + const regionSeq = + features.length && shouldFetchReferenceSequence(opts.colorBy?.type) + ? await fetchSequence(region) + : undefined + + const bins = [] as { + refbase?: string + total: number + all: number + ref: number + '-1': 0 + '0': 0 + '1': 0 + lowqual: BinType + cov: BinType + delskips: BinType + noncov: BinType + }[] + + for (let i = 0; i < features.length; i++) { + const feature = features[i] + const fstart = feature.get('start') + const fend = feature.get('end') + const fstrand = feature.get('strand') as -1 | 0 | 1 + + for (let j = fstart; j < fend + 1; j++) { + const i = j - region.start + if (i >= 0 && i < binMax) { + if (bins[i] === undefined) { + bins[i] = { + total: 0, + all: 0, + ref: 0, + '-1': 0, + '0': 0, + '1': 0, + lowqual: {} as BinType, + cov: {} as BinType, + delskips: {} as BinType, + noncov: {} as BinType, + } + } + if (j !== fend) { + bins[i].total++ + bins[i].all++ + bins[i].ref++ + bins[i][fstrand]++ + } + } + } + + if (colorBy?.type === 'modifications') { + const seq = feature.get('seq') as string + const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || '' + const ops = parseCigar(feature.get('CIGAR')) + const fend = feature.get('end') + + getModificationPositions(mm, seq, fstrand).forEach( + ({ type, positions }) => { + const mod = `mod_${type}` + for (const pos of getNextRefPos(ops, positions)) { + const epos = pos + fstart - region.start + if (epos >= 0 && epos < bins.length && pos + fstart < fend) { + const bin = bins[epos] + if (bin) { + inc(bin, fstrand, 'cov', mod) + } else { + console.warn( + 'Undefined position in modifications snpcoverage encountered', + ) + } + } + } + }, + ) + } + + // methylation based coloring takes into account both reference + // sequence CpG detection and reads + else if (colorBy?.type === 'methylation') { + if (!regionSeq) { + throw new Error( + 'no region sequence detected, need sequenceAdapter configuration', + ) + } + const seq = feature.get('seq') + const mm = getTagAlt(feature, 'MM', 'Mm') || '' + const methBins = new Array(region.end - region.start).fill(0) + const ops = parseCigar(feature.get('CIGAR')) + + getModificationPositions(mm, seq, fstrand).forEach( + ({ type, positions }) => { + // we are processing methylation + if (type === 'm') { + for (const pos of getNextRefPos(ops, positions)) { + const epos = pos + fstart - region.start + if (epos >= 0 && epos < methBins.length) { + methBins[epos] = 1 + } + } + } + }, + ) + + for (let j = fstart; j < fend; j++) { + const i = j - region.start + if (i >= 0 && i < bins.length - 1) { + const l1 = regionSeq[i].toLowerCase() + const l2 = regionSeq[i + 1].toLowerCase() + const bin = bins[i] + const bin1 = bins[i + 1] + + // color + if (l1 === 'c' && l2 === 'g') { + if (methBins[i] || methBins[i + 1]) { + inc(bin, fstrand, 'cov', 'meth') + inc(bin1, fstrand, 'cov', 'meth') + bins[i].ref-- + bins[i][fstrand]-- + bins[i + 1].ref-- + bins[i + 1][fstrand]-- + } else { + inc(bin, fstrand, 'cov', 'unmeth') + inc(bin1, fstrand, 'cov', 'unmeth') + bins[i].ref-- + bins[i][fstrand]-- + bins[i + 1].ref-- + bins[i + 1][fstrand]-- + } + } + } + } + } + + // normal SNP based coloring + const mismatches = (feature.get('mismatches') as Mismatch[]) || [] + const colorSNPs = + colorBy?.type !== 'modifications' && colorBy?.type !== 'methylation' + + for (let i = 0; i < mismatches.length; i++) { + const mismatch = mismatches[i] + const mstart = fstart + mismatch.start + const mlen = mismatchLen(mismatch) + const mend = mstart + mlen + for (let j = mstart; j < mstart + mlen; j++) { + const epos = j - region.start + if (epos >= 0 && epos < bins.length) { + const bin = bins[epos] + const { base, type } = mismatch + const interbase = isInterbase(type) + if (!interbase) { + bin.ref-- + bin[fstrand]-- + } else { + inc(bin, fstrand, 'noncov', type) + } + + if (type === 'deletion' || type === 'skip') { + inc(bin, fstrand, 'delskips', type) + bin.total-- + } else if (!interbase && colorSNPs) { + inc(bin, fstrand, 'cov', base) + bin.refbase = mismatch.altbase + } + } + } + + if (mismatch.type === 'skip') { + const hash = `${mstart}_${mend}_${fstrand}` + if (skipmap[hash] === undefined) { + skipmap[hash] = { + feature: feature, + start: mstart, + end: mend, + strand: fstrand, + xs: getTag(feature, 'XS') || getTag(feature, 'TS'), + score: 0, + } + } + skipmap[hash].score++ + } + } + } + + return { bins, skipmap } +} diff --git a/plugins/alignments/src/SNPCoverageAdapter/index.ts b/plugins/alignments/src/SNPCoverageAdapter/index.ts index 9ee962b5ee..886d96e163 100644 --- a/plugins/alignments/src/SNPCoverageAdapter/index.ts +++ b/plugins/alignments/src/SNPCoverageAdapter/index.ts @@ -1,23 +1,20 @@ import PluginManager from '@jbrowse/core/PluginManager' import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' -import configSchemaFactory from './configSchema' +import configSchema from './configSchema' import { capabilities } from './SNPCoverageAdapter' -export default (pluginManager: PluginManager) => { - pluginManager.addAdapterType( - () => - new AdapterType({ - name: 'SNPCoverageAdapter', - adapterMetadata: { - category: null, - displayName: null, - hiddenFromGUI: true, - description: null, - }, - getAdapterClass: () => - import('./SNPCoverageAdapter').then(r => r.default), - configSchema: configSchemaFactory(pluginManager), - adapterCapabilities: capabilities, - }), - ) +export default function (pluginManager: PluginManager) { + pluginManager.addAdapterType(() => { + return new AdapterType({ + name: 'SNPCoverageAdapter', + displayName: 'SNPCoverage adapter', + adapterMetadata: { + hiddenFromGUI: true, + }, + getAdapterClass: () => + import('./SNPCoverageAdapter').then(r => r.default), + configSchema, + adapterCapabilities: capabilities, + }) + }) } diff --git a/plugins/alignments/src/__snapshots__/index.test.ts.snap b/plugins/alignments/src/__snapshots__/index.test.ts.snap index 463d523aec..a10c09c9d1 100644 --- a/plugins/alignments/src/__snapshots__/index.test.ts.snap +++ b/plugins/alignments/src/__snapshots__/index.test.ts.snap @@ -1,3 +1,3 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`plugin in a stock JBrowse 1`] = `Object {}`; +exports[`plugin in a stock JBrowse 1`] = `{}`; diff --git a/plugins/alignments/src/index.ts b/plugins/alignments/src/index.ts index 0506b1b749..ddefb9d66b 100644 --- a/plugins/alignments/src/index.ts +++ b/plugins/alignments/src/index.ts @@ -1,9 +1,5 @@ -import { FileLocation } from '@jbrowse/core/util/types' import Plugin from '@jbrowse/core/Plugin' import PluginManager from '@jbrowse/core/PluginManager' -import * as MismatchParser from './BamAdapter/MismatchParser' -import { LinearPileupDisplayModel } from './LinearPileupDisplay/model' - import BamAdapterF from './CramAdapter' import CramAdapterF from './BamAdapter' import HtsgetBamAdapterF from './HtsgetBamAdapter' @@ -12,24 +8,18 @@ import SNPCoverageRendererF from './SNPCoverageRenderer' import PileupRendererF from './PileupRenderer' import LinearAlignmentsDisplayF from './LinearAlignmentsDisplay' import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay' -import LinearPileupDisplayF from './LinearPileupDisplay' +import LinearReadArcsDisplayF from './LinearReadArcsDisplay' +import LinearReadCloudDisplayF from './LinearReadCloudDisplay' import AlignmentsTrackF from './AlignmentsTrack' import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail' - -import { - PileupGetGlobalValueForTag, - PileupGetVisibleModifications, -} from './PileupRPC/rpcMethods' -import { - makeIndex, - makeIndexType, - getFileName, - AdapterGuesser, - TrackTypeGuesser, -} from '@jbrowse/core/util/tracks' - -export { MismatchParser } -export type { LinearPileupDisplayModel } +import PileupRPCMethodsF from './PileupRPC' +import GuessAlignmentsTypesF from './GuessAlignmentsTypes' +import LinearPileupDisplayF, { + linearPileupDisplayStateModelFactory, + linearPileupDisplayConfigSchemaFactory, +} from './LinearPileupDisplay' +import { LinearPileupDisplayModel } from './LinearPileupDisplay/model' +import * as MismatchParser from './MismatchParser' export default class AlignmentsPlugin extends Plugin { name = 'AlignmentsPlugin' @@ -44,84 +34,20 @@ export default class AlignmentsPlugin extends Plugin { SNPCoverageAdapterF, HtsgetBamAdapterF, PileupRendererF, + PileupRPCMethodsF, SNPCoverageRendererF, + LinearReadArcsDisplayF, + LinearReadCloudDisplayF, LinearAlignmentsDisplayF, AlignmentsFeatureWidgetF, + GuessAlignmentsTypesF, ].map(f => f(pluginManager)) - - pluginManager.addToExtensionPoint( - 'Core-guessAdapterForLocation', - (adapterGuesser: AdapterGuesser) => { - return ( - file: FileLocation, - index?: FileLocation, - adapterHint?: string, - ) => { - const regexGuess = /\.cram$/i - const adapterName = 'CramAdapter' - const fileName = getFileName(file) - const obj = { - type: adapterName, - cramLocation: file, - craiLocation: index || makeIndex(file, '.crai'), - } - if (regexGuess.test(fileName) && !adapterHint) { - return obj - } else if (adapterHint === adapterName) { - return obj - } - return adapterGuesser(file, index, adapterHint) - } - }, - ) - - pluginManager.addToExtensionPoint( - 'Core-guessAdapterForLocation', - (adapterGuesser: AdapterGuesser) => { - return ( - file: FileLocation, - index?: FileLocation, - adapterHint?: string, - ) => { - const regexGuess = /\.bam$/i - const adapterName = 'BamAdapter' - const fileName = getFileName(file) - const indexName = index && getFileName(index) - - const obj = { - type: adapterName, - bamLocation: file, - index: { - location: index || makeIndex(file, '.bai'), - indexType: makeIndexType(indexName, 'CSI', 'BAI'), - }, - } - if (regexGuess.test(fileName) && !adapterHint) { - return obj - } else if (adapterHint === adapterName) { - return obj - } - return adapterGuesser(file, index, adapterHint) - } - }, - ) - pluginManager.addToExtensionPoint( - 'Core-guessTrackTypeForLocation', - (trackTypeGuesser: TrackTypeGuesser) => { - return (adapterName: string) => { - if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') { - return 'AlignmentsTrack' - } - return trackTypeGuesser(adapterName) - } - }, - ) - - pluginManager.addRpcMethod( - () => new PileupGetGlobalValueForTag(pluginManager), - ) - pluginManager.addRpcMethod( - () => new PileupGetVisibleModifications(pluginManager), - ) } } + +export { + linearPileupDisplayConfigSchemaFactory, + linearPileupDisplayStateModelFactory, + MismatchParser, +} +export type { LinearPileupDisplayModel } diff --git a/plugins/alignments/src/LinearPileupDisplay/components/FilterByTag.tsx b/plugins/alignments/src/shared/FilterByTag.tsx similarity index 87% rename from plugins/alignments/src/LinearPileupDisplay/components/FilterByTag.tsx rename to plugins/alignments/src/shared/FilterByTag.tsx index 7e2629ad7b..b6d875c886 100644 --- a/plugins/alignments/src/LinearPileupDisplay/components/FilterByTag.tsx +++ b/plugins/alignments/src/shared/FilterByTag.tsx @@ -2,31 +2,21 @@ import React, { useState } from 'react' import { observer } from 'mobx-react' import { Button, - Dialog, DialogActions, DialogContent, - DialogTitle, - IconButton, Link, Paper, TextField, Typography, } from '@mui/material' +import { Dialog } from '@jbrowse/core/ui' import { makeStyles } from 'tss-react/mui' -import CloseIcon from '@mui/icons-material/Close' - const useStyles = makeStyles()(theme => ({ paper: { padding: theme.spacing(2), margin: theme.spacing(2), }, - closeButton: { - position: 'absolute', - right: theme.spacing(1), - top: theme.spacing(1), - color: theme.palette.grey[500], - }, field: { margin: theme.spacing(2), }, @@ -105,17 +95,7 @@ function FilterByTagDlg(props: { const site = 'https://broadinstitute.github.io/picard/explain-flags.html' return ( - - - Filter options - - - - + Set filter bitmask options. Refer to {site}{' '} @@ -143,9 +123,7 @@ function FilterByTagDlg(props: { { - setTag(event.target.value) - }} + onChange={event => setTag(event.target.value)} placeholder="Enter tag name" inputProps={{ maxLength: 2, @@ -158,9 +136,7 @@ function FilterByTagDlg(props: { { - setTagValue(event.target.value) - }} + onChange={event => setTagValue(event.target.value)} placeholder="Enter tag value" inputProps={{ 'data-testid': 'color-tag-name-input', @@ -173,9 +149,7 @@ function FilterByTagDlg(props: { { - setReadName(event.target.value) - }} + onChange={event => setReadName(event.target.value)} placeholder="Enter read name" inputProps={{ 'data-testid': 'color-tag-readname-input', diff --git a/plugins/alignments/src/shared/color.ts b/plugins/alignments/src/shared/color.ts new file mode 100644 index 0000000000..ecdb37cd1f --- /dev/null +++ b/plugins/alignments/src/shared/color.ts @@ -0,0 +1,47 @@ +import { orientationTypes } from '../util' +import { ChainStats } from './fetchChains' + +const alignmentColoring: { [key: string]: string } = { + color_pair_lr: '#c8c8c8', + color_pair_rr: 'navy', + color_pair_rl: 'teal', + color_pair_ll: 'green', +} + +export function getInsertSizeColor( + f1: { refName: string; tlen?: number }, + f2: { refName: string }, + stats?: ChainStats, +) { + const sameRef = f1.refName === f2.refName + const tlen = Math.abs(f1.tlen || 0) + if (sameRef && tlen > (stats?.upper || 0)) { + return 'red' + } else if (sameRef && tlen < (stats?.lower || 0)) { + return '#f0f' + } else if (!sameRef) { + return 'purple' + } + return '' +} + +export function getInsertSizeAndOrientationColor( + f1: { refName: string; pair_orientation?: string; tlen?: number }, + f2: { refName: string }, + stats?: ChainStats, +) { + return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1) +} + +export function getOrientationColor(f: { pair_orientation?: string }) { + const type = orientationTypes['fr'] + const orientation = type[f.pair_orientation || ''] + const map = { + LR: 'color_pair_lr', + RR: 'color_pair_rr', + RL: 'color_pair_rl', + LL: 'color_pair_ll', + } + const val = map[orientation as keyof typeof map] + return alignmentColoring[val] || 'grey' +} diff --git a/plugins/alignments/src/shared/fetchChains.ts b/plugins/alignments/src/shared/fetchChains.ts new file mode 100644 index 0000000000..287a99cf24 --- /dev/null +++ b/plugins/alignments/src/shared/fetchChains.ts @@ -0,0 +1,63 @@ +import { + getContainingTrack, + getContainingView, + getSession, +} from '@jbrowse/core/util' +import { getSnapshot, IAnyStateTreeNode } from 'mobx-state-tree' +import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' + +type LGV = LinearGenomeViewModel + +export interface ReducedFeature { + name: string + strand: number + refName: string + start: number + end: number + id: string + flags: number + tlen: number + pair_orientation: string + next_ref?: string + next_pos?: number + clipPos: number + SA?: string +} + +export interface ChainStats { + max: number + min: number + upper: number + lower: number +} + +export interface ChainData { + chains: ReducedFeature[][] + stats?: ChainStats +} + +export async function fetchChains(self: IAnyStateTreeNode) { + try { + const { rpcSessionId: sessionId } = getContainingTrack(self) + const { rpcManager } = getSession(self) + const view = getContainingView(self) as LGV + + if (!view.initialized || self.error) { + return + } + self.setLoading(true) + + const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', { + sessionId, + regions: view.staticBlocks.contentBlocks, + filterBy: getSnapshot(self.filterBy), + adapterConfig: self.adapterConfig, + })) as ChainData + + self.setChainData(ret) + self.setLoading(false) + } catch (e) { + console.error(e) + self.setError(e) + } +} diff --git a/plugins/alignments/src/shared.ts b/plugins/alignments/src/shared/index.ts similarity index 77% rename from plugins/alignments/src/shared.ts rename to plugins/alignments/src/shared/index.ts index 68ec5f1b45..af2e47e64e 100644 --- a/plugins/alignments/src/shared.ts +++ b/plugins/alignments/src/shared/index.ts @@ -1,9 +1,8 @@ +import { types, IAnyStateTreeNode } from 'mobx-state-tree' import { BlockSet } from '@jbrowse/core/util/blockTypes' - import { getSession } from '@jbrowse/core/util' import { getRpcSessionId } from '@jbrowse/core/util/tracks' -import { IAnyStateTreeNode } from 'mobx-state-tree' -import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema' +import { AnyConfigurationModel } from '@jbrowse/core/configuration' export async function getUniqueTagValues( self: IAnyStateTreeNode & { adapterConfig: AnyConfigurationModel }, @@ -32,9 +31,11 @@ export async function getUniqueTagValues( return values as string[] } +type Track = IAnyStateTreeNode & { configuration: AnyConfigurationModel } + export async function getUniqueModificationValues( self: IAnyStateTreeNode & { - parentTrack: IAnyStateTreeNode & { configuration: AnyConfigurationModel } + parentTrack: Track }, adapterConfig: AnyConfigurationModel, colorScheme: { type: string; tag?: string }, @@ -60,3 +61,15 @@ export async function getUniqueModificationValues( ) return values as string[] } + +export const FilterModel = types.model({ + flagInclude: types.optional(types.number, 0), + flagExclude: types.optional(types.number, 1540), + readName: types.maybe(types.string), + tagFilter: types.maybe( + types.model({ + tag: types.string, + value: types.string, + }), + ), +}) diff --git a/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam new file mode 100644 index 0000000000..c1443c7988 Binary files /dev/null and b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam differ diff --git a/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam.bai b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam.bai new file mode 100644 index 0000000000..116269c5ea Binary files /dev/null and b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam.bai differ diff --git a/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam.conf b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam.conf new file mode 100644 index 0000000000..69815dda78 --- /dev/null +++ b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.bam.conf @@ -0,0 +1,9 @@ +[ tracks . volvox-long_reads ] +key = BAM - volvox-longreads.bam +storeClass = JBrowse/Store/SeqFeature/BAM +urlTemplate = ../../raw/volvox//volvox-long-reads.fastq.sorted.bam +metadata.category = BAM +metadata.Description = BAM-format alignments of simulated long reads. +type = JBrowse/View/Track/Alignments2 +renderAlignment = true +cacheMismatches = true diff --git a/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.cram b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.cram new file mode 100644 index 0000000000..5aff63a524 Binary files /dev/null and b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.cram differ diff --git a/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.cram.crai b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.cram.crai new file mode 100644 index 0000000000..a40cebc4df Binary files /dev/null and b/plugins/alignments/test_data/volvox-long-reads.fastq.sorted.cram.crai differ diff --git a/plugins/arc/package.json b/plugins/arc/package.json index 4166d09820..ed3c0f842c 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/arc", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", @@ -47,8 +47,8 @@ "mobx": "^6.0.0", "mobx-react": "^7.0.0", "mobx-state-tree": "^5.0.0", - "prop-types": "^15.0.0", "react": ">=16.8.0", + "react-dom": ">=16.8.0", "rxjs": "^6.0.0" }, "private": true, diff --git a/plugins/arc/src/ArcRenderer/ArcRenderer.tsx b/plugins/arc/src/ArcRenderer/ArcRenderer.ts similarity index 100% rename from plugins/arc/src/ArcRenderer/ArcRenderer.tsx rename to plugins/arc/src/ArcRenderer/ArcRenderer.ts diff --git a/plugins/arc/src/ArcRenderer/configSchema.tsx b/plugins/arc/src/ArcRenderer/configSchema.ts similarity index 100% rename from plugins/arc/src/ArcRenderer/configSchema.tsx rename to plugins/arc/src/ArcRenderer/configSchema.ts diff --git a/plugins/arc/src/ArcRenderer/index.ts b/plugins/arc/src/ArcRenderer/index.ts new file mode 100644 index 0000000000..156bda52f0 --- /dev/null +++ b/plugins/arc/src/ArcRenderer/index.ts @@ -0,0 +1,17 @@ +import PluginManager from '@jbrowse/core/PluginManager' + +import ReactComponent from './ArcRendering' +import configSchema from './configSchema' +import ArcRenderer from './ArcRenderer' + +export default (pluginManager: PluginManager) => { + pluginManager.addRendererType( + () => + new ArcRenderer({ + name: 'ArcRenderer', + ReactComponent, + configSchema, + pluginManager, + }), + ) +} diff --git a/plugins/arc/src/ArcRenderer/index.tsx b/plugins/arc/src/ArcRenderer/index.tsx deleted file mode 100644 index 6b1bd96681..0000000000 --- a/plugins/arc/src/ArcRenderer/index.tsx +++ /dev/null @@ -1,3 +0,0 @@ -export { default as ReactComponent } from './ArcRendering' -export { default as configSchema } from './configSchema' -export { default } from './ArcRenderer' diff --git a/plugins/arc/src/LinearArcDisplay/configSchema.tsx b/plugins/arc/src/LinearArcDisplay/configSchema.ts similarity index 76% rename from plugins/arc/src/LinearArcDisplay/configSchema.tsx rename to plugins/arc/src/LinearArcDisplay/configSchema.ts index 992e9661a5..3b08efb160 100644 --- a/plugins/arc/src/LinearArcDisplay/configSchema.tsx +++ b/plugins/arc/src/LinearArcDisplay/configSchema.ts @@ -1,15 +1,12 @@ import PluginManager from '@jbrowse/core/PluginManager' import { types } from 'mobx-state-tree' import { ConfigurationSchema } from '@jbrowse/core/configuration' +import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view' /** * #config LinearArcDisplay */ export function configSchemaFactory(pluginManager: PluginManager) { - const LGVPlugin = pluginManager.getPlugin( - 'LinearGenomeViewPlugin', - ) as import('@jbrowse/plugin-linear-genome-view').default - const { baseLinearDisplayConfigSchema } = LGVPlugin.exports return ConfigurationSchema( 'LinearArcDisplay', { diff --git a/plugins/arc/src/LinearArcDisplay/index.ts b/plugins/arc/src/LinearArcDisplay/index.ts new file mode 100644 index 0000000000..d8ae623505 --- /dev/null +++ b/plugins/arc/src/LinearArcDisplay/index.ts @@ -0,0 +1,20 @@ +import PluginManager from '@jbrowse/core/PluginManager' +import { DisplayType } from '@jbrowse/core/pluggableElementTypes' +import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view' + +import { configSchemaFactory } from './configSchema' +import { stateModelFactory } from './model' + +export default (pluginManager: PluginManager) => { + pluginManager.addDisplayType(() => { + const configSchema = configSchemaFactory(pluginManager) + return new DisplayType({ + name: 'LinearArcDisplay', + configSchema, + stateModel: stateModelFactory(configSchema), + trackType: 'FeatureTrack', + viewType: 'LinearGenomeView', + ReactComponent: BaseLinearDisplayComponent, + }) + }) +} diff --git a/plugins/arc/src/LinearArcDisplay/index.tsx b/plugins/arc/src/LinearArcDisplay/index.tsx deleted file mode 100644 index bb7c3318c0..0000000000 --- a/plugins/arc/src/LinearArcDisplay/index.tsx +++ /dev/null @@ -1,2 +0,0 @@ -export { configSchemaFactory } from './configSchema' -export { stateModelFactory } from './model' diff --git a/plugins/arc/src/LinearArcDisplay/model.tsx b/plugins/arc/src/LinearArcDisplay/model.ts similarity index 71% rename from plugins/arc/src/LinearArcDisplay/model.tsx rename to plugins/arc/src/LinearArcDisplay/model.ts index 71c6afe8ea..b868f3e1fe 100644 --- a/plugins/arc/src/LinearArcDisplay/model.tsx +++ b/plugins/arc/src/LinearArcDisplay/model.ts @@ -2,18 +2,10 @@ import { AnyConfigurationSchemaType, ConfigurationReference, } from '@jbrowse/core/configuration/configurationSchema' -import PluginManager from '@jbrowse/core/PluginManager' import { types } from 'mobx-state-tree' +import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view' -export function stateModelFactory( - configSchema: AnyConfigurationSchemaType, - pluginManager: PluginManager, -) { - const LGVPlugin = pluginManager.getPlugin( - 'LinearGenomeViewPlugin', - ) as import('@jbrowse/plugin-linear-genome-view').default - // @ts-ignore - const { BaseLinearDisplay } = LGVPlugin.exports +export function stateModelFactory(configSchema: AnyConfigurationSchemaType) { return types .compose( 'LinearArcDisplay', diff --git a/plugins/arc/src/index.ts b/plugins/arc/src/index.ts index b43f29c3ca..823154ef13 100644 --- a/plugins/arc/src/index.ts +++ b/plugins/arc/src/index.ts @@ -1,53 +1,18 @@ import Plugin from '@jbrowse/core/Plugin' import PluginManager from '@jbrowse/core/PluginManager' -import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType' -import { - configSchemaFactory as linearArcDisplayConfigSchemaFactory, - stateModelFactory as LinearArcDisplayStateModelFactory, -} from './LinearArcDisplay' -import ArcRenderer, { - configSchema as ArcRendererConfigSchema, - ReactComponent as ArcRendererReactComponent, -} from './ArcRenderer' +import LinearArcDisplayF from './LinearArcDisplay' +import ArcRendererF from './ArcRenderer' +import { Feature } from '@jbrowse/core/util' -export default class MyProjectPlugin extends Plugin { +export default class ArcPlugin extends Plugin { name = 'ArcRenderer' install(pluginManager: PluginManager) { - const LGVPlugin = pluginManager.getPlugin( - 'LinearGenomeViewPlugin', - ) as import('@jbrowse/plugin-linear-genome-view').default - // @ts-ignore - const { BaseLinearDisplayComponent } = LGVPlugin.exports - - pluginManager.addRendererType( - () => - // @ts-ignore error "expected 0 arguments, but got 1"? - new ArcRenderer({ - name: 'ArcRenderer', - ReactComponent: ArcRendererReactComponent, - configSchema: ArcRendererConfigSchema, - pluginManager, - }), - ) - pluginManager.addDisplayType(() => { - const configSchema = linearArcDisplayConfigSchemaFactory(pluginManager) - return new DisplayType({ - name: 'LinearArcDisplay', - configSchema, - stateModel: LinearArcDisplayStateModelFactory( - configSchema, - pluginManager, - ), - trackType: 'FeatureTrack', - viewType: 'LinearGenomeView', - ReactComponent: BaseLinearDisplayComponent, - }) - }) + ArcRendererF(pluginManager) + LinearArcDisplayF(pluginManager) pluginManager.jexl.addFunction( 'logThickness', - // eslint-disable-next-line @typescript-eslint/no-explicit-any - (feature: any, attributeName: string) => { + (feature: Feature, attributeName: string) => { return Math.log(feature.get(attributeName) + 1) }, ) diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index d102c58243..f19af61948 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/authentication", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", @@ -37,18 +37,16 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { + "generic-filehandle": "^3.0.0", "jwt-decode": "^3.1.2" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", "@mui/material": "^5.0.0", "crypto-js": "^3.0.0", - "electron": "^15.0.0", - "generic-filehandle": "^3.0.0", "mobx": "^6.0.0", "mobx-react": "^7.0.0", "mobx-state-tree": "^5.0.0", - "prop-types": "^15.0.0", "react": ">=16.8.0", "react-dom": ">=16.8.0", "rxjs": "^6.0.0" diff --git a/plugins/authentication/src/ExternalTokenModel/ExternalTokenEntryForm.tsx b/plugins/authentication/src/ExternalTokenModel/ExternalTokenEntryForm.tsx index 1f887bc987..6f7d8375b1 100644 --- a/plugins/authentication/src/ExternalTokenModel/ExternalTokenEntryForm.tsx +++ b/plugins/authentication/src/ExternalTokenModel/ExternalTokenEntryForm.tsx @@ -1,10 +1,6 @@ import React, { useState } from 'react' -import Button from '@mui/material/Button' -import Dialog from '@mui/material/Dialog' -import DialogContent from '@mui/material/DialogContent' -import DialogTitle from '@mui/material/DialogTitle' -import DialogActions from '@mui/material/DialogActions' -import TextField from '@mui/material/TextField' +import { Button, DialogContent, DialogActions, TextField } from '@mui/material' +import { Dialog } from '@jbrowse/core/ui' export const ExternalTokenEntryForm = ({ internetAccountId, @@ -17,17 +13,19 @@ export const ExternalTokenEntryForm = ({ return ( <> - - Enter Token for {internetAccountId} + { - setToken(event.target.value) - }} + onChange={event => setToken(event.target.value)} margin="dense" /> @@ -48,9 +46,7 @@ export const ExternalTokenEntryForm = ({ diff --git a/plugins/authentication/src/OAuthModel/configSchema.ts b/plugins/authentication/src/OAuthModel/configSchema.ts index 5595bbd746..e68c8d60bf 100644 --- a/plugins/authentication/src/OAuthModel/configSchema.ts +++ b/plugins/authentication/src/OAuthModel/configSchema.ts @@ -58,6 +58,14 @@ const OAuthConfigSchema = ConfigurationSchema( type: 'string', defaultValue: '', }, + /** + * #slot + */ + state: { + description: 'optional state for the authorization call', + type: 'string', + defaultValue: '', + }, /** * #slot */ diff --git a/plugins/authentication/src/OAuthModel/model.tsx b/plugins/authentication/src/OAuthModel/model.tsx index a3edce9ab1..badd20308a 100644 --- a/plugins/authentication/src/OAuthModel/model.tsx +++ b/plugins/authentication/src/OAuthModel/model.tsx @@ -15,6 +15,7 @@ interface OAuthData { code_challenge?: string code_challenge_method?: string token_access_type?: string + state?: string } function fixup(buf: string) { @@ -70,6 +71,13 @@ const stateModelFactory = (configSchema: OAuthInternetAccountConfigModel) => { get scopes(): string { return getConf(self, 'scopes') }, + /** + * OAuth state parameter: https://www.rfc-editor.org/rfc/rfc6749#section-4.1.1 + * Can override or extend if dynamic state is needed. + */ + state(): string | undefined { + return getConf(self, 'state') || undefined + }, get responseType(): 'token' | 'code' { return getConf(self, 'responseType') }, @@ -155,7 +163,7 @@ const stateModelFactory = (configSchema: OAuthInternetAccountConfigModel) => { if (obj.error === 'invalid_grant') { this.removeRefreshToken() } - text ??= obj?.error_description + text = obj?.error_description ?? text } catch (e) { /* just use original text as error */ } @@ -184,6 +192,8 @@ const stateModelFactory = (configSchema: OAuthInternetAccountConfigModel) => { reject: (error: Error) => void, ) { listener = event => { + // this should probably get better handling, but ignored for now + // eslint-disable-next-line @typescript-eslint/no-floating-promises this.finishOAuthWindow(event, resolve, reject) } window.addEventListener('message', listener) @@ -256,6 +266,10 @@ const stateModelFactory = (configSchema: OAuthInternetAccountConfigModel) => { response_type: self.responseType || 'code', } + if (self.state()) { + data.state = self.state() + } + if (self.scopes) { data.scope = self.scopes } @@ -293,6 +307,8 @@ const stateModelFactory = (configSchema: OAuthInternetAccountConfigModel) => { const eventFromDesktop = new MessageEvent('message', { data: { name: eventName, redirectUri: redirectUri }, }) + // may want to improve handling + // eslint-disable-next-line @typescript-eslint/no-floating-promises this.finishOAuthWindow(eventFromDesktop, resolve, reject) } else { const options = `width=500,height=600,left=0,top=0` @@ -309,6 +325,8 @@ const stateModelFactory = (configSchema: OAuthInternetAccountConfigModel) => { resolve(await self.exchangeRefreshForAccessToken(refreshToken)) } this.addMessageChannel(resolve, reject) + // may want to improve handling + // eslint-disable-next-line @typescript-eslint/no-floating-promises this.useEndpointForAuthorization(resolve, reject) }, async validateToken( diff --git a/plugins/authentication/src/__snapshots__/index.test.js.snap b/plugins/authentication/src/__snapshots__/index.test.js.snap index d2547f69f2..eb80d6e762 100644 --- a/plugins/authentication/src/__snapshots__/index.test.js.snap +++ b/plugins/authentication/src/__snapshots__/index.test.js.snap @@ -1,7 +1,7 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`initialized correctly 1`] = ` -Object { +{ "internetAccountId": "HTTPBasicTest", "type": "HTTPBasicInternetAccount", } diff --git a/plugins/bed/package.json b/plugins/bed/package.json index bed3cf75bb..f540fe006e 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/bed", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", diff --git a/plugins/bed/src/BedAdapter/BedAdapter.test.ts b/plugins/bed/src/BedAdapter/BedAdapter.test.ts index d772b882e3..ba3289df5e 100644 --- a/plugins/bed/src/BedAdapter/BedAdapter.test.ts +++ b/plugins/bed/src/BedAdapter/BedAdapter.test.ts @@ -2,11 +2,6 @@ import { toArray } from 'rxjs/operators' import BedAdapter from './BedAdapter' import MyConfigSchema from './configSchema' -import { TextDecoder } from 'web-encoding' -if (!window.TextDecoder) { - window.TextDecoder = TextDecoder -} - test('adapter can fetch features from volvox-bed12.bed', async () => { const adapter = new BedAdapter( MyConfigSchema.create({ diff --git a/plugins/bed/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap b/plugins/bed/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap index d3ebe037c2..2f5f70a16d 100644 --- a/plugins/bed/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap +++ b/plugins/bed/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap @@ -1,71 +1,71 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`adapter can fetch bed with header 1`] = ` -Array [ - Object { +[ + { "end": 3009, "refName": "contigA", "start": 3000, "strand": 0, "uniqueId": "test-contigA-0", }, - Object { + { "end": 3114, "refName": "contigA", "start": 3105, "strand": 0, "uniqueId": "test-contigA-1", }, - Object { + { "end": 3161, "refName": "contigA", "start": 3152, "strand": 0, "uniqueId": "test-contigA-2", }, - Object { + { "end": 3180, "refName": "contigA", "start": 3171, "strand": 0, "uniqueId": "test-contigA-3", }, - Object { + { "end": 3183, "refName": "contigA", "start": 3174, "strand": 0, "uniqueId": "test-contigA-4", }, - Object { + { "end": 3222, "refName": "contigA", "start": 3213, "strand": 0, "uniqueId": "test-contigA-5", }, - Object { + { "end": 3474, "refName": "contigA", "start": 3465, "strand": 0, "uniqueId": "test-contigA-6", }, - Object { + { "end": 3804, "refName": "contigA", "start": 3795, "strand": 0, "uniqueId": "test-contigA-7", }, - Object { + { "end": 4044, "refName": "contigA", "start": 4035, "strand": 0, "uniqueId": "test-contigA-8", }, - Object { + { "end": 4082, "refName": "contigA", "start": 4073, @@ -76,8 +76,8 @@ Array [ `; exports[`adapter can fetch features bed with autosql 1`] = ` -Array [ - Object { +[ + { "Entrez_Gene_Id": "2782", "Hugo_Symbol": "GNB1", "Matched_Norm_Sample_Barcode": "TCGA-OR-A5KB-11A-11D-A30A-10", @@ -108,8 +108,8 @@ Array [ "score": 1, "start": 1, "strand": 0, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 2, "parentId": "test-ctgA-0", "start": 1, @@ -127,71 +127,71 @@ Array [ `; exports[`adapter can fetch features from volvox.sort.bed simple bed3 1`] = ` -Array [ - Object { +[ + { "end": 3009, "refName": "contigA", "start": 3000, "strand": 0, "uniqueId": "test-contigA-0", }, - Object { + { "end": 3114, "refName": "contigA", "start": 3105, "strand": 0, "uniqueId": "test-contigA-1", }, - Object { + { "end": 3161, "refName": "contigA", "start": 3152, "strand": 0, "uniqueId": "test-contigA-2", }, - Object { + { "end": 3180, "refName": "contigA", "start": 3171, "strand": 0, "uniqueId": "test-contigA-3", }, - Object { + { "end": 3183, "refName": "contigA", "start": 3174, "strand": 0, "uniqueId": "test-contigA-4", }, - Object { + { "end": 3222, "refName": "contigA", "start": 3213, "strand": 0, "uniqueId": "test-contigA-5", }, - Object { + { "end": 3474, "refName": "contigA", "start": 3465, "strand": 0, "uniqueId": "test-contigA-6", }, - Object { + { "end": 3804, "refName": "contigA", "start": 3795, "strand": 0, "uniqueId": "test-contigA-7", }, - Object { + { "end": 4044, "refName": "contigA", "start": 4035, "strand": 0, "uniqueId": "test-contigA-8", }, - Object { + { "end": 4082, "refName": "contigA", "start": 4073, @@ -202,8 +202,8 @@ Array [ `; exports[`adapter can fetch features from volvox-bed12.bed 1`] = ` -Array [ - Object { +[ + { "end": 9000, "itemRgb": "0,0,0", "name": "EDEN.1", @@ -211,8 +211,8 @@ Array [ "score": 1000, "start": 1049, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1200, "parentId": "test-ctgA-0", "start": 1049, @@ -220,7 +220,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-ctgA-0-0", }, - Object { + { "end": 1500, "parentId": "test-ctgA-0", "start": 1200, @@ -228,7 +228,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-0-1", }, - Object { + { "end": 3902, "parentId": "test-ctgA-0", "start": 2999, @@ -236,7 +236,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-0-2", }, - Object { + { "end": 5500, "parentId": "test-ctgA-0", "start": 4999, @@ -244,7 +244,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-0-3", }, - Object { + { "end": 7608, "parentId": "test-ctgA-0", "start": 6999, @@ -252,7 +252,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-0-4", }, - Object { + { "end": 9000, "parentId": "test-ctgA-0", "start": 7608, @@ -264,7 +264,7 @@ Array [ "type": "mRNA", "uniqueId": "test-ctgA-0", }, - Object { + { "end": 9000, "itemRgb": "0,0,0", "name": "EDEN.2", @@ -272,8 +272,8 @@ Array [ "score": 1000, "start": 1049, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1200, "parentId": "test-ctgA-1", "start": 1049, @@ -281,7 +281,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-ctgA-1-0", }, - Object { + { "end": 1500, "parentId": "test-ctgA-1", "start": 1200, @@ -289,7 +289,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-1-1", }, - Object { + { "end": 5500, "parentId": "test-ctgA-1", "start": 4999, @@ -297,7 +297,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-1-2", }, - Object { + { "end": 7608, "parentId": "test-ctgA-1", "start": 6999, @@ -305,7 +305,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-1-3", }, - Object { + { "end": 9000, "parentId": "test-ctgA-1", "start": 7608, @@ -317,7 +317,7 @@ Array [ "type": "mRNA", "uniqueId": "test-ctgA-1", }, - Object { + { "end": 9000, "itemRgb": "0,0,0", "name": "EDEN.3", @@ -325,8 +325,8 @@ Array [ "score": 1000, "start": 1299, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1500, "parentId": "test-ctgA-2", "start": 1299, @@ -334,7 +334,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-ctgA-2-0", }, - Object { + { "end": 3300, "parentId": "test-ctgA-2", "start": 2999, @@ -342,7 +342,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-ctgA-2-1", }, - Object { + { "end": 3902, "parentId": "test-ctgA-2", "start": 3300, @@ -350,7 +350,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-2-2", }, - Object { + { "end": 5500, "parentId": "test-ctgA-2", "start": 4999, @@ -358,7 +358,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-2-3", }, - Object { + { "end": 7600, "parentId": "test-ctgA-2", "start": 6999, @@ -366,7 +366,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-2-4", }, - Object { + { "end": 9000, "parentId": "test-ctgA-2", "start": 7600, @@ -378,7 +378,7 @@ Array [ "type": "mRNA", "uniqueId": "test-ctgA-2", }, - Object { + { "end": 23000, "itemRgb": "0,0,0", "name": "rna-Apple3", @@ -386,8 +386,8 @@ Array [ "score": 1000, "start": 17399, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 17999, "parentId": "test-ctgA-3", "start": 17399, @@ -395,7 +395,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-ctgA-3-0", }, - Object { + { "end": 18800, "parentId": "test-ctgA-3", "start": 17999, @@ -403,7 +403,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-3-1", }, - Object { + { "end": 19500, "parentId": "test-ctgA-3", "start": 18999, @@ -411,7 +411,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-3-2", }, - Object { + { "end": 21200, "parentId": "test-ctgA-3", "start": 20999, @@ -419,7 +419,7 @@ Array [ "type": "CDS", "uniqueId": "test-ctgA-3-3", }, - Object { + { "end": 23000, "parentId": "test-ctgA-3", "start": 21200, @@ -434,4 +434,4 @@ Array [ ] `; -exports[`adapter can use gwas header 1`] = `Array []`; +exports[`adapter can use gwas header 1`] = `[]`; diff --git a/plugins/bed/src/BedAdapter/index.ts b/plugins/bed/src/BedAdapter/index.ts index 7703441d29..2ef6bc4b71 100644 --- a/plugins/bed/src/BedAdapter/index.ts +++ b/plugins/bed/src/BedAdapter/index.ts @@ -1 +1,16 @@ -export { default as configSchema } from './configSchema' +import PluginManager from '@jbrowse/core/PluginManager' +import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' + +import configSchema from './configSchema' + +export default (pluginManager: PluginManager) => { + pluginManager.addAdapterType( + () => + new AdapterType({ + name: 'BedAdapter', + displayName: 'BED adapter', + configSchema, + getAdapterClass: () => import('./BedAdapter').then(r => r.default), + }), + ) +} diff --git a/plugins/bed/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap b/plugins/bed/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap index 8314d85069..fae983a3f1 100644 --- a/plugins/bed/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap +++ b/plugins/bed/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap @@ -1,71 +1,71 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`adapter can fetch bed with header 1`] = ` -Array [ - Object { +[ + { "end": 3009, "refName": "contigA", "start": 3000, "strand": 0, "uniqueId": "test-163098", }, - Object { + { "end": 3114, "refName": "contigA", "start": 3105, "strand": 0, "uniqueId": "test-163116", }, - Object { + { "end": 3161, "refName": "contigA", "start": 3152, "strand": 0, "uniqueId": "test-163134", }, - Object { + { "end": 3180, "refName": "contigA", "start": 3171, "strand": 0, "uniqueId": "test-163152", }, - Object { + { "end": 3183, "refName": "contigA", "start": 3174, "strand": 0, "uniqueId": "test-163170", }, - Object { + { "end": 3222, "refName": "contigA", "start": 3213, "strand": 0, "uniqueId": "test-163188", }, - Object { + { "end": 3474, "refName": "contigA", "start": 3465, "strand": 0, "uniqueId": "test-163206", }, - Object { + { "end": 3804, "refName": "contigA", "start": 3795, "strand": 0, "uniqueId": "test-163224", }, - Object { + { "end": 4044, "refName": "contigA", "start": 4035, "strand": 0, "uniqueId": "test-163242", }, - Object { + { "end": 4082, "refName": "contigA", "start": 4073, @@ -76,8 +76,8 @@ Array [ `; exports[`adapter can fetch features bed with autosql 1`] = ` -Array [ - Object { +[ + { "Entrez_Gene_Id": "2782", "Hugo_Symbol": "GNB1", "Matched_Norm_Sample_Barcode": "TCGA-OR-A5KB-11A-11D-A30A-10", @@ -108,8 +108,8 @@ Array [ "score": 1, "start": 1, "strand": 0, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 2, "parentId": "test-52985", "start": 1, @@ -127,71 +127,71 @@ Array [ `; exports[`adapter can fetch features from volvox.sort.bed.gz simple bed3 1`] = ` -Array [ - Object { +[ + { "end": 3009, "refName": "contigA", "start": 3000, "strand": 0, "uniqueId": "test-155162", }, - Object { + { "end": 3114, "refName": "contigA", "start": 3105, "strand": 0, "uniqueId": "test-155180", }, - Object { + { "end": 3161, "refName": "contigA", "start": 3152, "strand": 0, "uniqueId": "test-155198", }, - Object { + { "end": 3180, "refName": "contigA", "start": 3171, "strand": 0, "uniqueId": "test-155216", }, - Object { + { "end": 3183, "refName": "contigA", "start": 3174, "strand": 0, "uniqueId": "test-155234", }, - Object { + { "end": 3222, "refName": "contigA", "start": 3213, "strand": 0, "uniqueId": "test-155252", }, - Object { + { "end": 3474, "refName": "contigA", "start": 3465, "strand": 0, "uniqueId": "test-155270", }, - Object { + { "end": 3804, "refName": "contigA", "start": 3795, "strand": 0, "uniqueId": "test-155288", }, - Object { + { "end": 4044, "refName": "contigA", "start": 4035, "strand": 0, "uniqueId": "test-155306", }, - Object { + { "end": 4082, "refName": "contigA", "start": 4073, @@ -202,8 +202,8 @@ Array [ `; exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = ` -Array [ - Object { +[ + { "end": 9000, "itemRgb": "0,0,0", "name": "EDEN.1", @@ -211,8 +211,8 @@ Array [ "score": 1000, "start": 1049, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1200, "parentId": "test-45689", "start": 1049, @@ -220,7 +220,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-45689-0", }, - Object { + { "end": 1500, "parentId": "test-45689", "start": 1200, @@ -228,7 +228,7 @@ Array [ "type": "CDS", "uniqueId": "test-45689-1", }, - Object { + { "end": 3902, "parentId": "test-45689", "start": 2999, @@ -236,7 +236,7 @@ Array [ "type": "CDS", "uniqueId": "test-45689-2", }, - Object { + { "end": 5500, "parentId": "test-45689", "start": 4999, @@ -244,7 +244,7 @@ Array [ "type": "CDS", "uniqueId": "test-45689-3", }, - Object { + { "end": 7608, "parentId": "test-45689", "start": 6999, @@ -252,7 +252,7 @@ Array [ "type": "CDS", "uniqueId": "test-45689-4", }, - Object { + { "end": 9000, "parentId": "test-45689", "start": 7608, @@ -264,7 +264,7 @@ Array [ "type": "mRNA", "uniqueId": "test-45689", }, - Object { + { "end": 9000, "itemRgb": "0,0,0", "name": "EDEN.2", @@ -272,8 +272,8 @@ Array [ "score": 1000, "start": 1049, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1200, "parentId": "test-45786", "start": 1049, @@ -281,7 +281,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-45786-0", }, - Object { + { "end": 1500, "parentId": "test-45786", "start": 1200, @@ -289,7 +289,7 @@ Array [ "type": "CDS", "uniqueId": "test-45786-1", }, - Object { + { "end": 5500, "parentId": "test-45786", "start": 4999, @@ -297,7 +297,7 @@ Array [ "type": "CDS", "uniqueId": "test-45786-2", }, - Object { + { "end": 7608, "parentId": "test-45786", "start": 6999, @@ -305,7 +305,7 @@ Array [ "type": "CDS", "uniqueId": "test-45786-3", }, - Object { + { "end": 9000, "parentId": "test-45786", "start": 7608, @@ -317,7 +317,7 @@ Array [ "type": "mRNA", "uniqueId": "test-45786", }, - Object { + { "end": 9000, "itemRgb": "0,0,0", "name": "EDEN.3", @@ -325,8 +325,8 @@ Array [ "score": 1000, "start": 1299, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1500, "parentId": "test-45874", "start": 1299, @@ -334,7 +334,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-45874-0", }, - Object { + { "end": 3300, "parentId": "test-45874", "start": 2999, @@ -342,7 +342,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-45874-1", }, - Object { + { "end": 3902, "parentId": "test-45874", "start": 3300, @@ -350,7 +350,7 @@ Array [ "type": "CDS", "uniqueId": "test-45874-2", }, - Object { + { "end": 5500, "parentId": "test-45874", "start": 4999, @@ -358,7 +358,7 @@ Array [ "type": "CDS", "uniqueId": "test-45874-3", }, - Object { + { "end": 7600, "parentId": "test-45874", "start": 6999, @@ -366,7 +366,7 @@ Array [ "type": "CDS", "uniqueId": "test-45874-4", }, - Object { + { "end": 9000, "parentId": "test-45874", "start": 7600, @@ -378,7 +378,7 @@ Array [ "type": "mRNA", "uniqueId": "test-45874", }, - Object { + { "end": 23000, "itemRgb": "0,0,0", "name": "rna-Apple3", @@ -386,8 +386,8 @@ Array [ "score": 1000, "start": 17399, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 17999, "parentId": "test-45971", "start": 17399, @@ -395,7 +395,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-45971-0", }, - Object { + { "end": 18800, "parentId": "test-45971", "start": 17999, @@ -403,7 +403,7 @@ Array [ "type": "CDS", "uniqueId": "test-45971-1", }, - Object { + { "end": 19500, "parentId": "test-45971", "start": 18999, @@ -411,7 +411,7 @@ Array [ "type": "CDS", "uniqueId": "test-45971-2", }, - Object { + { "end": 21200, "parentId": "test-45971", "start": 20999, @@ -419,7 +419,7 @@ Array [ "type": "CDS", "uniqueId": "test-45971-3", }, - Object { + { "end": 23000, "parentId": "test-45971", "start": 21200, @@ -434,4 +434,4 @@ Array [ ] `; -exports[`adapter can use gwas header 1`] = `Array []`; +exports[`adapter can use gwas header 1`] = `[]`; diff --git a/plugins/bed/src/BedTabixAdapter/index.ts b/plugins/bed/src/BedTabixAdapter/index.ts index 7703441d29..5259107705 100644 --- a/plugins/bed/src/BedTabixAdapter/index.ts +++ b/plugins/bed/src/BedTabixAdapter/index.ts @@ -1 +1,16 @@ -export { default as configSchema } from './configSchema' +import PluginManager from '@jbrowse/core/PluginManager' +import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' + +import configSchema from './configSchema' + +export default (pluginManager: PluginManager) => { + pluginManager.addAdapterType( + () => + new AdapterType({ + name: 'BedTabixAdapter', + displayName: 'BED tabix adapter', + configSchema, + getAdapterClass: () => import('./BedTabixAdapter').then(r => r.default), + }), + ) +} diff --git a/plugins/bed/src/BedpeAdapter/BedpeAdapter.ts b/plugins/bed/src/BedpeAdapter/BedpeAdapter.ts new file mode 100644 index 0000000000..5aca48c55d --- /dev/null +++ b/plugins/bed/src/BedpeAdapter/BedpeAdapter.ts @@ -0,0 +1,204 @@ +import { + BaseFeatureDataAdapter, + BaseOptions, +} from '@jbrowse/core/data_adapters/BaseAdapter' +import { openLocation } from '@jbrowse/core/util/io' +import { ObservableCreate } from '@jbrowse/core/util/rxjs' +import { Region, Feature, SimpleFeature } from '@jbrowse/core/util' +import IntervalTree from '@flatten-js/interval-tree' +import { unzip } from '@gmod/bgzf-filehandle' + +function isGzip(buf: Buffer) { + return buf[0] === 31 && buf[1] === 139 && buf[2] === 8 +} + +export function featureData( + line: string, + uniqueId: string, + flip: boolean, + names?: string[], +) { + const l = line.split('\t') + const ref1 = l[flip ? 3 : 0] + const start1 = +l[flip ? 4 : 1] + const end1 = +l[flip ? 5 : 2] + const ref2 = +l[!flip ? 3 : 0] + const start2 = +l[!flip ? 4 : 1] + const end2 = +l[!flip ? 5 : 2] + const name = l[6] + const score = +l[7] + const strand1 = parseStrand(l[8]) + const strand2 = parseStrand(l[9]) + const extra = l.slice(9) + const rest = names + ? Object.fromEntries(names.slice(9).map((n, idx) => [n, extra[idx]])) + : extra + + return new SimpleFeature({ + start: start1, + end: end1, + refName: ref1, + strand: strand1, + name, + ...rest, + score, + uniqueId, + mate: { refName: ref2, start: start2, end: end2, strand: strand2 }, + }) +} + +function parseStrand(strand: string) { + if (strand === '+') { + return 1 + } else if (strand === '-') { + return -1 + } else if (strand === '.') { + return 0 + } else { + return undefined + } +} + +export default class BedpeAdapter extends BaseFeatureDataAdapter { + protected bedpeFeatures?: Promise<{ + header: string + feats1: Record + feats2: Record + columnNames: string[] + }> + + protected intervalTrees: { + [key: string]: Promise | undefined + } = {} + + public static capabilities = ['getFeatures', 'getRefNames'] + + private async loadDataP(opts: BaseOptions = {}) { + const pm = this.pluginManager + const bedLoc = this.getConf('bedpeLocation') + const buf = await openLocation(bedLoc, pm).readFile(opts) + const buffer = isGzip(buf) ? await unzip(buf) : buf + // 512MB max chrome string length is 512MB + if (buffer.length > 536_870_888) { + throw new Error('Data exceeds maximum string length (512MB)') + } + const data = new TextDecoder('utf8', { fatal: true }).decode(buffer) + const lines = data.split(/\n|\r\n|\r/).filter(f => !!f) + const headerLines = [] + let i = 0 + for (; i < lines.length && lines[i].startsWith('#'); i++) { + headerLines.push(lines[i]) + } + const header = headerLines.join('\n') + const feats1 = {} as Record + const feats2 = {} as Record + for (; i < lines.length; i++) { + const line = lines[i] + const cols = line.split('\t') + const r1 = cols[0] + const r2 = cols[3] + if (!feats1[r1]) { + feats1[r1] = [] + } + if (!feats2[r2]) { + feats2[r2] = [] + } + feats1[r1].push(line) + feats2[r2].push(line) + } + const columnNames = this.getConf('columnNames') + + return { + header, + feats1, + feats2, + columnNames, + } + } + + private async loadData(opts: BaseOptions = {}) { + if (!this.bedpeFeatures) { + this.bedpeFeatures = this.loadDataP(opts).catch(e => { + this.bedpeFeatures = undefined + throw e + }) + } + + return this.bedpeFeatures + } + + public async getRefNames(opts: BaseOptions = {}) { + const { feats1, feats2 } = await this.loadData(opts) + return [...new Set([...Object.keys(feats1), ...Object.keys(feats2)])] + } + + async getHeader(opts: BaseOptions = {}) { + const { header } = await this.loadData(opts) + return header + } + + async getNames() { + const { header, columnNames } = await this.loadData() + if (columnNames.length) { + return columnNames + } + const defs = header.split(/\n|\r\n|\r/).filter(f => !!f) + const defline = defs[defs.length - 1] + return defline?.includes('\t') + ? defline + .slice(1) + .split('\t') + .map(field => field.trim()) + : undefined + } + + private async loadFeatureTreeP(refName: string) { + const { feats1, feats2 } = await this.loadData() + const lines1 = feats1[refName] + const lines2 = feats2[refName] + const names = await this.getNames() + + const intervalTree = new IntervalTree() + const ret1 = lines1?.map((f, i) => { + const uniqueId = `${this.id}-${refName}-${i}` + return featureData(f, uniqueId, false, names) + }) + const ret2 = lines2?.map((f, i) => { + const uniqueId = `${this.id}-${refName}-${i}` + return featureData(f, uniqueId, true, names) + }) + + for (let i = 0; i < ret1.length; i++) { + const obj = ret1[i] + intervalTree.insert([obj.get('start'), obj.get('end')], obj) + } + + for (let i = 0; i < ret2.length; i++) { + const obj = ret2[i] + intervalTree.insert([obj.get('start'), obj.get('end')], obj) + } + + return intervalTree + } + + private async loadFeatureTree(refName: string) { + if (!this.intervalTrees[refName]) { + this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch(e => { + this.intervalTrees[refName] = undefined + throw e + }) + } + return this.intervalTrees[refName] + } + + public getFeatures(query: Region, opts: BaseOptions = {}) { + return ObservableCreate(async observer => { + const { start, end, refName } = query + const intervalTree = await this.loadFeatureTree(refName) + intervalTree?.search([start, end]).forEach(f => observer.next(f)) + observer.complete() + }, opts.signal) + } + + public freeResources(): void {} +} diff --git a/plugins/bed/src/BedpeAdapter/configSchema.ts b/plugins/bed/src/BedpeAdapter/configSchema.ts new file mode 100644 index 0000000000..e9d9d26905 --- /dev/null +++ b/plugins/bed/src/BedpeAdapter/configSchema.ts @@ -0,0 +1,34 @@ +import { ConfigurationSchema } from '@jbrowse/core/configuration' + +/** + * #config BedpeAdapter + * intended for SVs in a single assembly + */ +function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars + +const BedpeAdapter = ConfigurationSchema( + 'BedpeAdapter', + { + /** + * #slot + * can be plaintext or gzipped, not indexed so loaded into memory on startup + */ + bedpeLocation: { + type: 'fileLocation', + defaultValue: { + uri: '/path/to/my.bedpe.gz', + locationType: 'UriLocation', + }, + }, + /** + * #slot + */ + columnNames: { + type: 'stringArray', + description: 'List of column names', + defaultValue: [], + }, + }, + { explicitlyTyped: true }, +) +export default BedpeAdapter diff --git a/plugins/bed/src/BedpeAdapter/index.ts b/plugins/bed/src/BedpeAdapter/index.ts new file mode 100644 index 0000000000..7c0019b823 --- /dev/null +++ b/plugins/bed/src/BedpeAdapter/index.ts @@ -0,0 +1,16 @@ +import PluginManager from '@jbrowse/core/PluginManager' +import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' + +import configSchema from './configSchema' + +export default (pluginManager: PluginManager) => { + pluginManager.addAdapterType( + () => + new AdapterType({ + name: 'BedpeAdapter', + displayName: 'BEDPE adapter', + configSchema, + getAdapterClass: () => import('./BedpeAdapter').then(r => r.default), + }), + ) +} diff --git a/plugins/bed/src/BigBedAdapter/__snapshots__/BigBedAdapter.test.ts.snap b/plugins/bed/src/BigBedAdapter/__snapshots__/BigBedAdapter.test.ts.snap index 02dd30e369..4667e1634e 100644 --- a/plugins/bed/src/BigBedAdapter/__snapshots__/BigBedAdapter.test.ts.snap +++ b/plugins/bed/src/BigBedAdapter/__snapshots__/BigBedAdapter.test.ts.snap @@ -1,8 +1,8 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`adapter can fetch features from volvox.bb 1`] = ` -Array [ - Object { +[ + { "end": 9000, "geneBioType": "-", "geneId": "EDEN", @@ -14,8 +14,8 @@ Array [ "score": 1000, "start": 1049, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1200, "parentId": "test-bb-358912", "start": 1049, @@ -23,7 +23,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-bb-358912-0", }, - Object { + { "end": 1500, "parentId": "test-bb-358912", "start": 1200, @@ -31,7 +31,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-358912-1", }, - Object { + { "end": 3902, "parentId": "test-bb-358912", "start": 2999, @@ -39,7 +39,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-358912-2", }, - Object { + { "end": 5500, "parentId": "test-bb-358912", "start": 4999, @@ -47,7 +47,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-358912-3", }, - Object { + { "end": 7608, "parentId": "test-bb-358912", "start": 6999, @@ -55,7 +55,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-358912-4", }, - Object { + { "end": 9000, "parentId": "test-bb-358912", "start": 7608, @@ -68,7 +68,7 @@ Array [ "type": "mRNA", "uniqueId": "test-bb-358912", }, - Object { + { "end": 9000, "geneBioType": "-", "geneId": "EDEN", @@ -80,8 +80,8 @@ Array [ "score": 1000, "start": 1049, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1200, "parentId": "test-bb-359006", "start": 1049, @@ -89,7 +89,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-bb-359006-0", }, - Object { + { "end": 1500, "parentId": "test-bb-359006", "start": 1200, @@ -97,7 +97,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359006-1", }, - Object { + { "end": 5500, "parentId": "test-bb-359006", "start": 4999, @@ -105,7 +105,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359006-2", }, - Object { + { "end": 7608, "parentId": "test-bb-359006", "start": 6999, @@ -113,7 +113,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359006-3", }, - Object { + { "end": 9000, "parentId": "test-bb-359006", "start": 7608, @@ -126,7 +126,7 @@ Array [ "type": "mRNA", "uniqueId": "test-bb-359006", }, - Object { + { "end": 9000, "geneBioType": "-", "geneId": "EDEN", @@ -138,8 +138,8 @@ Array [ "score": 1000, "start": 1299, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 1500, "parentId": "test-bb-359091", "start": 1299, @@ -147,7 +147,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-bb-359091-0", }, - Object { + { "end": 3300, "parentId": "test-bb-359091", "start": 2999, @@ -155,7 +155,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-bb-359091-1", }, - Object { + { "end": 3902, "parentId": "test-bb-359091", "start": 3300, @@ -163,7 +163,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359091-2", }, - Object { + { "end": 5500, "parentId": "test-bb-359091", "start": 4999, @@ -171,7 +171,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359091-3", }, - Object { + { "end": 7600, "parentId": "test-bb-359091", "start": 6999, @@ -179,7 +179,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359091-4", }, - Object { + { "end": 9000, "parentId": "test-bb-359091", "start": 7600, @@ -192,7 +192,7 @@ Array [ "type": "mRNA", "uniqueId": "test-bb-359091", }, - Object { + { "end": 23000, "geneBioType": "-", "geneId": "rna-Apple3", @@ -204,8 +204,8 @@ Array [ "score": 1000, "start": 17399, "strand": 1, - "subfeatures": Array [ - Object { + "subfeatures": [ + { "end": 17999, "parentId": "test-bb-359185", "start": 17399, @@ -213,7 +213,7 @@ Array [ "type": "five_prime_UTR", "uniqueId": "test-bb-359185-0", }, - Object { + { "end": 18800, "parentId": "test-bb-359185", "start": 17999, @@ -221,7 +221,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359185-1", }, - Object { + { "end": 19500, "parentId": "test-bb-359185", "start": 18999, @@ -229,7 +229,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359185-2", }, - Object { + { "end": 21200, "parentId": "test-bb-359185", "start": 20999, @@ -237,7 +237,7 @@ Array [ "type": "CDS", "uniqueId": "test-bb-359185-3", }, - Object { + { "end": 23000, "parentId": "test-bb-359185", "start": 21200, diff --git a/plugins/bed/src/BigBedAdapter/index.ts b/plugins/bed/src/BigBedAdapter/index.ts index 7703441d29..b453ca806b 100644 --- a/plugins/bed/src/BigBedAdapter/index.ts +++ b/plugins/bed/src/BigBedAdapter/index.ts @@ -1 +1,16 @@ -export { default as configSchema } from './configSchema' +import PluginManager from '@jbrowse/core/PluginManager' +import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' + +import configSchema from './configSchema' + +export default (pluginManager: PluginManager) => { + pluginManager.addAdapterType( + () => + new AdapterType({ + name: 'BigBedAdapter', + displayName: 'BigBed adapter', + configSchema, + getAdapterClass: () => import('./BigBedAdapter').then(r => r.default), + }), + ) +} diff --git a/plugins/bed/src/__snapshots__/index.test.js.snap b/plugins/bed/src/__snapshots__/index.test.js.snap index 463d523aec..a10c09c9d1 100644 --- a/plugins/bed/src/__snapshots__/index.test.js.snap +++ b/plugins/bed/src/__snapshots__/index.test.js.snap @@ -1,3 +1,3 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`plugin in a stock JBrowse 1`] = `Object {}`; +exports[`plugin in a stock JBrowse 1`] = `{}`; diff --git a/plugins/bed/src/index.ts b/plugins/bed/src/index.ts index 0ed1c2890d..6dfd2be536 100644 --- a/plugins/bed/src/index.ts +++ b/plugins/bed/src/index.ts @@ -1,9 +1,9 @@ -import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType' import Plugin from '@jbrowse/core/Plugin' import PluginManager from '@jbrowse/core/PluginManager' -import { configSchema as bigBedAdapterConfigSchema } from './BigBedAdapter' -import { configSchema as bedTabixAdapterConfigSchema } from './BedTabixAdapter' -import { configSchema as bedAdapterConfigSchema } from './BedAdapter' +import BigBedAdapterF from './BigBedAdapter' +import BedpeAdapterF from './BedpeAdapter' +import BedTabixAdapterF from './BedTabixAdapter' +import BedAdapterF from './BedAdapter' import { FileLocation } from '@jbrowse/core/util/types' import { getFileName, @@ -16,15 +16,10 @@ export default class BedPlugin extends Plugin { name = 'BedPlugin' install(pluginManager: PluginManager) { - pluginManager.addAdapterType( - () => - new AdapterType({ - name: 'BigBedAdapter', - configSchema: bigBedAdapterConfigSchema, - getAdapterClass: () => - import('./BigBedAdapter/BigBedAdapter').then(r => r.default), - }), - ) + BigBedAdapterF(pluginManager) + BedAdapterF(pluginManager) + BedpeAdapterF(pluginManager) + BedTabixAdapterF(pluginManager) pluginManager.addToExtensionPoint( 'Core-guessAdapterForLocation', (adapterGuesser: AdapterGuesser) => { @@ -51,25 +46,28 @@ export default class BedPlugin extends Plugin { }, ) - pluginManager.addAdapterType( - () => - new AdapterType({ - name: 'BedTabixAdapter', - configSchema: bedTabixAdapterConfigSchema, - getAdapterClass: () => - import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default), - }), + pluginManager.addToExtensionPoint( + 'Core-guessAdapterForLocation', + (adapterGuesser: AdapterGuesser) => { + return ( + file: FileLocation, + index?: FileLocation, + adapterHint?: string, + ) => { + const regexGuess = /\.bedpe\.gz$/i + const adapterName = 'BedpeAdapter' + const fileName = getFileName(file) + if (regexGuess.test(fileName) || adapterHint === adapterName) { + return { + type: adapterName, + bedpeLocation: file, + } + } + return adapterGuesser(file, index, adapterHint) + } + }, ) - pluginManager.addAdapterType( - () => - new AdapterType({ - name: 'BedAdapter', - configSchema: bedAdapterConfigSchema, - getAdapterClass: () => - import('./BedAdapter/BedAdapter').then(r => r.default), - }), - ) pluginManager.addToExtensionPoint( 'Core-guessAdapterForLocation', (adapterGuesser: AdapterGuesser) => { diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index 2a9248addf..4a20d311c4 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/breakpoint-split-view", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", @@ -37,7 +37,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@gmod/vcf": "^5.0.5", + "@gmod/vcf": "^5.0.9", "@mui/icons-material": "^5.0.1", "svg-path-generator": "^1.1.0" }, @@ -49,7 +49,7 @@ "mobx-react": "^7.0.0", "mobx-state-tree": "^5.0.0", "react": ">=16.8.4", - "tss-react": "^3.0.0" + "tss-react": "^4.0.0" }, "private": true, "distModule": "esm/index.js", diff --git a/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/index.ts b/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/index.ts index ae0efdfd11..7104154f39 100644 --- a/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/index.ts +++ b/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/index.ts @@ -1,6 +1,9 @@ +import { lazy } from 'react' import { ConfigurationSchema } from '@jbrowse/core/configuration' +import PluginManager from '@jbrowse/core/PluginManager' import { ElementId } from '@jbrowse/core/util/types/mst' import { types } from 'mobx-state-tree' +import { WidgetType } from '@jbrowse/core/pluggableElementTypes' const configSchema = ConfigurationSchema('BreakpointAlignmentsWidget', {}) @@ -19,4 +22,14 @@ const stateModel = types }, })) -export { configSchema, stateModel } +export default (pluginManager: PluginManager) => { + pluginManager.addWidgetType(() => { + return new WidgetType({ + name: 'BreakpointAlignmentsWidget', + heading: 'Breakpoint feature details', + configSchema, + stateModel, + ReactComponent: lazy(() => import('./BreakpointAlignmentsFeatureDetail')), + }) + }) +} diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView.ts similarity index 84% rename from plugins/breakpoint-split-view/src/BreakpointSplitView.ts rename to plugins/breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView.ts index ee69cc0c93..27a54fcbcf 100644 --- a/plugins/breakpoint-split-view/src/BreakpointSplitView.ts +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView.ts @@ -1,16 +1,13 @@ import { getSession, Feature } from '@jbrowse/core/util' -import PluginManager from '@jbrowse/core/PluginManager' import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType' -import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import { Assembly } from '@jbrowse/core/assemblyManager/assembly' import { parseBreakend } from '@gmod/vcf' +import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' -// locals -import BreakpointSplitViewComponent from './components/BreakpointSplitView' -import BreakpointSplitViewModel from './model' +type LGV = LinearGenomeViewModel -class BreakpointSplitViewType extends ViewType { - snapshotFromBreakendFeature(feature: Feature, view: LinearGenomeViewModel) { +export default class BreakpointSplitViewType extends ViewType { + snapshotFromBreakendFeature(feature: Feature, view: LGV) { const alt = feature.get('ALT')?.[0] const bnd = alt ? parseBreakend(alt) : undefined const startPos = feature.get('start') @@ -105,15 +102,3 @@ class BreakpointSplitViewType extends ViewType { return snapshot } } - -export default (pluginManager: PluginManager) => { - const { load } = pluginManager - - const { stateModel } = load(BreakpointSplitViewModel) - - return new BreakpointSplitViewType({ - name: 'BreakpointSplitView', - stateModel, - ReactComponent: BreakpointSplitViewComponent, - }) -} diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx new file mode 100644 index 0000000000..4c9ba100f7 --- /dev/null +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx @@ -0,0 +1,165 @@ +import React, { useMemo, useState } from 'react' +import Path from 'svg-path-generator' +import { observer } from 'mobx-react' +import { getSnapshot } from 'mobx-state-tree' +import { getSession } from '@jbrowse/core/util' + +// locals +import { + getBadlyPairedAlignments, + getMatchedAlignmentFeatures, + hasPairedReads, +} from './util' +import { yPos, useNextFrame, getPxFromCoordinate } from '../util' +import { BreakpointViewModel } from '../model' + +const [LEFT, , RIGHT] = [0, 1, 2, 3] + +const AlignmentConnections = observer(function ({ + model, + trackId, + parentRef, +}: { + model: BreakpointViewModel + trackId: string + parentRef: React.RefObject +}) { + const { views, showIntraviewLinks } = model + + const session = getSession(model) + const snap = getSnapshot(model) + const { assemblyManager } = session + const assembly = assemblyManager.get(views[0].assemblyNames[0]) + useNextFrame(snap) + const totalFeatures = model.getTrackFeatures(trackId) + const hasPaired = useMemo( + () => hasPairedReads(totalFeatures), + [totalFeatures], + ) + + const layoutMatches = useMemo(() => { + const layoutMatches = model.getMatchedFeaturesInLayout( + trackId, + hasPaired + ? getBadlyPairedAlignments(totalFeatures) + : getMatchedAlignmentFeatures(totalFeatures), + ) + if (!hasPaired) { + layoutMatches.forEach(m => { + m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos')) + }) + } + return layoutMatches + }, [totalFeatures, trackId, hasPaired, model]) + + const [mouseoverElt, setMouseoverElt] = useState() + + let yOffset = 0 + if (parentRef.current) { + const rect = parentRef.current.getBoundingClientRect() + yOffset = rect.top + } + + if (!assembly) { + return null + } + + return ( + + {layoutMatches.map(chunk => { + const ret = [] + // we follow a path in the list of chunks, not from top to bottom, just in series + // following x1,y1 -> x2,y2 + for (let i = 0; i < chunk.length - 1; i++) { + const { layout: c1, feature: f1, level: level1 } = chunk[i] + const { layout: c2, feature: f2, level: level2 } = chunk[i + 1] + + if (!c1 || !c2) { + console.warn('received null layout for a overlay feature') + return null + } + + // disable rendering connections in a single level + if (!showIntraviewLinks && level1 === level2) { + return null + } + const f1ref = assembly.getCanonicalRefName(f1.get('refName')) + const f2ref = assembly.getCanonicalRefName(f2.get('refName')) + + if (!f1ref || !f2ref) { + throw new Error(`unable to find ref for ${f1ref || f2ref}`) + } + + const s1 = f1.get('strand') + const s2 = f2.get('strand') + const p1 = c1[s1 === -1 ? LEFT : RIGHT] + const p2 = hasPaired + ? c2[s2 === -1 ? LEFT : RIGHT] + : c2[s2 === -1 ? RIGHT : LEFT] + const x1 = getPxFromCoordinate(views[level1], f1ref, p1) + const x2 = getPxFromCoordinate(views[level2], f2ref, p2) + const reversed1 = views[level1].pxToBp(x1).reversed + const reversed2 = views[level2].pxToBp(x2).reversed + + const tracks = views.map(v => v.getTrack(trackId)) + + const y1 = yPos(trackId, level1, views, tracks, c1) - yOffset + const y2 = yPos(trackId, level2, views, tracks, c2) - yOffset + + // possible todo: use totalCurveHeight to possibly make alternative + // squiggle if the S is too small + const path = Path() + .moveTo(x1, y1) + .curveTo( + x1 + 200 * f1.get('strand') * (reversed1 ? -1 : 1), + y1, + x2 - + 200 * + f2.get('strand') * + (reversed2 ? -1 : 1) * + (hasPaired ? -1 : 1), + y2, + x2, + y2, + ) + .end() + const id = `${f1.id()}-${f2.id()}` + ret.push( + { + const featureWidget = session.addWidget?.( + 'BreakpointAlignmentsWidget', + 'breakpointAlignments', + { + featureData: { + feature1: ( + totalFeatures.get(f1.id()) || { toJSON: () => {} } + ).toJSON(), + feature2: ( + totalFeatures.get(f2.id()) || { toJSON: () => {} } + ).toJSON(), + }, + }, + ) + session.showWidget?.(featureWidget) + }} + onMouseOver={() => setMouseoverElt(id)} + onMouseOut={() => setMouseoverElt(undefined)} + />, + ) + } + return ret + })} + + ) +}) + +export default AlignmentConnections diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Breakends.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Breakends.tsx new file mode 100644 index 0000000000..6b0598d8cb --- /dev/null +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Breakends.tsx @@ -0,0 +1,134 @@ +import React, { useState, useMemo } from 'react' +import Path from 'svg-path-generator' +import { getSession } from '@jbrowse/core/util' +import { observer } from 'mobx-react' +import { getSnapshot } from 'mobx-state-tree' + +// locals +import { findMatchingAlt, getMatchedBreakendFeatures } from './util' +import { yPos, getPxFromCoordinate, useNextFrame } from '../util' +import { BreakpointViewModel } from '../model' + +const [LEFT] = [0, 1, 2, 3] + +const Breakends = observer(function ({ + model, + trackId, + parentRef: ref, +}: { + model: BreakpointViewModel + trackId: string + parentRef: React.RefObject +}) { + const { views } = model + const session = getSession(model) + const { assemblyManager } = session + const totalFeatures = model.getTrackFeatures(trackId) + const layoutMatches = useMemo( + () => + model.getMatchedFeaturesInLayout( + trackId, + getMatchedBreakendFeatures(totalFeatures), + ), + [totalFeatures, trackId, model], + ) + + const [mouseoverElt, setMouseoverElt] = useState() + const snap = getSnapshot(model) + useNextFrame(snap) + const assembly = assemblyManager.get(views[0].assemblyNames[0]) + + if (!assembly) { + return null + } + + let yoff = 0 + if (ref.current) { + const rect = ref.current.getBoundingClientRect() + yoff = rect.top + } + + return ( + + {layoutMatches.map(chunk => { + const ret = [] + // we follow a path in the list of chunks, not from top to bottom, just + // in series following x1,y1 -> x2,y2 + for (let i = 0; i < chunk.length - 1; i += 1) { + const { layout: c1, feature: f1, level: level1 } = chunk[i] + const { layout: c2, feature: f2, level: level2 } = chunk[i + 1] + const id = f1.id() + + const relevantAlt = findMatchingAlt(f1, f2) + if (!c1 || !c2) { + return null + } + const f1origref = f1.get('refName') + const f2origref = f2.get('refName') + const f1ref = assembly.getCanonicalRefName(f1origref) + const f2ref = assembly.getCanonicalRefName(f2origref) + if (!f1ref || !f2ref) { + throw new Error(`unable to find ref for ${f1ref || f2ref}`) + } + const x1 = getPxFromCoordinate(views[level1], f1ref, c1[LEFT]) + const x2 = getPxFromCoordinate(views[level2], f2ref, c2[LEFT]) + const reversed1 = views[level1].pxToBp(x1).reversed + const reversed2 = views[level2].pxToBp(x2).reversed + + const tracks = views.map(v => v.getTrack(trackId)) + const y1 = yPos(trackId, level1, views, tracks, c1) - yoff + const y2 = yPos(trackId, level2, views, tracks, c2) - yoff + if (!relevantAlt) { + console.warn('the relevant ALT allele was not found, cannot render') + } else { + const path = Path() + .moveTo( + x1 - + 20 * + (relevantAlt.Join === 'left' ? -1 : 1) * + (reversed1 ? -1 : 1), + y1, + ) + .lineTo(x1, y1) + .lineTo(x2, y2) + .lineTo( + x2 - + 20 * + (relevantAlt.MateDirection === 'left' ? 1 : -1) * + (reversed2 ? -1 : 1), + y2, + ) + .end() + ret.push( + { + const featureWidget = session.addWidget?.( + 'VariantFeatureWidget', + 'variantFeature', + { + featureData: totalFeatures.get(id)?.toJSON(), + }, + ) + session.showWidget?.(featureWidget) + }} + onMouseOver={() => setMouseoverElt(id)} + onMouseOut={() => setMouseoverElt(undefined)} + />, + ) + } + } + return ret + })} + + ) +}) + +export default Breakends diff --git a/plugins/breakpoint-split-view/src/components/BreakpointSplitView.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/BreakpointSplitView.tsx similarity index 83% rename from plugins/breakpoint-split-view/src/components/BreakpointSplitView.tsx rename to plugins/breakpoint-split-view/src/BreakpointSplitView/components/BreakpointSplitView.tsx index 5cfbf82518..795045920c 100644 --- a/plugins/breakpoint-split-view/src/components/BreakpointSplitView.tsx +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/BreakpointSplitView.tsx @@ -44,30 +44,25 @@ const useStyles = makeStyles()(theme => ({ }, })) -const Overlay = observer( - (props: { - parentRef: React.RefObject - model: BreakpointViewModel - trackId: string - }) => { - const { model, trackId } = props - const tracks = model.getMatchedTracks(trackId) - if ( - tracks[0]?.type === 'PileupTrack' || - tracks[0]?.type === 'AlignmentsTrack' - ) { - return - } - if (tracks[0]?.type === 'VariantTrack') { - return model.hasTranslocations(trackId) ? ( - - ) : ( - - ) - } - return null - }, -) +const Overlay = observer(function (props: { + parentRef: React.RefObject + model: BreakpointViewModel + trackId: string +}) { + const { model, trackId } = props + const tracks = model.getMatchedTracks(trackId) + if (tracks[0]?.type === 'AlignmentsTrack') { + return + } + if (tracks[0]?.type === 'VariantTrack') { + return model.hasTranslocations(trackId) ? ( + + ) : ( + + ) + } + return null +}) const BreakpointSplitView = observer( ({ model }: { model: BreakpointViewModel }) => { diff --git a/plugins/breakpoint-split-view/src/components/Header.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Header.tsx similarity index 81% rename from plugins/breakpoint-split-view/src/components/Header.tsx rename to plugins/breakpoint-split-view/src/BreakpointSplitView/components/Header.tsx index 94c00cbfff..3299b38891 100644 --- a/plugins/breakpoint-split-view/src/components/Header.tsx +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Header.tsx @@ -11,9 +11,10 @@ import LeakRemove from '@mui/icons-material/LeakRemove' import LinkIcon from '@mui/icons-material/Link' import LinkOffIcon from '@mui/icons-material/LinkOff' +// locals import { BreakpointViewModel } from '../model' -const useStyles = makeStyles()(theme => ({ +const useStyles = makeStyles()({ headerBar: { gridArea: '1/1/auto/span 2', display: 'flex', @@ -21,20 +22,22 @@ const useStyles = makeStyles()(theme => ({ spacer: { flexGrow: 1, }, -})) +}) -const InteractWithSquiggles = observer( - ({ model }: { model: BreakpointViewModel }) => { - return ( - model.toggleInteract()} - title="Toggle interacting with the overlay" - > - {model.interactToggled ? : } - - ) - }, -) +const InteractWithSquiggles = observer(function ({ + model, +}: { + model: BreakpointViewModel +}) { + return ( + model.toggleInteract()} + title="Toggle interacting with the overlay" + > + {model.interactToggled ? : } + + ) +}) const LinkViews = observer(({ model }: { model: BreakpointViewModel }) => { return ( diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Translocations.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Translocations.tsx new file mode 100644 index 0000000000..7f16b618f3 --- /dev/null +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Translocations.tsx @@ -0,0 +1,141 @@ +import React, { useState, useMemo } from 'react' +import { getSession } from '@jbrowse/core/util' +import { observer } from 'mobx-react' +import { getSnapshot } from 'mobx-state-tree' +import Path from 'svg-path-generator' + +// locals +import { getMatchedTranslocationFeatures } from './util' +import { yPos, getPxFromCoordinate, useNextFrame } from '../util' +import { BreakpointViewModel, LayoutRecord } from '../model' + +const [LEFT] = [0, 1, 2, 3] + +const Translocations = observer(function ({ + model, + trackId, + parentRef: ref, +}: { + model: BreakpointViewModel + trackId: string + parentRef: React.RefObject +}) { + const { views } = model + const session = getSession(model) + const { assemblyManager } = session + const totalFeatures = model.getTrackFeatures(trackId) + const layoutMatches = useMemo( + () => + model.getMatchedFeaturesInLayout( + trackId, + getMatchedTranslocationFeatures(totalFeatures), + ), + + [totalFeatures, trackId, model], + ) + + const [mouseoverElt, setMouseoverElt] = useState() + const snap = getSnapshot(model) + useNextFrame(snap) + + const assembly = assemblyManager.get(views[0].assemblyNames[0]) + if (!assembly) { + return null + } + + let yOffset = 0 + if (ref.current) { + const rect = ref.current.getBoundingClientRect() + yOffset = rect.top + } + + // we hardcode the TRA to go to the "other view" and if there is none, we + // just return null here note: would need to do processing of the INFO + // CHR2/END and see which view could contain those coordinates to really + // do it properly + if (views.length < 2) { + return null + } + return ( + + {layoutMatches.map(chunk => { + // we follow a path in the list of chunks, not from top to bottom, + // just in series following x1,y1 -> x2,y2 + const ret = [] + for (let i = 0; i < chunk.length; i += 1) { + const { layout: c1, feature: f1, level: level1 } = chunk[i] + const level2 = level1 === 0 ? 1 : 0 + const id = f1.id() + if (!c1) { + return null + } + + const info = f1.get('INFO') + const chr2 = info.CHR2[0] + const end2 = info.END[0] + const [myDirection, mateDirection] = info.STRANDS[0].split('') + + const r = getPxFromCoordinate(views[level2], chr2, end2) + if (r) { + const c2: LayoutRecord = [r, 0, r + 1, 0] + const x1 = getPxFromCoordinate( + views[level1], + f1.get('refName'), + c1[LEFT], + ) + const x2 = r + const reversed1 = views[level1].pxToBp(x1).reversed + const reversed2 = views[level2].pxToBp(x2).reversed + + const tracks = views.map(v => v.getTrack(trackId)) + const y1 = yPos(trackId, level1, views, tracks, c1) - yOffset + const y2 = yPos(trackId, level2, views, tracks, c2) - yOffset + + const path = Path() + .moveTo( + x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1), + y1, + ) + .lineTo(x1, y1) + .lineTo(x2, y2) + .lineTo( + x2 - + 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1), + y2, + ) + .end() + ret.push( + { + const featureWidget = session.addWidget?.( + 'VariantFeatureWidget', + 'variantFeature', + { + featureData: ( + totalFeatures.get(id) || { toJSON: () => {} } + ).toJSON(), + }, + ) + session.showWidget?.(featureWidget) + }} + onMouseOver={() => setMouseoverElt(id)} + onMouseOut={() => setMouseoverElt(undefined)} + />, + ) + } + } + return ret + })} + + ) +}) + +export default Translocations diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/util.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/util.ts new file mode 100644 index 0000000000..ac52bc7241 --- /dev/null +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/util.ts @@ -0,0 +1,120 @@ +import { Feature } from '@jbrowse/core/util' + +import { parseBreakend, Breakend } from '@gmod/vcf' + +// this finds candidate alignment features, aimed at plotting split reads +// from BAM/CRAM files +export function getBadlyPairedAlignments(features: Map) { + const candidates: Record = {} + const alreadySeen = new Set() + + // this finds candidate features that share the same name + for (const feature of features.values()) { + const flags = feature.get('flags') + const id = feature.id() + const unmapped = flags & 4 + const correctlyPaired = flags & 2 + + if (!alreadySeen.has(id) && !correctlyPaired && !unmapped) { + const n = feature.get('name') + if (!candidates[n]) { + candidates[n] = [] + } + candidates[n].push(feature) + } + alreadySeen.add(feature.id()) + } + + return Object.values(candidates).filter(v => v.length > 1) +} + +// this finds candidate alignment features, aimed at plotting split reads +// from BAM/CRAM files +export function getMatchedAlignmentFeatures(features: Map) { + const candidates: Record = {} + const alreadySeen = new Set() + + // this finds candidate features that share the same name + for (const feature of features.values()) { + const id = feature.id() + const unmapped = feature.get('flags') & 4 + if (!alreadySeen.has(id) && !unmapped) { + const n = feature.get('name') + if (!candidates[n]) { + candidates[n] = [] + } + candidates[n].push(feature) + } + alreadySeen.add(feature.id()) + } + + return Object.values(candidates).filter(v => v.length > 1) +} + +export function hasPairedReads(features: Map) { + for (const f of features.values()) { + if (f.get('flags') & 1) { + return true + } + } + return false +} + +export function findMatchingAlt(feat1: Feature, feat2: Feature) { + const alts = feat1.get('ALT') as string[] | undefined + if (alts) { + return Object.fromEntries( + alts + ?.map(alt => parseBreakend(alt)) + .filter((f): f is Breakend => !!f) + .map(bnd => [bnd.MatePosition, bnd]), + )[`${feat2.get('refName')}:${feat2.get('start') + 1}`] + } + return undefined +} + +// Returns paired BND features across multiple views by inspecting +// the ALT field to get exact coordinate matches +export function getMatchedBreakendFeatures(feats: Map) { + const candidates: Record = {} + const alreadySeen = new Set() + + for (const f of feats.values()) { + if (!alreadySeen.has(f.id())) { + if (f.get('type') === 'breakend') { + const alts = f.get('ALT') as string[] | undefined + alts?.forEach(a => { + const cur = `${f.get('refName')}:${f.get('start') + 1}` + const bnd = parseBreakend(a) + if (bnd) { + if (!candidates[cur]) { + candidates[bnd.MatePosition || 'none'] = [f] + } else { + candidates[cur].push(f) + } + } + }) + } + } + alreadySeen.add(f.id()) + } + + return Object.values(candidates).filter(v => v.length > 1) +} + +// Getting "matched" TRA means just return all TRA +export function getMatchedTranslocationFeatures(feats: Map) { + const ret: Feature[][] = [] + const alreadySeen = new Set() + + for (const f of feats.values()) { + if (!alreadySeen.has(f.id())) { + if (f.get('ALT')[0] === '') { + ret.push([f]) + } + } + alreadySeen.add(f.id()) + } + + return ret +} diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/index.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/index.ts new file mode 100644 index 0000000000..32d6158464 --- /dev/null +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/index.ts @@ -0,0 +1,17 @@ +import PluginManager from '@jbrowse/core/PluginManager' + +// locals +import BreakpointSplitViewComponent from './components/BreakpointSplitView' +import BreakpointSplitView from './BreakpointSplitView' +import stateModelFactory from './model' + +export default (pluginManager: PluginManager) => { + pluginManager.addViewType(() => { + return new BreakpointSplitView({ + name: 'BreakpointSplitView', + displayName: 'Breakpoint split view', + stateModel: stateModelFactory(pluginManager), + ReactComponent: BreakpointSplitViewComponent, + }) + }) +} diff --git a/plugins/breakpoint-split-view/src/model.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts similarity index 83% rename from plugins/breakpoint-split-view/src/model.ts rename to plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts index 679a8f30ff..9d36fe6147 100644 --- a/plugins/breakpoint-split-view/src/model.ts +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts @@ -1,8 +1,3 @@ -import { - LinearGenomeViewModel, - LinearGenomeViewStateModel, -} from '@jbrowse/plugin-linear-genome-view' -import PluginManager from '@jbrowse/core/PluginManager' import { types, getParent, @@ -11,25 +6,28 @@ import { getPath, Instance, } from 'mobx-state-tree' +import { autorun } from 'mobx' + +// jbrowse +import { + LinearGenomeViewModel, + LinearGenomeViewStateModel, +} from '@jbrowse/plugin-linear-genome-view' +import PluginManager from '@jbrowse/core/PluginManager' import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models' import { getSession, Feature } from '@jbrowse/core/util' import { AnyConfigurationModel, getConf } from '@jbrowse/core/configuration' -import { autorun } from 'mobx' -// https://stackoverflow.com/a/49186706/2129219 the array-intersection package -// on npm has a large kb size, and we are just intersecting open track ids so -// simple is better -function intersect( - cb: (l: T) => string, - a1: T[] = [], - a2: T[] = [], - ...rest: T[][] -): T[] { - const ids = a2.map(elt => cb(elt)) - const a12 = a1.filter(value => ids.includes(cb(value))) - return rest.length === 0 ? a12 : intersect(cb, a12, ...rest) +// locals +import { intersect } from './util' + +// eslint-disable-next-line @typescript-eslint/no-explicit-any +function calc(track: any, feat: Feature): LayoutRecord { + return track.displays[0].searchFeatureByID(feat.id()) } +type LGV = LinearGenomeViewModel + export interface Breakend { MateDirection: string Join: string @@ -136,28 +134,26 @@ export default function stateModelFactory(pluginManager: PluginManager) { // use reverse to search the second track first const tracks = this.getMatchedTracks(trackConfigId) - // eslint-disable-next-line @typescript-eslint/no-explicit-any - const calc = (track: any, feat: Feature) => { - return track.displays[0].searchFeatureByID(feat.id()) - } - return features.map(c => c .map(feature => { const level = tracks.findIndex(track => calc(track, feature)) - if (level !== -1) { - const layout = calc(tracks[level], feature) - return { - feature, - layout, - level, - } - } - return undefined + return level !== -1 + ? { + feature, + layout: calc(tracks[level], feature), + level, + } + : undefined }) .filter( - // eslint-disable-next-line @typescript-eslint/no-explicit-any - (f): f is { feature: Feature; layout: any; level: number } => !!f, + ( + f, + ): f is { + feature: Feature + layout: LayoutRecord + level: number + } => !!f, ), ) }, @@ -212,7 +208,7 @@ export default function stateModelFactory(pluginManager: PluginManager) { self.views.forEach(v => v.setWidth(newWidth)) }, - removeView(view: LinearGenomeViewModel) { + removeView(view: LGV) { self.views.remove(view) }, @@ -263,11 +259,8 @@ export default function stateModelFactory(pluginManager: PluginManager) { }, })) - const stateModel = types.compose(BaseViewModel, model) - - return { stateModel } + return types.compose(BaseViewModel, model) } -export type BreakpointView = ReturnType -export type BreakpointViewStateModel = BreakpointView['stateModel'] +export type BreakpointViewStateModel = ReturnType export type BreakpointViewModel = Instance diff --git a/plugins/breakpoint-split-view/src/util.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts similarity index 78% rename from plugins/breakpoint-split-view/src/util.ts rename to plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts index 9ea921b55c..1d370d4b56 100644 --- a/plugins/breakpoint-split-view/src/util.ts +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts @@ -37,7 +37,6 @@ export function yPos( height: number scrollTop: number SNPCoverageDisplay?: { height: number } - showCoverage?: boolean }, ] }[], // basic track requirements @@ -47,8 +46,8 @@ export function yPos( const min = 0 const max = display.height let offset = 0 - const { showCoverage, SNPCoverageDisplay } = display - if (SNPCoverageDisplay && showCoverage) { + const { SNPCoverageDisplay } = display + if (SNPCoverageDisplay) { offset = SNPCoverageDisplay.height } return ( @@ -68,3 +67,17 @@ export const useNextFrame = (variable: unknown) => { setNextFrameState(variable) }, [variable]) } + +// https://stackoverflow.com/a/49186706/2129219 the array-intersection package +// on npm has a large kb size, and we are just intersecting open track ids so +// simple is better +export function intersect( + cb: (l: T) => string, + a1: T[] = [], + a2: T[] = [], + ...rest: T[][] +): T[] { + const ids = a2.map(elt => cb(elt)) + const a12 = a1.filter(value => ids.includes(cb(value))) + return rest.length === 0 ? a12 : intersect(cb, a12, ...rest) +} diff --git a/plugins/breakpoint-split-view/src/components/AlignmentConnections.tsx b/plugins/breakpoint-split-view/src/components/AlignmentConnections.tsx deleted file mode 100644 index accba9ced6..0000000000 --- a/plugins/breakpoint-split-view/src/components/AlignmentConnections.tsx +++ /dev/null @@ -1,218 +0,0 @@ -import React, { useMemo, useState } from 'react' -import Path from 'svg-path-generator' -import { observer } from 'mobx-react' -import { getSnapshot } from 'mobx-state-tree' -import { getSession, Feature } from '@jbrowse/core/util' - -// locals -import { yPos, useNextFrame, getPxFromCoordinate } from '../util' -import { BreakpointViewModel } from '../model' - -const [LEFT, , RIGHT] = [0, 1, 2, 3] - -// this finds candidate alignment features, aimed at plotting split reads -// from BAM/CRAM files -function getBadlyPairedAlignments(features: Map) { - const candidates: Record = {} - const alreadySeen = new Set() - - // this finds candidate features that share the same name - for (const feature of features.values()) { - const flags = feature.get('flags') - const id = feature.id() - const unmapped = flags & 4 - const correctlyPaired = flags & 2 - - if (!alreadySeen.has(id) && !correctlyPaired && !unmapped) { - const n = feature.get('name') - if (!candidates[n]) { - candidates[n] = [] - } - candidates[n].push(feature) - } - alreadySeen.add(feature.id()) - } - - return Object.values(candidates).filter(v => v.length > 1) -} - -// this finds candidate alignment features, aimed at plotting split reads -// from BAM/CRAM files -function getMatchedAlignmentFeatures(features: Map) { - const candidates: Record = {} - const alreadySeen = new Set() - - // this finds candidate features that share the same name - for (const feature of features.values()) { - const id = feature.id() - const unmapped = feature.get('flags') & 4 - if (!alreadySeen.has(id) && !unmapped) { - const n = feature.get('name') - if (!candidates[n]) { - candidates[n] = [] - } - candidates[n].push(feature) - } - alreadySeen.add(feature.id()) - } - - return Object.values(candidates).filter(v => v.length > 1) -} - -function hasPairedReads(features: Map) { - return [...features.values()].find(f => f.get('flags') & 64) -} - -const AlignmentConnections = observer( - ({ - model, - trackId, - parentRef, - }: { - model: BreakpointViewModel - trackId: string - parentRef: React.RefObject - }) => { - const { views, showIntraviewLinks } = model - - const session = getSession(model) - const snap = getSnapshot(model) - const { assemblyManager } = session - const assembly = assemblyManager.get(views[0].assemblyNames[0]) - useNextFrame(snap) - const totalFeatures = model.getTrackFeatures(trackId) - const hasPaired = useMemo( - () => hasPairedReads(totalFeatures), - [totalFeatures], - ) - - const layoutMatches = useMemo(() => { - const features = hasPaired - ? getBadlyPairedAlignments(totalFeatures) - : getMatchedAlignmentFeatures(totalFeatures) - const layoutMatches = model.getMatchedFeaturesInLayout(trackId, features) - if (!hasPaired) { - layoutMatches.forEach(m => { - m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos')) - }) - } - return layoutMatches - }, [totalFeatures, trackId, hasPaired, model]) - - const [mouseoverElt, setMouseoverElt] = useState() - - let yOffset = 0 - if (parentRef.current) { - const rect = parentRef.current.getBoundingClientRect() - yOffset = rect.top - } - - if (!assembly) { - console.warn('Unable to read assembly') - return null - } - - return ( - - {layoutMatches.map(chunk => { - const ret = [] - // we follow a path in the list of chunks, not from top to bottom, just in series - // following x1,y1 -> x2,y2 - for (let i = 0; i < chunk.length - 1; i += 1) { - const { layout: c1, feature: f1, level: level1 } = chunk[i] - const { layout: c2, feature: f2, level: level2 } = chunk[i + 1] - - if (!c1 || !c2) { - console.warn('received null layout for a overlay feature') - return null - } - - // disable rendering connections in a single level - if (!showIntraviewLinks && level1 === level2) { - return null - } - const f1origref = f1.get('refName') - const f2origref = f2.get('refName') - const f1ref = assembly.getCanonicalRefName(f1origref) - const f2ref = assembly.getCanonicalRefName(f2origref) - - if (!f1ref || !f2ref) { - throw new Error(`unable to find ref for ${f1ref || f2ref}`) - } - - const s1 = f1.get('strand') - const s2 = f2.get('strand') - const p1 = hasPaired - ? c1[s1 === -1 ? LEFT : RIGHT] - : c1[s1 === -1 ? LEFT : RIGHT] - const p2 = hasPaired - ? c2[s2 === -1 ? LEFT : RIGHT] - : c2[s2 === -1 ? RIGHT : LEFT] - const x1 = getPxFromCoordinate(views[level1], f1ref, p1) - const x2 = getPxFromCoordinate(views[level2], f2ref, p2) - const reversed1 = views[level1].pxToBp(x1).reversed - const reversed2 = views[level2].pxToBp(x2).reversed - - const tracks = views.map(v => v.getTrack(trackId)) - - const y1 = yPos(trackId, level1, views, tracks, c1) - yOffset - const y2 = yPos(trackId, level2, views, tracks, c2) - yOffset - - // possible todo: use totalCurveHeight to possibly make alternative - // squiggle if the S is too small - const path = Path() - .moveTo(x1, y1) - .curveTo( - x1 + 200 * f1.get('strand') * (reversed1 ? -1 : 1), - y1, - x2 - - 200 * - f2.get('strand') * - (reversed2 ? -1 : 1) * - (hasPaired ? -1 : 1), - y2, - x2, - y2, - ) - .end() - const id = `${f1.id()}-${f2.id()}` - ret.push( - { - const featureWidget = session.addWidget?.( - 'BreakpointAlignmentsWidget', - 'breakpointAlignments', - { - featureData: { - feature1: ( - totalFeatures.get(f1.id()) || { toJSON: () => {} } - ).toJSON(), - feature2: ( - totalFeatures.get(f2.id()) || { toJSON: () => {} } - ).toJSON(), - }, - }, - ) - session.showWidget?.(featureWidget) - }} - onMouseOver={() => setMouseoverElt(id)} - onMouseOut={() => setMouseoverElt(undefined)} - />, - ) - } - return ret - })} - - ) - }, -) - -export default AlignmentConnections diff --git a/plugins/breakpoint-split-view/src/components/Breakends.tsx b/plugins/breakpoint-split-view/src/components/Breakends.tsx deleted file mode 100644 index e7a2543961..0000000000 --- a/plugins/breakpoint-split-view/src/components/Breakends.tsx +++ /dev/null @@ -1,180 +0,0 @@ -import React, { useState, useMemo } from 'react' -import Path from 'svg-path-generator' -import { getSession, Feature } from '@jbrowse/core/util' -import { observer } from 'mobx-react' -import { getSnapshot } from 'mobx-state-tree' -import { parseBreakend, Breakend } from '@gmod/vcf' - -// locals -import { yPos, getPxFromCoordinate, useNextFrame } from '../util' -import { BreakpointViewModel } from '../model' - -const [LEFT] = [0, 1, 2, 3] - -function findMatchingAlt(feat1: Feature, feat2: Feature) { - const alts = feat1.get('ALT') as string[] | undefined - if (alts) { - return Object.fromEntries( - alts - ?.map(alt => parseBreakend(alt)) - .filter((f): f is Breakend => !!f) - .map(bnd => [bnd.MatePosition, bnd]), - )[`${feat2.get('refName')}:${feat2.get('start') + 1}`] - } - return undefined -} - -// Returns paired BND features across multiple views by inspecting -// the ALT field to get exact coordinate matches -function getMatchedBreakendFeatures(features: Map) { - const candidates: Record = {} - const alreadySeen = new Set() - - for (const f of features.values()) { - if (!alreadySeen.has(f.id())) { - if (f.get('type') === 'breakend') { - const alts = f.get('ALT') as string[] | undefined - alts?.forEach(a => { - const cur = `${f.get('refName')}:${f.get('start') + 1}` - const bnd = parseBreakend(a) - if (bnd) { - if (!candidates[cur]) { - candidates[bnd.MatePosition || 'none'] = [f] - } else { - candidates[cur].push(f) - } - } - }) - } - } - alreadySeen.add(f.id()) - } - - return Object.values(candidates).filter(v => v.length > 1) -} - -const Breakends = observer( - ({ - model, - trackId, - parentRef: ref, - }: { - model: BreakpointViewModel - trackId: string - parentRef: React.RefObject - }) => { - const { views } = model - const session = getSession(model) - const { assemblyManager } = session - const totalFeatures = model.getTrackFeatures(trackId) - const layoutMatches = useMemo( - () => - model.getMatchedFeaturesInLayout( - trackId, - getMatchedBreakendFeatures(totalFeatures), - ), - [totalFeatures, trackId, model], - ) - - const [mouseoverElt, setMouseoverElt] = useState() - const snap = getSnapshot(model) - useNextFrame(snap) - const assembly = assemblyManager.get(views[0].assemblyNames[0]) - - if (!assembly) { - return null - } - - let yoff = 0 - if (ref.current) { - const rect = ref.current.getBoundingClientRect() - yoff = rect.top - } - - return ( - - {layoutMatches.map(chunk => { - const ret = [] - // we follow a path in the list of chunks, not from top to bottom, just - // in series following x1,y1 -> x2,y2 - for (let i = 0; i < chunk.length - 1; i += 1) { - const { layout: c1, feature: f1, level: level1 } = chunk[i] - const { layout: c2, feature: f2, level: level2 } = chunk[i + 1] - const id = f1.id() - - const relevantAlt = findMatchingAlt(f1, f2) - if (!c1 || !c2) { - return null - } - const f1origref = f1.get('refName') - const f2origref = f2.get('refName') - const f1ref = assembly.getCanonicalRefName(f1origref) - const f2ref = assembly.getCanonicalRefName(f2origref) - if (!f1ref || !f2ref) { - throw new Error(`unable to find ref for ${f1ref || f2ref}`) - } - const x1 = getPxFromCoordinate(views[level1], f1ref, c1[LEFT]) - const x2 = getPxFromCoordinate(views[level2], f2ref, c2[LEFT]) - const reversed1 = views[level1].pxToBp(x1).reversed - const reversed2 = views[level2].pxToBp(x2).reversed - - const tracks = views.map(v => v.getTrack(trackId)) - const y1 = yPos(trackId, level1, views, tracks, c1) - yoff - const y2 = yPos(trackId, level2, views, tracks, c2) - yoff - if (!relevantAlt) { - console.warn( - 'the relevant ALT allele was not found, cannot render', - ) - } else { - const path = Path() - .moveTo( - x1 - - 20 * - (relevantAlt.Join === 'left' ? -1 : 1) * - (reversed1 ? -1 : 1), - y1, - ) - .lineTo(x1, y1) - .lineTo(x2, y2) - .lineTo( - x2 - - 20 * - (relevantAlt.MateDirection === 'left' ? 1 : -1) * - (reversed2 ? -1 : 1), - y2, - ) - .end() - ret.push( - { - const featureWidget = session.addWidget?.( - 'VariantFeatureWidget', - 'variantFeature', - { - featureData: totalFeatures.get(id)?.toJSON(), - }, - ) - session.showWidget?.(featureWidget) - }} - onMouseOver={() => setMouseoverElt(id)} - onMouseOut={() => setMouseoverElt(undefined)} - />, - ) - } - } - return ret - })} - - ) - }, -) - -export default Breakends diff --git a/plugins/breakpoint-split-view/src/components/Translocations.tsx b/plugins/breakpoint-split-view/src/components/Translocations.tsx deleted file mode 100644 index b53a42d454..0000000000 --- a/plugins/breakpoint-split-view/src/components/Translocations.tsx +++ /dev/null @@ -1,164 +0,0 @@ -import React, { useState, useMemo } from 'react' -import { getSession, Feature } from '@jbrowse/core/util' -import { observer } from 'mobx-react' -import { getSnapshot } from 'mobx-state-tree' -import Path from 'svg-path-generator' - -// locals -import { yPos, getPxFromCoordinate, useNextFrame } from '../util' -import { BreakpointViewModel, LayoutRecord } from '../model' - -const [LEFT] = [0, 1, 2, 3] - -// Getting "matched" TRA means just return all TRA -function getMatchedTranslocationFeatures(features: Map) { - const feats: Feature[][] = [] - const alreadySeen = new Set() - - for (const f of features.values()) { - if (!alreadySeen.has(f.id())) { - if (f.get('ALT')[0] === '') { - feats.push([f]) - } - } - alreadySeen.add(f.id()) - } - - return feats -} - -const Translocations = observer( - ({ - model, - trackId, - parentRef: ref, - }: { - model: BreakpointViewModel - trackId: string - parentRef: React.RefObject - }) => { - const { views } = model - const session = getSession(model) - const { assemblyManager } = session - const totalFeatures = model.getTrackFeatures(trackId) - const layoutMatches = useMemo( - () => - model.getMatchedFeaturesInLayout( - trackId, - getMatchedTranslocationFeatures(totalFeatures), - ), - - [totalFeatures, trackId, model], - ) - - const [mouseoverElt, setMouseoverElt] = useState() - const snap = getSnapshot(model) - useNextFrame(snap) - - const assembly = assemblyManager.get(views[0].assemblyNames[0]) - if (!assembly) { - console.warn('Unable to read assembly') - return null - } - - let yOffset = 0 - if (ref.current) { - const rect = ref.current.getBoundingClientRect() - yOffset = rect.top - } - - // we hardcode the TRA to go to the "other view" and if there is none, we - // just return null here note: would need to do processing of the INFO - // CHR2/END and see which view could contain those coordinates to really - // do it properly - if (views.length < 2) { - return null - } - return ( - - {layoutMatches.map(chunk => { - // we follow a path in the list of chunks, not from top to bottom, - // just in series following x1,y1 -> x2,y2 - const ret = [] - for (let i = 0; i < chunk.length; i += 1) { - const { layout: c1, feature: f1, level: level1 } = chunk[i] - const level2 = level1 === 0 ? 1 : 0 - const id = f1.id() - if (!c1) { - return null - } - - const info = f1.get('INFO') - const chr2 = info.CHR2[0] - const end2 = info.END[0] - const [myDirection, mateDirection] = info.STRANDS[0].split('') - - const r = getPxFromCoordinate(views[level2], chr2, end2) - if (r) { - const c2: LayoutRecord = [r, 0, r + 1, 0] - - const x1 = getPxFromCoordinate( - views[level1], - f1.get('refName'), - c1[LEFT], - ) - const x2 = r - const reversed1 = views[level1].pxToBp(x1).reversed - const reversed2 = views[level2].pxToBp(x2).reversed - - const tracks = views.map(v => v.getTrack(trackId)) - const y1 = yPos(trackId, level1, views, tracks, c1) - yOffset - const y2 = yPos(trackId, level2, views, tracks, c2) - yOffset - - const path = Path() - .moveTo( - x1 - - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1), - y1, - ) - .lineTo(x1, y1) - .lineTo(x2, y2) - .lineTo( - x2 - - 20 * - (mateDirection === '+' ? 1 : -1) * - (reversed2 ? -1 : 1), - y2, - ) - .end() - ret.push( - { - const featureWidget = session.addWidget?.( - 'VariantFeatureWidget', - 'variantFeature', - { - featureData: ( - totalFeatures.get(id) || { toJSON: () => {} } - ).toJSON(), - }, - ) - session.showWidget?.(featureWidget) - }} - onMouseOver={() => setMouseoverElt(id)} - onMouseOut={() => setMouseoverElt(undefined)} - />, - ) - } - } - return ret - })} - - ) - }, -) - -export default Translocations diff --git a/plugins/breakpoint-split-view/src/index.ts b/plugins/breakpoint-split-view/src/index.ts index ea7f6645c8..5cd3c81930 100644 --- a/plugins/breakpoint-split-view/src/index.ts +++ b/plugins/breakpoint-split-view/src/index.ts @@ -1,35 +1,14 @@ -import { lazy } from 'react' -import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType' import PluginManager from '@jbrowse/core/PluginManager' import Plugin from '@jbrowse/core/Plugin' -import { - configSchema as alignmentsFeatureDetailConfigSchema, - stateModel as alignmentsFeatureDetailStateModel, -} from './BreakpointAlignmentsFeatureDetail' -import BreakpointSplitViewFactory from './BreakpointSplitView' +import BreakpointAlignmentsWidgetF from './BreakpointAlignmentsFeatureDetail' +import BreakpointSplitViewF from './BreakpointSplitView' export default class BreakpointSplitViewPlugin extends Plugin { name = 'BreakpointSplitViewPlugin' install(pluginManager: PluginManager) { - pluginManager.addViewType(() => - pluginManager.jbrequire(BreakpointSplitViewFactory), - ) - pluginManager.addWidgetType( - () => - new WidgetType({ - name: 'BreakpointAlignmentsWidget', - heading: 'Breakpoint feature details', - configSchema: alignmentsFeatureDetailConfigSchema, - stateModel: alignmentsFeatureDetailStateModel, - ReactComponent: lazy( - () => - import( - './BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail' - ), - ), - }), - ) + BreakpointSplitViewF(pluginManager) + BreakpointAlignmentsWidgetF(pluginManager) } configure() {} diff --git a/plugins/canvas/package.json b/plugins/canvas/package.json index a6e25e56df..899f18efca 100644 --- a/plugins/canvas/package.json +++ b/plugins/canvas/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-canvas", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 plugin for canvas features", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/README.md b/plugins/circular-view/README.md index ad7630f26f..dbe58874f3 100644 --- a/plugins/circular-view/README.md +++ b/plugins/circular-view/README.md @@ -2,12 +2,21 @@ ## slices -A slice is a range in angle (theta) space. Start radians, end radians. The start is always less than or equal to the end. If the slice goes through the origin, the end coordinate may be greater than 2π. +A slice is a range in angle (theta) space. Start radians, end radians. The start +is always less than or equal to the end. If the slice goes through the origin, +the end coordinate may be greater than 2π. -Each circular view is divided into "slices", one or more per displayed region. Slices are roughly equivalent to the "blocks" in linear tracks, except they each have their own polar coordinate system. All drawing in the slice is done relative to the slice's coordinate system, which will have its own origin and figure radius. +Each circular view is divided into "slices", one or more per displayed region. +Slices are roughly equivalent to the "blocks" in linear tracks, except they each +have their own polar coordinate system. All drawing in the slice is done +relative to the slice's coordinate system, which will have its own origin and +figure radius. -Tracks that draw "around the circle" will want to use these slices to draw, while tracks that draw arcs "across the circle" or other whole-figure overlays will probably not want to use these slices. +Tracks that draw "around the circle" will want to use these slices to draw, +while tracks that draw arcs "across the circle" or other whole-figure overlays +will probably not want to use these slices. ## sections -A section is a range in both angle (theta) and radius (rho) space. Start and end in theta have the same rules as slices. +A section is a range in both angle (theta) and radius (rho) space. Start and end +in theta have the same rules as slices. diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index c9a238f81d..dd9ab29014 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/circular-view", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", @@ -37,7 +37,8 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@mui/icons-material": "^5.0.1" + "@mui/icons-material": "^5.0.1", + "clone": "^2.1.2" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", @@ -47,7 +48,7 @@ "mobx-state-tree": "^5.0.0", "react": ">=16.8.0", "react-dom": ">=16.8.0", - "tss-react": "^3.0.0" + "tss-react": "^4.0.0" }, "publishConfig": { "access": "public" diff --git a/plugins/circular-view/src/BaseChordDisplay/components/BaseChordDisplay.tsx b/plugins/circular-view/src/BaseChordDisplay/components/BaseChordDisplay.tsx index e1bdd38a2f..2bfc4be5d5 100644 --- a/plugins/circular-view/src/BaseChordDisplay/components/BaseChordDisplay.tsx +++ b/plugins/circular-view/src/BaseChordDisplay/components/BaseChordDisplay.tsx @@ -1,16 +1,26 @@ import React from 'react' import { observer } from 'mobx-react' + +// locals import Loading from './Loading' import DisplayError from './DisplayError' -import RpcRenderedSvgGroup from './RpcRenderedSvgGroup' -// eslint-disable-next-line @typescript-eslint/no-explicit-any -function BaseChordDisplay({ display }: any) { + +export default observer(function BaseChordDisplay({ + display, +}: { + display: { + filled: boolean + error: unknown + reactElement: React.ReactElement + renderProps: { radius: number } + } +}) { if (display.error) { return } if (!display.filled) { return } - return -} -export default observer(BaseChordDisplay) + + return display.reactElement +}) diff --git a/plugins/circular-view/src/BaseChordDisplay/components/DisplayError.tsx b/plugins/circular-view/src/BaseChordDisplay/components/DisplayError.tsx index 7237dd9380..93a048dcc3 100644 --- a/plugins/circular-view/src/BaseChordDisplay/components/DisplayError.tsx +++ b/plugins/circular-view/src/BaseChordDisplay/components/DisplayError.tsx @@ -1,49 +1,47 @@ import React from 'react' import { observer } from 'mobx-react' -const DisplayError = observer( - ({ - model, - }: { - model: { renderProps: { radius: number }; error: unknown } - }) => { - const { - renderProps: { radius }, - error, - } = model - return ( - - - - - - - - - + + - {String(error)} - - - ) - }, -) + + + + + + + {String(error)} + + + ) +}) export default DisplayError diff --git a/plugins/circular-view/src/BaseChordDisplay/components/Loading.tsx b/plugins/circular-view/src/BaseChordDisplay/components/Loading.tsx index 1c7c74397e..d90cbeaea2 100644 --- a/plugins/circular-view/src/BaseChordDisplay/components/Loading.tsx +++ b/plugins/circular-view/src/BaseChordDisplay/components/Loading.tsx @@ -48,66 +48,63 @@ const useStyles = makeStyles()(theme => { } }) -// 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)', -const Loading = observer( - ({ - model: { - renderProps: { radius }, - }, - }: { - model: { renderProps: { radius: number } } - }) => { - const { classes } = useStyles() +const Loading = observer(function ({ + model: { + renderProps: { radius }, + }, +}: { + model: { renderProps: { radius: number } } +}) { + const { classes } = useStyles() - // only show the loading message after 400ms to prevent excessive flickering - const [shown, setShown] = useState(false) - useEffect(() => { - const timeout = setTimeout(() => setShown(true), 400) - return () => clearTimeout(timeout) - }) + // only show the loading message after 400ms to prevent excessive flickering + const [shown, setShown] = useState(false) + useEffect(() => { + const timeout = setTimeout(() => setShown(true), 400) + return () => clearTimeout(timeout) + }) - return !shown ? null : ( - - - - - - - - - + + - Loading… - - - - ) - }, -) + + + + + + + Loading… + + + + ) +}) export default Loading diff --git a/plugins/circular-view/src/BaseChordDisplay/components/RpcRenderedSvgGroup.tsx b/plugins/circular-view/src/BaseChordDisplay/components/RpcRenderedSvgGroup.tsx deleted file mode 100644 index 8e1df84ba7..0000000000 --- a/plugins/circular-view/src/BaseChordDisplay/components/RpcRenderedSvgGroup.tsx +++ /dev/null @@ -1,69 +0,0 @@ -import React, { useEffect, useRef } from 'react' -import { isAlive } from 'mobx-state-tree' -import { observer } from 'mobx-react' -import { hydrate, unmountComponentAtNode } from 'react-dom' -import { rIC } from '@jbrowse/core/util' - -function RpcRenderedSvgGroup({ - model, -}: { - model: { - // eslint-disable-next-line @typescript-eslint/no-explicit-any - data: any - html: string - filled: boolean - // eslint-disable-next-line @typescript-eslint/no-explicit-any - renderingComponent: React.FC - renderProps: Function - } -}) { - const { data, html, filled, renderingComponent } = model - - const ssrContainerNode = useRef(null) - - useEffect(() => { - const domNode = ssrContainerNode.current - function doHydrate() { - if (domNode && filled) { - if (domNode.innerHTML) { - domNode.style.display = 'none' - unmountComponentAtNode(domNode) - } - - // setting outline:none fixes react "focusable" element issue. see - // https://github.com/GMOD/jbrowse-components/issues/2160 - domNode.style.outline = 'none' - domNode.innerHTML = html - // use requestIdleCallback to defer main-thread rendering - // and hydration for when we have some free time. helps - // keep the framerate up. - rIC(() => { - if (!isAlive(model)) { - return - } - const mainThreadRendering = React.createElement( - renderingComponent, - { ...data, ...model.renderProps() }, - null, - ) - rIC(() => { - if (!isAlive(model)) { - return - } - hydrate(mainThreadRendering, domNode) - }) - }) - } - } - doHydrate() - return () => { - if (domNode) { - unmountComponentAtNode(domNode) - } - } - }) - - return -} - -export default observer(RpcRenderedSvgGroup) diff --git a/plugins/circular-view/src/BaseChordDisplay/models/BaseChordDisplayModel.ts b/plugins/circular-view/src/BaseChordDisplay/models/BaseChordDisplayModel.ts index 6a3dab02c3..2fa8eb51de 100644 --- a/plugins/circular-view/src/BaseChordDisplay/models/BaseChordDisplayModel.ts +++ b/plugins/circular-view/src/BaseChordDisplay/models/BaseChordDisplayModel.ts @@ -1,4 +1,8 @@ import React from 'react' +import clone from 'clone' +import { getParent, isAlive, types } from 'mobx-state-tree' + +// jbrowse import { getConf } from '@jbrowse/core/configuration' import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models' import CircularChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType' @@ -7,17 +11,17 @@ import { getContainingView, getSession, getEnv, + isFeature, makeAbortableReaction, AnyReactComponentType, + Feature, + Region, } from '@jbrowse/core/util' -import { Feature, isFeature } from '@jbrowse/core/util/simpleFeature' import { getParentRenderProps, getRpcSessionId, getTrackAssemblyNames, } from '@jbrowse/core/util/tracks' -import { Region } from '@jbrowse/core/util/types' -import { getParent, isAlive, types } from 'mobx-state-tree' // locals import { renderReactionData, renderReactionEffect } from './renderReaction' @@ -27,252 +31,257 @@ import { CircularViewModel } from '../../CircularView/models/CircularView' * #stateModel BaseChordDisplay * extends `BaseDisplay` */ -function stateModelFactory() { - return types - .compose( - 'BaseChordDisplay', - BaseDisplay, - types.model({ - /** - * #property - */ - bezierRadiusRatio: 0.1, - /** - * #property - */ - assemblyName: types.maybe(types.string), - }), - ) - .volatile(() => { - return { - // NOTE: all this volatile stuff has to be filled in at once - // so that it stays consistent - filled: false, - reactElement: undefined as React.ReactElement | undefined, - data: undefined, - message: '', - renderingComponent: undefined as undefined | AnyReactComponentType, - refNameMap: undefined as Record | undefined, - } - }) - .actions(self => { - const { pluginManager } = getEnv(self) - const track = self - return { - /** - * #action - */ - onChordClick(feature: Feature) { - getConf(self, 'onChordClick', { feature, track, pluginManager }) - }, - } - }) - .views(self => ({ +function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars + +export const BaseChordDisplayModel = types + .compose( + 'BaseChordDisplay', + BaseDisplay, + types.model({ /** - * #getter + * #property */ - get blockDefinitions() { - const origSlices = (getContainingView(self) as CircularViewModel) - .staticSlices - if (!self.refNameMap) { - return origSlices - } + bezierRadiusRatio: 0.1, + /** + * #property + */ + assemblyName: types.maybe(types.string), + }), + ) + .volatile(() => { + return { + // NOTE: all this volatile stuff has to be filled in at once + // so that it stays consistent + filled: false, + reactElement: undefined as React.ReactElement | undefined, + data: undefined, + html: undefined as string | undefined, + message: '', + renderingComponent: undefined as undefined | AnyReactComponentType, + refNameMap: undefined as Record | undefined, + } + }) + .actions(self => { + const { pluginManager } = getEnv(self) + const track = self + return { + /** + * #action + */ + onChordClick(feature: Feature) { + getConf(self, 'onChordClick', { feature, track, pluginManager }) + }, + } + }) + .views(self => ({ + /** + * #getter + */ + get blockDefinitions() { + const origSlices = (getContainingView(self) as CircularViewModel) + .staticSlices + if (!self.refNameMap) { + return origSlices + } - const slices = JSON.parse(JSON.stringify(origSlices)) + const slices = clone(origSlices) - // eslint-disable-next-line @typescript-eslint/no-explicit-any - slices.forEach((slice: any) => { - const regions = slice.region.elided - ? slice.region.regions - : [slice.region] - regions.forEach((region: Region) => { - const renamed = self.refNameMap?.[region.refName] - if (renamed && region.refName !== renamed) { - region.refName = renamed - } - }) + // eslint-disable-next-line @typescript-eslint/no-explicit-any + slices.forEach((slice: any) => { + const regions = slice.region.elided + ? slice.region.regions + : [slice.region] + regions.forEach((region: Region) => { + const renamed = self.refNameMap?.[region.refName] + if (renamed && region.refName !== renamed) { + region.refName = renamed + } }) - return slices - }, + }) + return slices + }, - /** - * #method - */ - renderProps() { - const view = getContainingView(self) as CircularViewModel - return { - ...getParentRenderProps(self), - rpcDriverName: self.rpcDriverName, - displayModel: self, - bezierRadius: view.radiusPx * self.bezierRadiusRatio, - radius: view.radiusPx, - blockDefinitions: this.blockDefinitions, - onChordClick: self.onChordClick, - } - }, + /** + * #method + */ + renderProps() { + const view = getContainingView(self) as CircularViewModel + return { + ...getParentRenderProps(self), + rpcDriverName: self.rpcDriverName, + displayModel: self, + bezierRadius: view.radiusPx * self.bezierRadiusRatio, + radius: view.radiusPx, + blockDefinitions: this.blockDefinitions, + onChordClick: self.onChordClick, + } + }, - /** - * #getter - * the pluggable element type object for this diplay's - * renderer - */ - get rendererType() { - const display = self - const { pluginManager } = getEnv(self) - const ThisRendererType = pluginManager.getRendererType( - self.rendererTypeName, + /** + * #getter + * the pluggable element type object for this display's + * renderer + */ + get rendererType() { + const display = self + const { pluginManager } = getEnv(self) + const ThisRendererType = pluginManager.getRendererType( + self.rendererTypeName, + ) + if (!ThisRendererType) { + throw new Error(`renderer "${display.rendererTypeName}" not found`) + } + if (!ThisRendererType.ReactComponent) { + throw new Error( + `renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`, ) - if (!ThisRendererType) { - throw new Error(`renderer "${display.rendererTypeName}" not found`) - } - if (!ThisRendererType.ReactComponent) { - throw new Error( - `renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`, - ) - } - return ThisRendererType - }, + } + return ThisRendererType + }, - /** - * #method - */ - isCompatibleWithRenderer(renderer: RendererType) { - return !!(renderer instanceof CircularChordRendererType) - }, + /** + * #method + */ + isCompatibleWithRenderer(renderer: RendererType) { + return !!(renderer instanceof CircularChordRendererType) + }, - /** - * #getter - * returns a string feature ID if the globally-selected object - * is probably a feature - */ - get selectedFeatureId() { - if (!isAlive(self)) { - return undefined - } - const session = getSession(self) - if (!session) { - return undefined - } - const { selection } = session - // does it quack like a feature? - if (isFeature(selection)) { - return selection.id() - } + /** + * #getter + * returns a string feature ID if the globally-selected object + * is probably a feature + */ + get selectedFeatureId() { + if (!isAlive(self)) { return undefined - }, - })) - .actions(self => ({ - /** - * #action - */ - renderStarted() { + } + const session = getSession(self) + if (!session) { + return undefined + } + const { selection } = session + // does it quack like a feature? + if (isFeature(selection)) { + return selection.id() + } + return undefined + }, + })) + .actions(self => ({ + /** + * #action + */ + renderStarted() { + self.filled = false + self.message = '' + self.reactElement = undefined + self.data = undefined + self.html = undefined + self.error = undefined + self.renderingComponent = undefined + }, + /** + * #action + */ + renderSuccess({ + message, + data, + reactElement, + html, + renderingComponent, + }: { + message: string + // eslint-disable-next-line @typescript-eslint/no-explicit-any + data: any + html: string + reactElement: React.ReactElement + renderingComponent: AnyReactComponentType + }) { + if (message) { self.filled = false - self.message = '' + self.message = message self.reactElement = undefined self.data = undefined + self.html = undefined self.error = undefined self.renderingComponent = undefined - }, - /** - * #action - */ - renderSuccess({ - message, - data, - reactElement, - renderingComponent, - }: { - message: string - // eslint-disable-next-line @typescript-eslint/no-explicit-any - data: any - reactElement: React.ReactElement - renderingComponent: AnyReactComponentType - }) { - if (message) { - self.filled = false - self.message = message - self.reactElement = undefined - self.data = undefined - self.error = undefined - self.renderingComponent = undefined - } else { - self.filled = true - self.message = '' - self.reactElement = reactElement - self.data = data - self.error = undefined - self.renderingComponent = renderingComponent - } - }, - /** - * #action - */ - renderError(error: unknown) { - console.error(error) - // the rendering failed for some reason - self.filled = false + } else { + self.filled = true self.message = '' - self.reactElement = undefined - self.data = undefined - self.error = error - self.renderingComponent = undefined - }, + self.reactElement = reactElement + self.data = data + self.html = html + self.error = undefined + self.renderingComponent = renderingComponent + } + }, + /** + * #action + */ + renderError(error: unknown) { + console.error(error) + // the rendering failed for some reason + self.filled = false + self.message = '' + self.reactElement = undefined + self.html = undefined + self.data = undefined + self.error = error + self.renderingComponent = undefined + }, - /** - * #action - */ - setRefNameMap(refNameMap: Record) { - self.refNameMap = refNameMap - }, - })) - .actions(self => ({ - afterAttach() { - makeAbortableReaction( - self, - renderReactionData, + /** + * #action + */ + setRefNameMap(refNameMap: Record) { + self.refNameMap = refNameMap + }, + })) + .actions(self => ({ + afterAttach() { + makeAbortableReaction( + self, + renderReactionData, - // @ts-ignore - renderReactionEffect, - { - name: `${self.type} ${self.id} rendering`, - // delay: self.renderDelay || 300, - fireImmediately: true, - }, - self.renderStarted, - self.renderSuccess, - self.renderError, - ) - makeAbortableReaction( - self, - () => ({ - assemblyNames: getTrackAssemblyNames(self.parentTrack) as string[], - // eslint-disable-next-line @typescript-eslint/no-explicit-any - adapter: getConf(getParent(self, 2), 'adapter'), - assemblyManager: getSession(self).assemblyManager, - }), + // @ts-ignore + renderReactionEffect, + { + name: `${self.type} ${self.id} rendering`, + // delay: self.renderDelay || 300, + fireImmediately: true, + }, + self.renderStarted, + self.renderSuccess, + self.renderError, + ) + makeAbortableReaction( + self, + () => ({ + assemblyNames: getTrackAssemblyNames(self.parentTrack) as string[], // eslint-disable-next-line @typescript-eslint/no-explicit-any - async ({ assemblyNames, adapter, assemblyManager }: any, signal) => { - return assemblyManager.getRefNameMapForAdapter( - adapter, - assemblyNames[0], - { signal, sessionId: getRpcSessionId(self) }, - ) - }, - { - name: `${self.type} ${self.id} getting refNames`, - fireImmediately: true, - }, - () => {}, - refNameMap => { - self.setRefNameMap(refNameMap) - }, - error => { - console.error(error) - self.setError(error) - }, - ) - }, - })) -} - -export const BaseChordDisplayModel = stateModelFactory() + adapter: getConf(getParent(self, 2), 'adapter'), + assemblyManager: getSession(self).assemblyManager, + }), + // eslint-disable-next-line @typescript-eslint/no-explicit-any + async ({ assemblyNames, adapter, assemblyManager }: any, signal) => { + return assemblyManager.getRefNameMapForAdapter( + adapter, + assemblyNames[0], + { signal, sessionId: getRpcSessionId(self) }, + ) + }, + { + name: `${self.type} ${self.id} getting refNames`, + fireImmediately: true, + }, + () => {}, + refNameMap => { + self.setRefNameMap(refNameMap) + }, + error => { + console.error(error) + self.setError(error) + }, + ) + }, + })) diff --git a/plugins/circular-view/src/BaseChordDisplay/models/renderReaction.ts b/plugins/circular-view/src/BaseChordDisplay/models/renderReaction.ts index 20bdaed469..c1ef3a96e8 100644 --- a/plugins/circular-view/src/BaseChordDisplay/models/renderReaction.ts +++ b/plugins/circular-view/src/BaseChordDisplay/models/renderReaction.ts @@ -1,3 +1,4 @@ +import clone from 'clone' import { getRpcSessionId } from '@jbrowse/core/util/tracks' import { getSession, getContainingView } from '@jbrowse/core/util' @@ -13,9 +14,9 @@ export function renderReactionData(self: any) { renderProps: self.renderProps(), renderArgs: { assemblyName: view.displayedRegions[0]?.assemblyName, - adapterConfig: JSON.parse(JSON.stringify(self.adapterConfig)), + adapterConfig: clone(self.adapterConfig), rendererType: rendererType.name, - regions: JSON.parse(JSON.stringify(view.displayedRegions)), + regions: clone(view.displayedRegions), blockDefinitions: self.blockDefinitions, sessionId: getRpcSessionId(self), timeout: 1000000, @@ -68,5 +69,10 @@ export async function renderReactionEffect( signal, }) - return { html, data, renderingComponent: rendererType.ReactComponent } + return { + html, + data, + reactElement: data.reactElement, + renderingComponent: rendererType.ReactComponent, + } } diff --git a/plugins/circular-view/src/CircularView/components/CircularView.tsx b/plugins/circular-view/src/CircularView/components/CircularView.tsx index 002b56ad69..1038beb058 100644 --- a/plugins/circular-view/src/CircularView/components/CircularView.tsx +++ b/plugins/circular-view/src/CircularView/components/CircularView.tsx @@ -1,24 +1,14 @@ import React from 'react' import { observer } from 'mobx-react' -import { ResizeHandle, ErrorMessage } from '@jbrowse/core/ui' +import { ResizeHandle } from '@jbrowse/core/ui' import { assembleLocString } from '@jbrowse/core/util' -import { CircularViewModel } from '../models/CircularView' -import { IconButton } from '@mui/material' import { makeStyles } from 'tss-react/mui' -import { grey } from '@mui/material/colors' - -// icons -import ZoomOutIcon from '@mui/icons-material/ZoomOut' -import ZoomInIcon from '@mui/icons-material/ZoomIn' -import RotateLeftIcon from '@mui/icons-material/RotateLeft' -import RotateRightIcon from '@mui/icons-material/RotateRight' -import LockOpenIcon from '@mui/icons-material/LockOpen' -import LockIcon from '@mui/icons-material/Lock' -import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons' // locals import Ruler from './Ruler' +import Controls from './Controls' import ImportForm from './ImportForm' +import { CircularViewModel } from '../models/CircularView' const dragHandleHeight = 3 @@ -38,24 +28,6 @@ const useStyles = makeStyles()(theme => ({ boxSizing: 'content-box', display: 'block', }, - iconButton: { - padding: '4px', - margin: '0 2px 0 2px', - }, - controls: { - overflow: 'hidden', - whiteSpace: 'nowrap', - position: 'absolute', - background: grey[200], - boxSizing: 'border-box', - borderRight: '1px solid #a2a2a2', - borderBottom: '1px solid #a2a2a2', - left: 0, - top: 0, - }, - importFormContainer: { - marginBottom: theme.spacing(4), - }, })) const Slices = observer(({ model }: { model: CircularViewModel }) => { @@ -85,165 +57,84 @@ const Slices = observer(({ model }: { model: CircularViewModel }) => { ) }) -const Controls = observer( - ({ - model, - showingFigure, - }: { - model: CircularViewModel - showingFigure: boolean - }) => { - const { classes } = useStyles() - return ( -
    - - - - - - - - - - - - - - - - - - {model.lockedFitToWindow ? : } - - - {model.hideTrackSelectorButton ? null : ( - - - - )} -
    - ) - }, -) - const CircularView = observer(({ model }: { model: CircularViewModel }) => { - const { classes } = useStyles() const initialized = !!model.displayedRegions.length && !!model.figureWidth && - !!model.figureHeight + !!model.figureHeight && + model.initialized const showImportForm = !initialized && !model.disableImportForm const showFigure = initialized && !showImportForm return ( -
    - {model.error ? ( - - ) : ( - <> - {showImportForm ? : null} - <> - {!showFigure ? null : ( -
    -
    `${x}px`) - .join(' '), - }} - > - - - - - -
    -
    - )} - - {model.hideVerticalResizeHandle ? null : ( - - )} - - + <> + {showImportForm || model.error ? ( + + ) : showFigure ? ( + + ) : null} + + ) +}) + +const CircularViewLoaded = observer(function ({ + model, +}: { + model: CircularViewModel +}) { + const { + width, + height, + id, + offsetRadians, + centerXY, + figureWidth, + figureHeight, + hideVerticalResizeHandle, + } = model + const { classes } = useStyles() + return ( +
    +
    +
    `${x}px`).join(' '), + }} + > + + + + + +
    +
    + + {hideVerticalResizeHandle ? null : ( + )}
    ) diff --git a/plugins/circular-view/src/CircularView/components/Controls.tsx b/plugins/circular-view/src/CircularView/components/Controls.tsx new file mode 100644 index 0000000000..5b0942a771 --- /dev/null +++ b/plugins/circular-view/src/CircularView/components/Controls.tsx @@ -0,0 +1,106 @@ +import React from 'react' +import { observer } from 'mobx-react' +import { IconButton } from '@mui/material' +import { makeStyles } from 'tss-react/mui' +import { grey } from '@mui/material/colors' + +// icons +import ZoomOutIcon from '@mui/icons-material/ZoomOut' +import ZoomInIcon from '@mui/icons-material/ZoomIn' +import RotateLeftIcon from '@mui/icons-material/RotateLeft' +import RotateRightIcon from '@mui/icons-material/RotateRight' +import LockOpenIcon from '@mui/icons-material/LockOpen' +import LockIcon from '@mui/icons-material/Lock' +import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons' + +// locals +import { CircularViewModel } from '../models/CircularView' + +const useStyles = makeStyles()({ + iconButton: { + padding: '4px', + margin: '0 2px 0 2px', + }, + controls: { + overflow: 'hidden', + whiteSpace: 'nowrap', + position: 'absolute', + background: grey[200], + boxSizing: 'border-box', + borderRight: '1px solid #a2a2a2', + borderBottom: '1px solid #a2a2a2', + left: 0, + top: 0, + }, +}) + +const Controls = observer(function ({ model }: { model: CircularViewModel }) { + const { classes } = useStyles() + return ( +
    + + + + + + + + + + + + + + + + + + {model.lockedFitToWindow ? : } + + + {model.hideTrackSelectorButton ? null : ( + + + + )} +
    + ) +}) +export default Controls diff --git a/plugins/circular-view/src/CircularView/components/ImportForm.tsx b/plugins/circular-view/src/CircularView/components/ImportForm.tsx index a439aff0f1..6cf2343be0 100644 --- a/plugins/circular-view/src/CircularView/components/ImportForm.tsx +++ b/plugins/circular-view/src/CircularView/components/ImportForm.tsx @@ -7,7 +7,7 @@ import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui' const useStyles = makeStyles()(theme => ({ importFormContainer: { - marginBottom: theme.spacing(4), + padding: theme.spacing(6), }, })) @@ -15,10 +15,9 @@ const useStyles = makeStyles()(theme => ({ const ImportForm = observer(({ model }: { model: any }) => { const { classes } = useStyles() const session = getSession(model) - const { error: modelError } = model + const { error } = model const { assemblyNames, assemblyManager } = session const [selectedAsm, setSelectedAsm] = useState(assemblyNames[0]) - const [error, setError] = useState(modelError) const assembly = assemblyManager.get(selectedAsm) const assemblyError = assemblyNames.length ? assembly?.error @@ -39,7 +38,7 @@ const ImportForm = observer(({ model }: { model: any }) => { { - setError(undefined) + model.setError(undefined) setSelectedAsm(val) }} session={session} @@ -50,11 +49,15 @@ const ImportForm = observer(({ model }: { model: any }) => { diff --git a/plugins/circular-view/src/CircularView/index.ts b/plugins/circular-view/src/CircularView/index.ts new file mode 100644 index 0000000000..538c6102f0 --- /dev/null +++ b/plugins/circular-view/src/CircularView/index.ts @@ -0,0 +1,16 @@ +import { lazy } from 'react' +import PluginManager from '@jbrowse/core/PluginManager' +import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType' +import stateModelFactory from './models/CircularView' + +export default (pluginManager: PluginManager) => { + pluginManager.addViewType( + () => + new ViewType({ + ReactComponent: lazy(() => import('./components/CircularView')), + stateModel: stateModelFactory(pluginManager), + name: 'CircularView', + displayName: 'Circular view', + }), + ) +} diff --git a/plugins/circular-view/src/CircularView/models/CircularView.ts b/plugins/circular-view/src/CircularView/models/CircularView.ts index 70ad69d6bb..5b34e07c30 100644 --- a/plugins/circular-view/src/CircularView/models/CircularView.ts +++ b/plugins/circular-view/src/CircularView/models/CircularView.ts @@ -19,6 +19,7 @@ import { getSession, clamp, isSessionModelWithWidgets, + Region as IRegion, } from '@jbrowse/core/util' import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models' import { calculateStaticSlices, sliceIsVisible } from './slices' @@ -33,10 +34,10 @@ function stateModelFactory(pluginManager: PluginManager) { const minHeight = 40 const minWidth = 100 const defaultHeight = 400 - return types.compose( - BaseViewModel, - types - .model('CircularView', { + return types + .compose( + BaseViewModel, + types.model('CircularView', { /** * #property */ @@ -49,7 +50,7 @@ function stateModelFactory(pluginManager: PluginManager) { /** * #property */ - bpPerPx: 2000000, + bpPerPx: 200, /** * #property */ @@ -102,449 +103,464 @@ function stateModelFactory(pluginManager: PluginManager) { minimumBlockWidth: 20, trackSelectorType: 'hierarchical', - }) - .volatile(() => ({ - width: 0, - })) - .views(self => ({ - /** - * #getter - */ - get staticSlices() { - return calculateStaticSlices(self) - }, - - /** - * #getter - */ - get visibleSection() { - return viewportVisibleSection( - [ - self.scrollX, - self.scrollX + self.width, - self.scrollY, - self.scrollY + self.height, - ], - this.centerXY, - this.radiusPx, - ) - }, - /** - * #getter - */ - get circumferencePx() { - let elidedBp = 0 - for (const r of this.elidedRegions) { - elidedBp += r.widthBp - } - return ( - elidedBp / self.bpPerPx + self.spacingPx * this.elidedRegions.length - ) - }, - /** - * #getter - */ - get radiusPx() { - return this.circumferencePx / (2 * Math.PI) - }, - /** - * #getter - */ - get bpPerRadian() { - return self.bpPerPx * this.radiusPx - }, - /** - * #getter - */ - get pxPerRadian() { - return this.radiusPx - }, - /** - * #getter - */ - get centerXY(): [number, number] { - return [ - this.radiusPx + self.paddingPx, - this.radiusPx + self.paddingPx, - ] - }, - /** - * #getter - */ - get totalBp() { - let total = 0 - for (const region of self.displayedRegions) { - total += region.end - region.start - } - return total - }, - /** - * #getter - */ - get maximumRadiusPx() { - return self.lockedFitToWindow - ? Math.min(self.width, self.height) / 2 - self.lockedPaddingPx - : 1000000 - }, - /** - * #getter - */ - get maxBpPerPx() { - const minCircumferencePx = 2 * Math.PI * self.minimumRadiusPx - return this.totalBp / minCircumferencePx - }, - /** - * #getter - */ - get minBpPerPx() { - // min depends on window dimensions, clamp between old min(0.01) and max - const maxCircumferencePx = 2 * Math.PI * this.maximumRadiusPx - return clamp( - this.totalBp / maxCircumferencePx, - 0.0000000001, - this.maxBpPerPx, + }), + ) + .volatile(() => ({ + volatileWidth: undefined as number | undefined, + error: undefined as unknown, + })) + .views(self => ({ + /** + * #getter + */ + get width() { + if (self.volatileWidth === undefined) { + throw new Error( + 'wait for view to be initialized first before accessing width', ) - }, - /** - * #getter - */ - get atMaxBpPerPx() { - return self.bpPerPx >= this.maxBpPerPx - }, - /** - * #getter - */ - get atMinBpPerPx() { - return self.bpPerPx <= this.minBpPerPx - }, - /** - * #getter - */ - get tooSmallToLock() { - return this.minBpPerPx <= 0.0000000001 - }, - /** - * #getter - */ - get figureDimensions(): [number, number] { - return [ - this.radiusPx * 2 + 2 * self.paddingPx, - this.radiusPx * 2 + 2 * self.paddingPx, - ] - }, - /** - * #getter - */ - get figureWidth() { - return this.figureDimensions[0] - }, - /** - * #getter - */ - get figureHeight() { - return this.figureDimensions[1] - }, - /** - * #getter - * this is displayedRegions, post-processed to - * elide regions that are too small to see reasonably - */ - get elidedRegions() { - // eslint-disable-next-line @typescript-eslint/no-explicit-any - const visible: any[] = [] - self.displayedRegions.forEach(region => { - const widthBp = region.end - region.start - const widthPx = widthBp / self.bpPerPx - if (widthPx < self.minVisibleWidth) { - // too small to see, collapse into a single elision region - const lastVisible = visible[visible.length - 1] - if (lastVisible && lastVisible.elided) { - lastVisible.regions.push({ ...region }) - lastVisible.widthBp += widthBp - } else { - visible.push({ - elided: true, - widthBp, - regions: [{ ...region }], - }) - } - } else { - // big enough to see, display it - visible.push({ ...region, widthBp }) + } + return self.volatileWidth + }, + /** + * #getter + */ + get staticSlices() { + return calculateStaticSlices(self) + }, + + /** + * #getter + */ + get visibleSection() { + return viewportVisibleSection( + [ + self.scrollX, + self.scrollX + self.width, + self.scrollY, + self.scrollY + self.height, + ], + this.centerXY, + this.radiusPx, + ) + }, + /** + * #getter + */ + get circumferencePx() { + let elidedBp = 0 + + for (const r of this.elidedRegions) { + elidedBp += r.widthBp + } + return ( + elidedBp / self.bpPerPx + self.spacingPx * this.elidedRegions.length + ) + }, + /** + * #getter + */ + get radiusPx() { + return this.circumferencePx / (2 * Math.PI) + }, + /** + * #getter + */ + get bpPerRadian() { + return self.bpPerPx * this.radiusPx + }, + /** + * #getter + */ + get pxPerRadian() { + return this.radiusPx + }, + /** + * #getter + */ + get centerXY(): [number, number] { + return [this.radiusPx + self.paddingPx, this.radiusPx + self.paddingPx] + }, + /** + * #getter + */ + get totalBp() { + let total = 0 + for (const region of self.displayedRegions) { + total += region.end - region.start + } + return total + }, + /** + * #getter + */ + get maximumRadiusPx() { + return self.lockedFitToWindow + ? Math.min(self.width, self.height) / 2 - self.lockedPaddingPx + : 1000000 + }, + /** + * #getter + */ + get maxBpPerPx() { + const minCircumferencePx = 2 * Math.PI * self.minimumRadiusPx + return this.totalBp / minCircumferencePx + }, + /** + * #getter + */ + get minBpPerPx() { + // min depends on window dimensions, clamp between old min(0.01) and max + const maxCircumferencePx = 2 * Math.PI * this.maximumRadiusPx + return clamp( + this.totalBp / maxCircumferencePx, + 0.0000000001, + this.maxBpPerPx, + ) + }, + /** + * #getter + */ + get atMaxBpPerPx() { + return self.bpPerPx >= this.maxBpPerPx + }, + /** + * #getter + */ + get atMinBpPerPx() { + return self.bpPerPx <= this.minBpPerPx + }, + /** + * #getter + */ + get tooSmallToLock() { + return this.minBpPerPx <= 0.0000000001 + }, + /** + * #getter + */ + get figureDimensions(): [number, number] { + return [ + this.radiusPx * 2 + 2 * self.paddingPx, + this.radiusPx * 2 + 2 * self.paddingPx, + ] + }, + /** + * #getter + */ + get figureWidth() { + return this.figureDimensions[0] + }, + /** + * #getter + */ + get figureHeight() { + return this.figureDimensions[1] + }, + /** + * #getter + * this is displayedRegions, post-processed to + * elide regions that are too small to see reasonably + */ + get elidedRegions() { + const visible: ( + | { + elided: true + widthBp: number + regions: IRegion[] } - }) - - // remove any single-region elisions - for (let i = 0; i < visible.length; i += 1) { - const v = visible[i] - if (v.elided && v.regions.length === 1) { - delete v.elided - visible[i] = { ...v, ...v.regions[0] } + | { + elided: false + widthBp: number + start: number + end: number + refName: string } - } - return visible - }, - /** - * #getter - */ - get assemblyNames() { - const assemblyNames: string[] = [] - self.displayedRegions.forEach(displayedRegion => { - if (!assemblyNames.includes(displayedRegion.assemblyName)) { - assemblyNames.push(displayedRegion.assemblyName) + )[] = [] + self.displayedRegions.forEach(region => { + const widthBp = region.end - region.start + const widthPx = widthBp / self.bpPerPx + if (widthPx < self.minVisibleWidth) { + // too small to see, collapse into a single elision region + const lastVisible = visible[visible.length - 1] + if (lastVisible?.elided) { + lastVisible.regions.push({ ...region }) + lastVisible.widthBp += widthBp + } else { + visible.push({ + elided: true, + widthBp, + regions: [{ ...region }], + }) } - }) - return assemblyNames - }, - /** - * #getter - */ - get initialized() { - const { assemblyManager } = getSession(self) - return this.assemblyNames.every( - a => assemblyManager.get(a)?.initialized, - ) - }, - })) - .views(self => ({ - /** - * #getter - */ - get visibleStaticSlices() { - return self.staticSlices.filter(s => sliceIsVisible(self, s)) - }, - })) - .volatile(() => ({ - error: undefined as unknown, - })) - .actions(self => ({ - /** - * #action - */ - setWidth(newWidth: number) { - self.width = Math.max(newWidth, minWidth) - return self.width - }, - /** - * #action - */ - setHeight(newHeight: number) { - self.height = Math.max(newHeight, minHeight) - return self.height - }, - /** - * #action - */ - resizeHeight(distance: number) { - const oldHeight = self.height - const newHeight = this.setHeight(self.height + distance) - this.setModelViewWhenAdjust(!self.tooSmallToLock) - return newHeight - oldHeight - }, - /** - * #action - */ - resizeWidth(distance: number) { - const oldWidth = self.width - const newWidth = this.setWidth(self.width + distance) - this.setModelViewWhenAdjust(!self.tooSmallToLock) - return newWidth - oldWidth - }, - /** - * #action - */ - rotateClockwiseButton() { - this.rotateClockwise(Math.PI / 6) - }, + } else { + // big enough to see, display it + visible.push({ ...region, widthBp, elided: false }) + } + }) - /** - * #action - */ - rotateCounterClockwiseButton() { - this.rotateCounterClockwise(Math.PI / 6) - }, + // remove any single-region elisions + for (let i = 0; i < visible.length; i += 1) { + const v = visible[i] + if (v.elided && v.regions.length === 1) { + visible[i] = { ...v, ...v.regions[0], elided: false } + } + } + return visible + }, + /** + * #getter + */ + get assemblyNames() { + const assemblyNames: string[] = [] + self.displayedRegions.forEach(displayedRegion => { + if (!assemblyNames.includes(displayedRegion.assemblyName)) { + assemblyNames.push(displayedRegion.assemblyName) + } + }) + return assemblyNames + }, + /** + * #getter + */ + get initialized() { + const { assemblyManager } = getSession(self) + return ( + self.volatileWidth !== undefined && + this.assemblyNames.every(a => assemblyManager.get(a)?.initialized) + ) + }, + })) + .views(self => ({ + /** + * #getter + */ + get visibleStaticSlices() { + return self.staticSlices.filter(s => sliceIsVisible(self, s)) + }, + })) - /** - * #action - */ - rotateClockwise(distance = 0.17) { - self.offsetRadians += distance - }, + .actions(self => ({ + /** + * #action + */ + setWidth(newWidth: number) { + self.volatileWidth = Math.max(newWidth, minWidth) + return self.volatileWidth + }, + /** + * #action + */ + setHeight(newHeight: number) { + self.height = Math.max(newHeight, minHeight) + return self.height + }, + /** + * #action + */ + resizeHeight(distance: number) { + const oldHeight = self.height + const newHeight = this.setHeight(self.height + distance) + this.setModelViewWhenAdjust(!self.tooSmallToLock) + return newHeight - oldHeight + }, + /** + * #action + */ + resizeWidth(distance: number) { + const oldWidth = self.width + const newWidth = this.setWidth(self.width + distance) + this.setModelViewWhenAdjust(!self.tooSmallToLock) + return newWidth - oldWidth + }, + /** + * #action + */ + rotateClockwiseButton() { + this.rotateClockwise(Math.PI / 6) + }, - /** - * #action - */ - rotateCounterClockwise(distance = 0.17) { - self.offsetRadians -= distance - }, + /** + * #action + */ + rotateCounterClockwiseButton() { + this.rotateCounterClockwise(Math.PI / 6) + }, - /** - * #action - */ - zoomInButton() { - this.setBpPerPx(self.bpPerPx / 1.4) - }, + /** + * #action + */ + rotateClockwise(distance = 0.17) { + self.offsetRadians += distance + }, - /** - * #action - */ - zoomOutButton() { - this.setBpPerPx(self.bpPerPx * 1.4) - }, + /** + * #action + */ + rotateCounterClockwise(distance = 0.17) { + self.offsetRadians -= distance + }, - /** - * #action - */ - setBpPerPx(newVal: number) { - self.bpPerPx = clamp(newVal, self.minBpPerPx, self.maxBpPerPx) - }, + /** + * #action + */ + zoomInButton() { + this.setBpPerPx(self.bpPerPx / 1.4) + }, - /** - * #action - */ - setModelViewWhenAdjust(secondCondition: boolean) { - if (self.lockedFitToWindow && secondCondition) { - this.setBpPerPx(self.minBpPerPx) - } - }, + /** + * #action + */ + zoomOutButton() { + this.setBpPerPx(self.bpPerPx * 1.4) + }, - /** - * #action - */ - closeView() { - // eslint-disable-next-line @typescript-eslint/no-explicit-any - getParent(self, 2).removeView(self) - }, + /** + * #action + */ + setBpPerPx(newVal: number) { + self.bpPerPx = clamp(newVal, self.minBpPerPx, self.maxBpPerPx) + }, - /** - * #action - */ - setDisplayedRegions(regions: SnapshotOrInstance[]) { - const previouslyEmpty = self.displayedRegions.length === 0 - self.displayedRegions = cast(regions) + /** + * #action + */ + setModelViewWhenAdjust(secondCondition: boolean) { + if (self.lockedFitToWindow && secondCondition) { + this.setBpPerPx(self.minBpPerPx) + } + }, - if (previouslyEmpty) { - this.setBpPerPx(self.minBpPerPx) - } else { - this.setBpPerPx(self.bpPerPx) - } - }, + /** + * #action + */ + closeView() { + // eslint-disable-next-line @typescript-eslint/no-explicit-any + getParent(self, 2).removeView(self) + }, - /** - * #action - */ - activateTrackSelector() { - if (self.trackSelectorType === 'hierarchical') { - const session = getSession(self) - if (isSessionModelWithWidgets(session)) { - const selector = session.addWidget( - 'HierarchicalTrackSelectorWidget', - 'hierarchicalTrackSelector', - { view: self }, - ) - session.showWidget(selector) - return selector - } - } - throw new Error( - `invalid track selector type ${self.trackSelectorType}`, - ) - }, + /** + * #action + */ + setDisplayedRegions(regions: SnapshotOrInstance[]) { + const previouslyEmpty = self.displayedRegions.length === 0 + self.displayedRegions = cast(regions) - /** - * #action - */ - toggleTrack(trackId: string) { - // if we have any tracks with that configuration, turn them off - const hiddenCount = this.hideTrack(trackId) - // if none had that configuration, turn one on - if (!hiddenCount) { - this.showTrack(trackId) + if (previouslyEmpty) { + this.setBpPerPx(self.minBpPerPx) + } else { + this.setBpPerPx(self.bpPerPx) + } + }, + + /** + * #action + */ + activateTrackSelector() { + if (self.trackSelectorType === 'hierarchical') { + const session = getSession(self) + if (isSessionModelWithWidgets(session)) { + const selector = session.addWidget( + 'HierarchicalTrackSelectorWidget', + 'hierarchicalTrackSelector', + { view: self }, + ) + session.showWidget(selector) + return selector } - }, + } + throw new Error(`invalid track selector type ${self.trackSelectorType}`) + }, - /** - * #action - */ - setError(error: unknown) { - console.error(error) - self.error = error - }, + /** + * #action + */ + toggleTrack(trackId: string) { + // if we have any tracks with that configuration, turn them off + const hiddenCount = this.hideTrack(trackId) + // if none had that configuration, turn one on + if (!hiddenCount) { + this.showTrack(trackId) + } + }, - /** - * #action - */ - showTrack(trackId: string, initialSnapshot = {}) { - const schema = pluginManager.pluggableConfigSchemaType('track') - const conf = resolveIdentifier(schema, getRoot(self), trackId) - const trackType = pluginManager.getTrackType(conf.type) - if (!trackType) { - throw new Error(`unknown track type ${conf.type}`) - } - const viewType = pluginManager.getViewType(self.type) - const supportedDisplays = viewType.displayTypes.map(d => d.name) - const displayConf = conf.displays.find((d: AnyConfigurationModel) => - supportedDisplays.includes(d.type), - ) - const track = trackType.stateModel.create({ - ...initialSnapshot, - type: conf.type, - configuration: conf, - displays: [{ type: displayConf.type, configuration: displayConf }], - }) - self.tracks.push(track) - }, + /** + * #action + */ + setError(error: unknown) { + self.error = error + }, - /** - * #action - */ - addTrackConf( - configuration: AnyConfigurationModel, - initialSnapshot = {}, - ) { - const { type } = configuration - const name = readConfObject(configuration, 'name') - const trackType = pluginManager.getTrackType(type) - if (!trackType) { - throw new Error(`unknown track type ${configuration.type}`) - } - const viewType = pluginManager.getViewType(self.type) - const supportedDisplays = viewType.displayTypes.map(d => d.name) - const displayConf = configuration.displays.find( - (d: AnyConfigurationModel) => supportedDisplays.includes(d.type), - ) - const track = trackType.stateModel.create({ - ...initialSnapshot, - name, - type, - configuration, - displays: [{ type: displayConf.type, configuration: displayConf }], - }) - self.tracks.push(track) - }, + /** + * #action + */ + showTrack(trackId: string, initialSnapshot = {}) { + const schema = pluginManager.pluggableConfigSchemaType('track') + const conf = resolveIdentifier(schema, getRoot(self), trackId) + const trackType = pluginManager.getTrackType(conf.type) + if (!trackType) { + throw new Error(`unknown track type ${conf.type}`) + } + const viewType = pluginManager.getViewType(self.type) + const supportedDisplays = viewType.displayTypes.map(d => d.name) + const displayConf = conf.displays.find((d: AnyConfigurationModel) => + supportedDisplays.includes(d.type), + ) + const track = trackType.stateModel.create({ + ...initialSnapshot, + type: conf.type, + configuration: conf, + displays: [{ type: displayConf.type, configuration: displayConf }], + }) + self.tracks.push(track) + }, - /** - * #action - */ - hideTrack(trackId: string) { - const schema = pluginManager.pluggableConfigSchemaType('track') - const conf = resolveIdentifier(schema, getRoot(self), trackId) - const t = self.tracks.filter(t => t.configuration === conf) - transaction(() => t.forEach(t => self.tracks.remove(t))) - return t.length - }, + /** + * #action + */ + addTrackConf(configuration: AnyConfigurationModel, initialSnapshot = {}) { + const { type } = configuration + const name = readConfObject(configuration, 'name') + const trackType = pluginManager.getTrackType(type) + if (!trackType) { + throw new Error(`unknown track type ${configuration.type}`) + } + const viewType = pluginManager.getViewType(self.type) + const supportedDisplays = viewType.displayTypes.map(d => d.name) + const displayConf = configuration.displays.find( + (d: AnyConfigurationModel) => supportedDisplays.includes(d.type), + ) + const track = trackType.stateModel.create({ + ...initialSnapshot, + name, + type, + configuration, + displays: [{ type: displayConf.type, configuration: displayConf }], + }) + self.tracks.push(track) + }, - /** - * #action - */ - toggleFitToWindowLock() { - // when going unlocked -> locked and circle is cut off, set to the locked minBpPerPx - self.lockedFitToWindow = !self.lockedFitToWindow - this.setModelViewWhenAdjust(self.atMinBpPerPx) - return self.lockedFitToWindow - }, - })), - ) + /** + * #action + */ + hideTrack(trackId: string) { + const schema = pluginManager.pluggableConfigSchemaType('track') + const conf = resolveIdentifier(schema, getRoot(self), trackId) + const t = self.tracks.filter(t => t.configuration === conf) + transaction(() => t.forEach(t => self.tracks.remove(t))) + return t.length + }, + + /** + * #action + */ + toggleFitToWindowLock() { + // when going unlocked -> locked and circle is cut off, set to the + // locked minBpPerPx + self.lockedFitToWindow = !self.lockedFitToWindow + this.setModelViewWhenAdjust(self.atMinBpPerPx) + return self.lockedFitToWindow + }, + })) } export type CircularViewStateModel = ReturnType diff --git a/plugins/circular-view/src/CircularView/models/__snapshots__/slices.test.js.snap b/plugins/circular-view/src/CircularView/models/__snapshots__/slices.test.js.snap index 69e684dec2..10cc11a1a4 100644 --- a/plugins/circular-view/src/CircularView/models/__snapshots__/slices.test.js.snap +++ b/plugins/circular-view/src/CircularView/models/__snapshots__/slices.test.js.snap @@ -1,14 +1,14 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`one slice 1`] = ` -Object { +{ "bpPerRadian": 1591.5494309189535, "endRadians": 6.283185307179586, "flipped": false, "key": "toast:1..10,000", "offsetRadians": 0, "radianWidth": 6.288185307179586, - "region": Object { + "region": { "end": 10000, "refName": "toast", "start": 0, @@ -19,15 +19,15 @@ Object { `; exports[`two slices 1`] = ` -Array [ - Object { +[ + { "bpPerRadian": 3183.098861837907, "endRadians": 3.141592653589793, "flipped": false, "key": "toast:1..10,000", "offsetRadians": 0, "radianWidth": 3.146592653589793, - "region": Object { + "region": { "end": 10000, "refName": "toast", "start": 0, @@ -35,14 +35,14 @@ Array [ }, "startRadians": 0, }, - Object { + { "bpPerRadian": 3183.098861837907, "endRadians": 6.288185307179586, "flipped": false, "key": "teest:1..10,000", "offsetRadians": 3.146592653589793, "radianWidth": 3.146592653589793, - "region": Object { + "region": { "end": 10000, "refName": "teest", "start": 0, @@ -54,15 +54,15 @@ Array [ `; exports[`volvox 1`] = ` -Array [ - Object { +[ + { "bpPerRadian": 8925.40920859349, "endRadians": 5.602096086738348, "flipped": false, "key": "{volvox}ctgA:1..50,001", "offsetRadians": 0, "radianWidth": 5.6070960867383475, - "region": Object { + "region": { "assemblyName": "volvox", "end": 50001, "refName": "ctgA", @@ -71,14 +71,14 @@ Array [ }, "startRadians": 0, }, - Object { + { "bpPerRadian": 8925.40920859349, "endRadians": 6.288185307179587, "flipped": false, "key": "{volvox}ctgB:1..6,079", "offsetRadians": 5.6070960867383475, "radianWidth": 0.6860892204412394, - "region": Object { + "region": { "assemblyName": "volvox", "end": 6079, "refName": "ctgB", diff --git a/plugins/circular-view/src/LaunchCircularView/index.ts b/plugins/circular-view/src/LaunchCircularView/index.ts new file mode 100644 index 0000000000..c1f223acc9 --- /dev/null +++ b/plugins/circular-view/src/LaunchCircularView/index.ts @@ -0,0 +1,48 @@ +import { when } from 'mobx' +import { AbstractSessionModel } from '@jbrowse/core/util' +import PluginManager from '@jbrowse/core/PluginManager' + +// locals +import { CircularViewModel } from '../CircularView/models/CircularView' + +type CGV = CircularViewModel + +export default (pluginManager: PluginManager) => { + pluginManager.addToExtensionPoint( + 'LaunchView-CircularView', + // @ts-ignore + async ({ + session, + assembly, + loc, + tracks = [], + }: { + session: AbstractSessionModel + assembly?: string + loc: string + tracks?: string[] + }) => { + const { assemblyManager } = session + const view = session.addView('CircularView', {}) as CGV + + await when(() => view.initialized) + + if (!assembly) { + throw new Error( + 'No assembly provided when launching circular genome view', + ) + } + + const asm = await assemblyManager.waitForAssembly(assembly) + if (!asm) { + throw new Error( + `Assembly "${assembly}" not found when launching circular genome view`, + ) + } + + view.setDisplayedRegions(asm.regions || []) + + tracks.forEach(track => view.showTrack(track)) + }, + ) +} diff --git a/plugins/circular-view/src/index.ts b/plugins/circular-view/src/index.ts index 04b7f54e71..64dcf8a3e1 100644 --- a/plugins/circular-view/src/index.ts +++ b/plugins/circular-view/src/index.ts @@ -1,69 +1,24 @@ -import { lazy } from 'react' -import { when } from 'mobx' import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util' import PluginManager from '@jbrowse/core/PluginManager' import Plugin from '@jbrowse/core/Plugin' -import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType' -import DataUsageIcon from '@mui/icons-material/DataUsage' -import stateModelFactory, { + +// locals +import { CircularViewModel, CircularViewStateModel, } from './CircularView/models/CircularView' +import CircularViewF from './CircularView' +import LaunchCircularViewF from './LaunchCircularView' -type CGV = CircularViewModel +// icons +import DataUsageIcon from '@mui/icons-material/DataUsage' export default class CircularViewPlugin extends Plugin { name = 'CircularViewPlugin' install(pluginManager: PluginManager) { - pluginManager.addViewType( - () => - new ViewType({ - ReactComponent: lazy( - () => import('./CircularView/components/CircularView'), - ), - stateModel: stateModelFactory(pluginManager), - name: 'CircularView', - }), - ) - - pluginManager.addToExtensionPoint( - 'LaunchView-CircularView', - // @ts-ignore - async ({ - session, - assembly, - loc, - tracks = [], - }: { - session: AbstractSessionModel - assembly?: string - loc: string - tracks?: string[] - }) => { - const { assemblyManager } = session - const view = session.addView('CircularView', {}) as CGV - - await when(() => view.initialized) - - if (!assembly) { - throw new Error( - 'No assembly provided when launching circular genome view', - ) - } - - const asm = await assemblyManager.waitForAssembly(assembly) - if (!asm) { - throw new Error( - `Assembly "${assembly}" not found when launching circular genome view`, - ) - } - - view.setDisplayedRegions(asm.regions || []) - - tracks.forEach(track => view.showTrack(track)) - }, - ) + CircularViewF(pluginManager) + LaunchCircularViewF(pluginManager) } configure(pluginManager: PluginManager) { @@ -80,8 +35,8 @@ export default class CircularViewPlugin extends Plugin { } export { - BaseChordDisplayModel, baseChordDisplayConfig, + BaseChordDisplayModel, BaseChordDisplayComponent, } from './BaseChordDisplay' diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 8187cc048d..e62eb68b44 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/comparative-adapters", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", diff --git a/plugins/comparative-adapters/src/ChainAdapter/index.ts b/plugins/comparative-adapters/src/ChainAdapter/index.ts index 57e9b9d513..eb3b5801b5 100644 --- a/plugins/comparative-adapters/src/ChainAdapter/index.ts +++ b/plugins/comparative-adapters/src/ChainAdapter/index.ts @@ -7,12 +7,10 @@ export default (pluginManager: PluginManager) => { () => new AdapterType({ name: 'ChainAdapter', + displayName: 'Liftover chain adapter', configSchema, adapterMetadata: { - category: null, hiddenFromGUI: true, - displayName: null, - description: null, }, getAdapterClass: () => import('./ChainAdapter').then(r => r.default), }), diff --git a/plugins/comparative-adapters/src/DeltaAdapter/index.ts b/plugins/comparative-adapters/src/DeltaAdapter/index.ts index 28fc87913c..68d3e51fd3 100644 --- a/plugins/comparative-adapters/src/DeltaAdapter/index.ts +++ b/plugins/comparative-adapters/src/DeltaAdapter/index.ts @@ -7,14 +7,11 @@ export default (pluginManager: PluginManager) => { () => new AdapterType({ name: 'DeltaAdapter', + displayName: 'MUMmer delta adapter', configSchema, adapterMetadata: { - category: null, hiddenFromGUI: true, - displayName: null, - description: null, }, - getAdapterClass: () => import('./DeltaAdapter').then(r => r.default), }), ) diff --git a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.test.ts b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.test.ts index 2637eef08a..cb1325ec8f 100644 --- a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.test.ts +++ b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.test.ts @@ -1,14 +1,7 @@ import { toArray } from 'rxjs/operators' import Adapter from './MCScanAnchorsAdapter' -import { TextEncoder, TextDecoder } from 'web-encoding' -import configSchema from './configSchema' -if (!window.TextEncoder) { - window.TextEncoder = TextEncoder -} -if (!window.TextDecoder) { - window.TextDecoder = TextDecoder -} +import configSchema from './configSchema' test('adapter can fetch features from mcscan anchors file', async () => { const adapter = new Adapter( diff --git a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts index 6ed01c5b39..ebea237900 100644 --- a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts +++ b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.ts @@ -2,11 +2,14 @@ import { BaseFeatureDataAdapter, BaseOptions, } from '@jbrowse/core/data_adapters/BaseAdapter' -import { Region } from '@jbrowse/core/util/types' import { openLocation } from '@jbrowse/core/util/io' -import { doesIntersect2 } from '@jbrowse/core/util' +import { + doesIntersect2, + SimpleFeature, + Feature, + Region, +} from '@jbrowse/core/util' import { ObservableCreate } from '@jbrowse/core/util/rxjs' -import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature' import { readFile, parseBed } from '../util' interface BareFeature { @@ -89,9 +92,10 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { // the adapter in the subadapters list const index = assemblyNames.indexOf(region.assemblyName) if (index !== -1) { + const flip = index === 0 feats.forEach(f => { const [r1, r2, score, rowNum] = f - const [f1, f2] = index === 1 ? [r2, r1] : [r1, r2] + const [f1, f2] = !flip ? [r2, r1] : [r1, r2] if ( f1.refName === region.refName && doesIntersect2(region.start, region.end, f1.start, f1.end) @@ -101,11 +105,16 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { ...f1, uniqueId: `${index}-${rowNum}`, syntenyId: rowNum, - // note: strand would be -1 if the two features are on opposite strands, - // indicating inverted alignment + + // note: strand would be -1 if the two features are on opposite + // strands, indicating inverted alignment strand: f1.strand * f2.strand, + assemblyName: assemblyNames[+!flip], score, - mate: f2 as BareFeature, + mate: { + ...f2, + assemblyName: assemblyNames[+flip], + }, }), ) } @@ -118,7 +127,7 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { /** * called to provide a hint that data tied to a certain region - * will not be needed for the forseeable future and can be purged + * will not be needed for the foreseeable future and can be purged * from caches, etc */ freeResources(/* { region } */): void {} diff --git a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/index.ts b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/index.ts index e5c8164a73..05fdd898e4 100644 --- a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/index.ts +++ b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/index.ts @@ -7,12 +7,10 @@ export default (pluginManager: PluginManager) => { () => new AdapterType({ name: 'MCScanAnchorsAdapter', + displayName: 'MCScan anchors adapter', configSchema, adapterMetadata: { - category: null, hiddenFromGUI: true, - displayName: null, - description: null, }, getAdapterClass: () => diff --git a/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts b/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts index d43a31f586..26e6ffdf93 100644 --- a/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts +++ b/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.ts @@ -106,6 +106,7 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { // the adapter in the subadapters list const index = assemblyNames.indexOf(region.assemblyName) if (index !== -1) { + const flip = index === 0 feats.forEach(f => { const [f11, f12, f21, f22, score, strand, rowNum] = f let r1 = { @@ -118,7 +119,7 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { start: Math.min(f21.start, f22.start), end: Math.max(f21.end, f22.end), } - if (index === 1) { + if (!flip) { ;[r2, r1] = [r1, r2] } if ( @@ -130,9 +131,13 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { ...r1, uniqueId: `${rowNum}`, syntenyId: rowNum, + assemblyName: assemblyNames[+!flip], score, strand, - mate: r2 as BareFeature, + mate: { + ...r2, + assemblyName: assemblyNames[+flip], + }, }), ) } @@ -145,7 +150,7 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter { /** * called to provide a hint that data tied to a certain region - * will not be needed for the forseeable future and can be purged + * will not be needed for the foreseeable future and can be purged * from caches, etc */ freeResources(/* { region } */): void {} diff --git a/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/index.ts b/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/index.ts index 0565c48f49..58df7ef8c5 100644 --- a/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/index.ts +++ b/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/index.ts @@ -7,12 +7,10 @@ export default (pluginManager: PluginManager) => { () => new AdapterType({ name: 'MCScanSimpleAnchorsAdapter', + displayName: 'MCScan anchors.simple adapter', configSchema, adapterMetadata: { - category: null, hiddenFromGUI: true, - displayName: null, - description: null, }, getAdapterClass: () => import('./MCScanSimpleAnchorsAdapter').then(r => r.default), diff --git a/plugins/comparative-adapters/src/MashMapAdapter/index.ts b/plugins/comparative-adapters/src/MashMapAdapter/index.ts index 309c47b28f..eacf8ea600 100644 --- a/plugins/comparative-adapters/src/MashMapAdapter/index.ts +++ b/plugins/comparative-adapters/src/MashMapAdapter/index.ts @@ -7,12 +7,10 @@ export default (pluginManager: PluginManager) => { () => new AdapterType({ name: 'MashMapAdapter', + displayName: 'MashMap adapter', configSchema, adapterMetadata: { - category: null, hiddenFromGUI: true, - displayName: null, - description: null, }, getAdapterClass: () => import('./MashMapAdapter').then(r => r.default), }), diff --git a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.test.ts b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.test.ts index ca7e9ba7bc..7c2b69daef 100644 --- a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.test.ts +++ b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.test.ts @@ -2,15 +2,6 @@ import { toArray } from 'rxjs/operators' import Adapter from './PAFAdapter' import MyConfigSchema from './configSchema' -import { TextEncoder, TextDecoder } from 'web-encoding' - -if (!window.TextEncoder) { - window.TextEncoder = TextEncoder -} -if (!window.TextDecoder) { - window.TextDecoder = TextDecoder -} - test('adapter can fetch features from peach_grape.paf', async () => { const adapter = new Adapter( MyConfigSchema.create({ diff --git a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts index 5478c4fe07..9a74c60c5e 100644 --- a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts +++ b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts @@ -6,131 +6,29 @@ import { Region } from '@jbrowse/core/util/types' import { doesIntersect2 } from '@jbrowse/core/util/range' import { openLocation } from '@jbrowse/core/util/io' import { ObservableCreate } from '@jbrowse/core/util/rxjs' -import { SimpleFeature, Feature } from '@jbrowse/core/util' +import { Feature } from '@jbrowse/core/util' import { AnyConfigurationModel, readConfObject, } from '@jbrowse/core/configuration' import { unzip } from '@gmod/bgzf-filehandle' +import { MismatchParser } from '@jbrowse/plugin-alignments' -export interface PAFRecord { - qname: string - qstart: number - qend: number - tname: string - tstart: number - tend: number - strand: number - extra: { - blockLen?: number - mappingQual: number - numMatches?: number - meanScore?: number - } -} - -function isGzip(buf: Buffer) { - return buf[0] === 31 && buf[1] === 139 && buf[2] === 8 -} - -function zip(a: number[], b: number[]) { - return a.map((e, i) => [e, b[i]] as [number, number]) -} - -// based on "weighted mean" method from dotPlotly -// https://github.com/tpoorten/dotPlotly -// License for dotPlotly reproduced here -// -// MIT License - -// Copyright (c) 2017 Tom Poorten - -// Permission is hereby granted, free of charge, to any person obtaining a copy -// of this software and associated documentation files (the "Software"), to deal -// in the Software without restriction, including without limitation the rights -// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -// copies of the Software, and to permit persons to whom the Software is -// furnished to do so, subject to the following conditions: - -// The above copyright notice and this permission notice shall be included in all -// copies or substantial portions of the Software. - -// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -// SOFTWARE. - -function getWeightedMeans(ret: PAFRecord[]) { - // in the weighted mean longer alignments factor in more - // heavily of all the fragments of a query vs the reference that it mapped - // to - // - // this uses a combined key query+'-'+ref to iteratively map all the - // alignments that match a particular ref from a particular query (so 1d - // array of what could be a 2d map) - // - // the result is a single number that says e.g. chr5 from human mapped to - // chr5 on mouse with 0.8 quality, and that0.8 is then attached to all the - // pieces of chr5 on human that mapped to chr5 on mouse. if chr5 on human - // also more weakly mapped to chr6 on mouse, then it would have another - // value e.g. 0.6. this can show strong and weak levels of synteny, - // especially in polyploidy situations - const scoreMap: { [key: string]: { quals: number[]; len: number[] } } = {} - for (let i = 0; i < ret.length; i++) { - const entry = ret[i] - const query = entry.qname - const target = entry.tname - const key = query + '-' + target - if (!scoreMap[key]) { - scoreMap[key] = { quals: [], len: [] } - } - scoreMap[key].quals.push(entry.extra.mappingQual) - scoreMap[key].len.push(entry.extra.blockLen || 1) - } - - const meanScoreMap = Object.fromEntries( - Object.entries(scoreMap).map(([key, val]) => { - const vals = zip(val.quals, val.len) - return [key, weightedMean(vals)] - }), - ) - for (let i = 0; i < ret.length; i++) { - const entry = ret[i] - const query = entry.qname - const target = entry.tname - const key = query + '-' + target - entry.extra.meanScore = meanScoreMap[key] - } - - let min = 10000 - let max = 0 - for (let i = 0; i < ret.length; i++) { - const entry = ret[i] - min = Math.min(entry.extra.meanScore || 0, min) - max = Math.max(entry.extra.meanScore || 0, max) - } - for (let i = 0; i < ret.length; i++) { - const entry = ret[i] - const b = entry.extra.meanScore || 0 - entry.extra.meanScore = (b - min) / (max - min) - } +// locals +import SyntenyFeature from './SyntenyFeature' +import { isGzip } from '../util' +import { + getWeightedMeans, + flipCigar, + parsePAF, + swapIndelCigar, + PAFRecord, +} from './util' - return ret -} +const { parseCigar } = MismatchParser -// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a -function weightedMean(tuples: [number, number][]) { - const [valueSum, weightSum] = tuples.reduce( - ([valueSum, weightSum], [value, weight]) => [ - valueSum + value * weight, - weightSum + weight, - ], - [0, 0], - ) - return valueSum / weightSum +interface PAFOptions extends BaseOptions { + config?: AnyConfigurationModel } export default class PAFAdapter extends BaseFeatureDataAdapter { @@ -158,52 +56,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter { throw new Error('Data exceeds maximum string length (512MB)') } const text = new TextDecoder('utf8', { fatal: true }).decode(buf) - - return text - .split(/\n|\r\n|\r/) - .filter(line => !!line) - .map(line => { - const [ - qname, - , - qstart, - qend, - strand, - tname, - , - tstart, - tend, - numMatches, - blockLen, - mappingQual, - ...fields - ] = line.split('\t') - - const rest = Object.fromEntries( - fields.map(field => { - const r = field.indexOf(':') - const fieldName = field.slice(0, r) - const fieldValue = field.slice(r + 3) - return [fieldName, fieldValue] - }), - ) - - return { - tname, - tstart: +tstart, - tend: +tend, - qname, - qstart: +qstart, - qend: +qend, - strand: strand === '-' ? -1 : 1, - extra: { - numMatches: +numMatches, - blockLen: +blockLen, - mappingQual: +mappingQual, - ...rest, - }, - } as PAFRecord - }) + return parsePAF(text) } async hasDataForRefName() { @@ -214,11 +67,11 @@ export default class PAFAdapter extends BaseFeatureDataAdapter { } getAssemblyNames() { - let assemblyNames = this.getConf('assemblyNames') as string[] + const assemblyNames = this.getConf('assemblyNames') as string[] if (assemblyNames.length === 0) { const query = this.getConf('queryAssembly') as string const target = this.getConf('targetAssembly') as string - assemblyNames = [query, target] + return [query, target] } return assemblyNames } @@ -240,77 +93,88 @@ export default class PAFAdapter extends BaseFeatureDataAdapter { return [] } - getFeatures( - region: Region, - opts: BaseOptions & { config?: AnyConfigurationModel } = {}, - ) { + getFeatures(query: Region, opts: PAFOptions = {}) { return ObservableCreate(async observer => { let pafRecords = await this.setup(opts) const { config } = opts + + // note: this is not the adapter config, it is responding to a display + // setting passed in via the opts parameter if (config && readConfObject(config, 'colorBy') === 'meanQueryIdentity') { pafRecords = getWeightedMeans(pafRecords) } const assemblyNames = this.getAssemblyNames() - const { assemblyName } = region - // The index of the assembly name in the region list corresponds to the + // The index of the assembly name in the query list corresponds to the // adapter in the subadapters list - const index = assemblyNames.indexOf(assemblyName) - if (index !== -1) { - for (let i = 0; i < pafRecords.length; i++) { - const r = pafRecords[i] - let start = 0 - let end = 0 - let refName = '' - let mateName = '' - let mateStart = 0 - let mateEnd = 0 - if (index === 0) { - start = r.qstart - end = r.qend - refName = r.qname - mateName = r.tname - mateStart = r.tstart - mateEnd = r.tend - } else { - start = r.tstart - end = r.tend - refName = r.tname - mateName = r.qname - mateStart = r.qstart - mateEnd = r.qend - } - const { extra, strand } = r - - if ( - refName === region.refName && - doesIntersect2(region.start, region.end, start, end) - ) { - const { numMatches, blockLen } = extra - observer.next( - new SimpleFeature({ - uniqueId: `${i}`, - start, - end, - refName, - strand, - revCigar: true, - // this is a special property of how to interpret CIGAR on PAF, - // intrinsic to the data format. the CIGAR is read backwards - // for features aligning to the negative strand of the target, - // which is actually different than how it works in e.g. - // BAM/SAM (which is visible during alignments track read vs ref) - assemblyName, + const index = assemblyNames.indexOf(query.assemblyName) + const { start: qstart, end: qend, refName: qref, assemblyName } = query + if (index === -1) { + console.warn(`${assemblyName} not found in this adapter`) + observer.complete() + } - // depending on whether the query or target is queried, the "rev" flag - flipInsDel: index === 0, - syntenyId: i, - identity: (numMatches || 0) / (blockLen || 1), - mate: { start: mateStart, end: mateEnd, refName: mateName }, - ...extra, - }), - ) + for (let i = 0; i < pafRecords.length; i++) { + const r = pafRecords[i] + let start = 0 + let end = 0 + let refName = '' + let mateName = '' + let mateStart = 0 + let mateEnd = 0 + const flip = index === 0 + const assemblyName = assemblyNames[+!flip] + if (index === 0) { + start = r.qstart + end = r.qend + refName = r.qname + mateName = r.tname + mateStart = r.tstart + mateEnd = r.tend + } else { + start = r.tstart + end = r.tend + refName = r.tname + mateName = r.qname + mateStart = r.qstart + mateEnd = r.qend + } + const { extra, strand } = r + if (refName === qref && doesIntersect2(qstart, qend, start, end)) { + const { numMatches = 0, blockLen = 1, cg, ...rest } = extra + + let CIGAR = extra.cg + if (extra.cg) { + if (flip && strand === -1) { + CIGAR = flipCigar(parseCigar(extra.cg)).join('') + } else if (flip) { + CIGAR = swapIndelCigar(extra.cg) + } } + + observer.next( + new SyntenyFeature({ + uniqueId: i + assemblyName, + assemblyName, + start, + end, + type: 'match', + refName, + strand, + ...rest, + CIGAR, + syntenyId: i, + identity: numMatches / blockLen, + numMatches, + blockLen, + mate: { + start: mateStart, + end: mateEnd, + refName: mateName, + assemblyName: assemblyNames[+flip], + }, + }), + ) } } @@ -318,5 +182,5 @@ export default class PAFAdapter extends BaseFeatureDataAdapter { }) } - freeResources(/* { region } */): void {} + freeResources(/* { query } */): void {} } diff --git a/plugins/comparative-adapters/src/PAFAdapter/SyntenyFeature.ts b/plugins/comparative-adapters/src/PAFAdapter/SyntenyFeature.ts new file mode 100644 index 0000000000..21261e8fc3 --- /dev/null +++ b/plugins/comparative-adapters/src/PAFAdapter/SyntenyFeature.ts @@ -0,0 +1,15 @@ +import { SimpleFeature } from '@jbrowse/core/util' +import { MismatchParser } from '@jbrowse/plugin-alignments' + +// locals +const { getMismatches } = MismatchParser + +export default class SyntenyFeature extends SimpleFeature { + // eslint-disable-next-line @typescript-eslint/no-explicit-any + get(arg: string): any { + if (arg === 'mismatches') { + return getMismatches(this.get('CIGAR')) + } + return super.get(arg) + } +} diff --git a/plugins/comparative-adapters/src/PAFAdapter/index.ts b/plugins/comparative-adapters/src/PAFAdapter/index.ts index 23660705b1..7fc0bbd0f7 100644 --- a/plugins/comparative-adapters/src/PAFAdapter/index.ts +++ b/plugins/comparative-adapters/src/PAFAdapter/index.ts @@ -7,12 +7,10 @@ export default (pluginManager: PluginManager) => { () => new AdapterType({ name: 'PAFAdapter', + displayName: 'PAF adapter', configSchema, adapterMetadata: { - category: null, hiddenFromGUI: true, - displayName: null, - description: null, }, getAdapterClass: () => import('./PAFAdapter').then(r => r.default), }), diff --git a/plugins/comparative-adapters/src/PAFAdapter/util.test.ts b/plugins/comparative-adapters/src/PAFAdapter/util.test.ts new file mode 100644 index 0000000000..c729f54060 --- /dev/null +++ b/plugins/comparative-adapters/src/PAFAdapter/util.test.ts @@ -0,0 +1,7 @@ +import { flipCigar } from './util' + +test('flip cigar', () => { + expect(flipCigar(['3', 'M', '5', 'D', '5', 'M', '5', 'I', '6', 'M'])).toEqual( + ['6', 'M', '5', 'D', '5', 'M', '5', 'I', '3', 'M'], + ) +}) diff --git a/plugins/comparative-adapters/src/PAFAdapter/util.ts b/plugins/comparative-adapters/src/PAFAdapter/util.ts new file mode 100644 index 0000000000..804d98d5cd --- /dev/null +++ b/plugins/comparative-adapters/src/PAFAdapter/util.ts @@ -0,0 +1,180 @@ +import { zip } from '../util' + +export interface PAFRecord { + qname: string + qstart: number + qend: number + tname: string + tstart: number + tend: number + strand: number + extra: { + cg?: string + blockLen?: number + mappingQual: number + numMatches?: number + meanScore?: number + } +} +// based on "weighted mean" method from https://github.com/tpoorten/dotPlotly +// License reproduced here +// +// MIT License + +// Copyright (c) 2017 Tom Poorten + +// Permission is hereby granted, free of charge, to any person obtaining a copy +// of this software and associated documentation files (the "Software"), to deal +// in the Software without restriction, including without limitation the rights +// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +// copies of the Software, and to permit persons to whom the Software is +// furnished to do so, subject to the following conditions: + +// The above copyright notice and this permission notice shall be included in all +// copies or substantial portions of the Software. + +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +// SOFTWARE. +// +// Notes: in the weighted mean longer alignments factor in more heavily of all +// the fragments of a query vs the reference that it mapped to +// +// this uses a combined key query+'-'+ref to iteratively map all the alignments +// that match a particular ref from a particular query (so 1d array of what +// could be a 2d map) +// +// the result is a single number that says e.g. chr5 from human mapped to chr5 +// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of +// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more +// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6. +// this can show strong and weak levels of synteny, especially in polyploidy +// situations + +export function getWeightedMeans(ret: PAFRecord[]) { + const scoreMap: { [key: string]: { quals: number[]; len: number[] } } = {} + for (let i = 0; i < ret.length; i++) { + const entry = ret[i] + const query = entry.qname + const target = entry.tname + const key = query + '-' + target + if (!scoreMap[key]) { + scoreMap[key] = { quals: [], len: [] } + } + scoreMap[key].quals.push(entry.extra.mappingQual) + scoreMap[key].len.push(entry.extra.blockLen || 1) + } + + const meanScoreMap = Object.fromEntries( + Object.entries(scoreMap).map(([key, val]) => { + const vals = zip(val.quals, val.len) + return [key, weightedMean(vals)] + }), + ) + for (let i = 0; i < ret.length; i++) { + const entry = ret[i] + const query = entry.qname + const target = entry.tname + const key = query + '-' + target + entry.extra.meanScore = meanScoreMap[key] + } + + let min = 10000 + let max = 0 + for (let i = 0; i < ret.length; i++) { + const entry = ret[i] + min = Math.min(entry.extra.meanScore || 0, min) + max = Math.max(entry.extra.meanScore || 0, max) + } + for (let i = 0; i < ret.length; i++) { + const entry = ret[i] + const b = entry.extra.meanScore || 0 + entry.extra.meanScore = (b - min) / (max - min) + } + + return ret +} + +// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a +function weightedMean(tuples: [number, number][]) { + const [valueSum, weightSum] = tuples.reduce( + ([valueSum, weightSum], [value, weight]) => [ + valueSum + value * weight, + weightSum + weight, + ], + [0, 0], + ) + return valueSum / weightSum +} + +export function parsePAF(text: string) { + return text + .split(/\n|\r\n|\r/) + .filter(line => !!line) + .map(line => { + const [ + qname, + , + qstart, + qend, + strand, + tname, + , + tstart, + tend, + numMatches, + blockLen, + mappingQual, + ...fields + ] = line.split('\t') + + const rest = Object.fromEntries( + fields.map(field => { + const r = field.indexOf(':') + const fieldName = field.slice(0, r) + const fieldValue = field.slice(r + 3) + return [fieldName, fieldValue] + }), + ) + + return { + tname, + tstart: +tstart, + tend: +tend, + qname, + qstart: +qstart, + qend: +qend, + strand: strand === '-' ? -1 : 1, + extra: { + numMatches: +numMatches, + blockLen: +blockLen, + mappingQual: +mappingQual, + ...rest, + }, + } as PAFRecord + }) +} + +export function flipCigar(cigar: string[]) { + const arr = [] + for (let i = cigar.length - 2; i >= 0; i -= 2) { + arr.push(cigar[i]) + const op = cigar[i + 1] + if (op === 'D') { + arr.push('I') + } else if (op === 'I') { + arr.push('D') + } else { + arr.push(op) + } + } + return arr +} + +export function swapIndelCigar(cigar: string) { + return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I') +} diff --git a/plugins/comparative-adapters/src/util.ts b/plugins/comparative-adapters/src/util.ts index 6131500e72..68e8762454 100644 --- a/plugins/comparative-adapters/src/util.ts +++ b/plugins/comparative-adapters/src/util.ts @@ -34,3 +34,7 @@ export async function readFile(file: GenericFilehandle, opts?: BaseOptions) { isGzip(buffer) ? await unzip(buffer) : buffer, ) } + +export function zip(a: number[], b: number[]) { + return a.map((e, i) => [e, b[i]] as [number, number]) +} diff --git a/plugins/config/package.json b/plugins/config/package.json index 30e8bc7b58..641688d120 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.1.7", + "version": "2.3.2", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", @@ -27,7 +27,7 @@ "build": "npm-run-all build:*", "test": "cd ../..; jest plugins/config", "prepublishOnly": "yarn test", - "prepack": "yarn build; yarn useDist", + "prepack": "yarn build && yarn useDist", "postpack": "yarn useSrc", "useDist": "node ../../scripts/useDist.js", "useSrc": "node ../../scripts/useSrc.js", @@ -46,11 +46,10 @@ "mobx": "^6.0.0", "mobx-react": "^7.0.0", "mobx-state-tree": "^5.0.0", - "prop-types": "^15.0.0", "react": ">=16.8.0", "react-dom": ">=16.8.0", "rxjs": "^6.0.0", - "tss-react": "^3.0.0" + "tss-react": "^4.0.0" }, "publishConfig": { "access": "public" diff --git a/plugins/config/src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap b/plugins/config/src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap index 37a46b8d1e..8fa5e217ff 100644 --- a/plugins/config/src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap +++ b/plugins/config/src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap @@ -2,7 +2,7 @@ exports[`ConfigurationEditor widget renders all the different types of built-in slots 1`] = `
    ) } diff --git a/products/jbrowse-web/src/Loader.tsx b/products/jbrowse-web/src/Loader.tsx index 33c660d351..39c0701ff5 100644 --- a/products/jbrowse-web/src/Loader.tsx +++ b/products/jbrowse-web/src/Loader.tsx @@ -9,7 +9,7 @@ import { useQueryParam, } from 'use-query-params' import { WindowHistoryAdapter } from 'use-query-params/adapters/window' -import { FatalErrorDialog } from '@jbrowse/core/ui' +import { LoadingEllipses, FatalErrorDialog } from '@jbrowse/core/ui' import '@fontsource/roboto' import 'requestidlecallback-polyfill' import shortid from 'shortid' @@ -36,6 +36,7 @@ const StartScreen = lazy(() => import('./StartScreen')) function NoConfigMessage() { const links = [ ['test_data/volvox/config.json', 'Volvox sample data'], + ['test_data/volvoxhub/config.json', 'Volvox hub sample data'], ['test_data/config.json', 'Human basic'], ['test_data/config_demo.json', 'Human sample data'], ['test_data/tomato/config.json', 'Tomato SVs'], @@ -46,6 +47,7 @@ function NoConfigMessage() { ['test_data/config_many_contigs.json', 'Many contigs'], ['test_data/config_honeybee.json', 'Honeybee'], ['test_data/config_wormbase.json', 'Wormbase'], + ['test_data/config_human_dotplot.json', 'Human dotplot'], ['test_data/wgbs/config.json', 'WGBS methylation'], ] return ( @@ -185,13 +187,13 @@ const StartScreenErrorMessage = ({ error }: { error: unknown }) => { > No config.json found. If you want to learn how to complete your setup, visit our{' '} - + quick start guide .
    ) : ( - Loading...
    }> + }> )} @@ -215,8 +217,8 @@ function ConfigTriaged({ loader.setConfigSnapshot({ ...session, id: shortid() }) handleClose() }} - onCancel={() => { - factoryReset() + onCancel={async () => { + await factoryReset() handleClose() }} reason={loader.sessionTriaged.reason} @@ -371,7 +373,7 @@ const Renderer = observer( } if (pm) { return !pm.rootModel?.session ? ( - Loading...
    }> + }> ) : ( diff --git a/products/jbrowse-web/src/SessionLoader.ts b/products/jbrowse-web/src/SessionLoader.ts index b5bfa33441..3eff2c3ddb 100644 --- a/products/jbrowse-web/src/SessionLoader.ts +++ b/products/jbrowse-web/src/SessionLoader.ts @@ -251,7 +251,14 @@ const SessionLoader = types }, async fetchConfig() { - const { configPath = 'config.json' } = self + let { configPath = 'config.json' } = self + + // @ts-ignore + // eslint-disable-next-line no-underscore-dangle + if (window.__jbrowseCacheBuster) { + configPath += `?rand=${Math.random()}` + } + const text = await openLocation({ uri: configPath, locationType: 'UriLocation', diff --git a/products/jbrowse-web/src/SessionWarningDialog.tsx b/products/jbrowse-web/src/SessionWarningDialog.tsx index 9fe169475c..ca6bb1cb3f 100644 --- a/products/jbrowse-web/src/SessionWarningDialog.tsx +++ b/products/jbrowse-web/src/SessionWarningDialog.tsx @@ -1,29 +1,13 @@ import React from 'react' -import { makeStyles } from 'tss-react/mui' +import { Dialog } from '@jbrowse/core/ui' import { Button, - Dialog, DialogContent, DialogContentText, - DialogTitle, - Divider, + DialogActions, } from '@mui/material' import WarningIcon from '@mui/icons-material/Warning' -const useStyles = makeStyles()(theme => ({ - main: { - textAlign: 'center', - margin: 8, // theme.spacing(2), - padding: 8, // theme.spacing(2), - borderWidth: 2, - borderRadius: 2, - }, - buttons: { - margin: 8, // theme.spacing(2), - color: theme.palette.text.primary, - }, -})) - export default function SessionWarningModal({ onConfirm, onCancel, @@ -33,50 +17,37 @@ export default function SessionWarningModal({ onCancel: () => void reason: { url: string }[] }) { - const { classes } = useStyles() return ( - Warning - -
    + - - - This link contains a session that has the following unknown plugins: -
      - {reason.map(r => ( -
    • URL: {r.url}
      • - ))} -
    - Please ensure you trust the source of this session. -     -     -
    - - -
    -
    + + This link contains a session that has the following unknown plugins: +
      + {reason.map(r => ( +
    • URL: {r.url}
      • + ))} +
    + Please ensure you trust the source of this session. +     + + + + +     ) } diff --git a/products/jbrowse-web/src/ShareButton.tsx b/products/jbrowse-web/src/ShareButton.tsx index 235374d7a1..eb13d54dec 100644 --- a/products/jbrowse-web/src/ShareButton.tsx +++ b/products/jbrowse-web/src/ShareButton.tsx @@ -1,15 +1,12 @@ import React, { useState, useEffect } from 'react' import { getSnapshot } from 'mobx-state-tree' import { observer } from 'mobx-react' -import copy from 'copy-to-clipboard' +import { Dialog } from '@jbrowse/core/ui' import { Button, - Dialog, DialogActions, DialogContent, DialogContentText, - DialogTitle, - Divider, IconButton, FormControl, FormControlLabel, @@ -18,6 +15,7 @@ import { TextField, Typography, } from '@mui/material' +import copy from 'copy-to-clipboard' import { alpha } from '@mui/material/styles' import { makeStyles } from 'tss-react/mui' @@ -27,7 +25,6 @@ import { AbstractSessionModel } from '@jbrowse/core/util' import ShareIcon from '@mui/icons-material/Share' import HelpOutlineIcon from '@mui/icons-material/HelpOutline' import SettingsIcon from '@mui/icons-material/Settings' -import CloseIcon from '@mui/icons-material/Close' import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons' // locals @@ -53,12 +50,6 @@ const useStyles = makeStyles()(theme => ({ loadingMessage: { padding: theme.spacing(5), }, - closeButton: { - position: 'absolute', - right: theme.spacing(1), - top: theme.spacing(1), - color: theme.palette.grey[500], - }, })) const SHARE_URL_LOCALSTORAGE_KEY = 'jbrowse-shareURL' @@ -68,7 +59,6 @@ function SettingsDialog(props: { onClose: Function currentSetting: string }) { - const { classes } = useStyles() const { onClose, open, currentSetting } = props const [setting, setSetting] = useState(currentSetting) const [infoDialogOpen, setInfoDialogOpen] = useState(false) @@ -80,15 +70,11 @@ function SettingsDialog(props: { return ( <> - - - Configure session sharing - {handleClose ? ( - - - - ) : null} - + Select between generating long or short URLs for the session sharing @@ -128,23 +114,14 @@ function SettingsDialog(props: { ) } function InfoDialog(props: { open: boolean; onClose: Function }) { - const { classes } = useStyles() const { onClose, open } = props - const handleClose = () => { - onClose() - } - return ( - - - Info about session URLs - {onClose ? ( - - - - ) : null} - + onClose()} + open={open} + title="Info about session URLs" + > Because everything about the JBrowse session is encoded in the URL @@ -171,132 +148,101 @@ function InfoDialog(props: { open: boolean; onClose: Function }) { ) } -const ShareDialog = observer( - ({ - handleClose, - session, - }: { - handleClose: () => void - session: AbstractSessionModel & { shareURL: string } - }) => { - const { classes } = useStyles() - const [shortUrl, setShortUrl] = useState('') - const [longUrl, setLongUrl] = useState('') - const [loading, setLoading] = useState(true) - const [error, setError] = useState() - const [settingsDialogOpen, setSettingsDialogOpen] = useState(false) - - const url = session.shareURL - const currentSetting = - localStorage.getItem(SHARE_URL_LOCALSTORAGE_KEY) || 'short' - const snap = getSnapshot(session) - - useEffect(() => { - let cancelled = false - ;(async () => { - if (currentSetting === 'short') { - try { - setLoading(true) - const locationUrl = new URL(window.location.href) - const result = await shareSessionToDynamo( - snap, - url, - locationUrl.href, - ) - if (!cancelled) { - const params = new URLSearchParams(locationUrl.search) - params.set('session', `share-${result.json.sessionId}`) - params.set('password', result.password) - locationUrl.search = params.toString() - setShortUrl(locationUrl.href) - } - } catch (e) { - setError(e) - } finally { - setLoading(false) - } - } - })() +const ShareDialog = observer(function ({ + handleClose, + session, +}: { + handleClose: () => void + session: AbstractSessionModel & { shareURL: string } +}) { + const [shortUrl, setShortUrl] = useState('') + const [longUrl, setLongUrl] = useState('') + const [loading, setLoading] = useState(true) + const [error, setError] = useState() + const [settingsDialogOpen, setSettingsDialogOpen] = useState(false) - return () => { - cancelled = true - } - }, [currentSetting, url, snap]) + const url = session.shareURL + const currentSetting = + localStorage.getItem(SHARE_URL_LOCALSTORAGE_KEY) || 'short' + const snap = getSnapshot(session) - useEffect(() => { - let cancelled = false - ;(async () => { + useEffect(() => { + let cancelled = false + // eslint-disable-next-line @typescript-eslint/no-floating-promises + ;(async () => { + if (currentSetting === 'short') { try { - // generate long URL - const sess = await toUrlSafeB64(JSON.stringify(getSnapshot(session))) - const longUrl = new URL(window.location.href) - const longParams = new URLSearchParams(longUrl.search) - longParams.set('session', `encoded-${sess}`) - longUrl.search = longParams.toString() + setLoading(true) + const locationUrl = new URL(window.location.href) + const result = await shareSessionToDynamo(snap, url, locationUrl.href) if (!cancelled) { - setLongUrl(longUrl.toString()) + const params = new URLSearchParams(locationUrl.search) + params.set('session', `share-${result.json.sessionId}`) + params.set('password', result.password) + locationUrl.search = params.toString() + setShortUrl(locationUrl.href) } } catch (e) { setError(e) + } finally { + setLoading(false) } - })() - return () => { - cancelled = true } - }, [session]) + })() - return ( - <> - - - JBrowse Shareable Link - {handleClose ? ( - - - - ) : null} - - + return () => { + cancelled = true + } + }, [currentSetting, url, snap]) - - - Copy the URL below to share your current JBrowse session. - setSettingsDialogOpen(true)}> - - - + useEffect(() => { + let cancelled = false + // eslint-disable-next-line @typescript-eslint/no-floating-promises + ;(async () => { + try { + const sess = await toUrlSafeB64(JSON.stringify(getSnapshot(session))) + const longUrl = new URL(window.location.href) + const longParams = new URLSearchParams(longUrl.search) + longParams.set('session', `encoded-${sess}`) + longUrl.search = longParams.toString() + if (!cancelled) { + setLongUrl(longUrl.toString()) + } + } catch (e) { + setError(e) + } + })() + return () => { + cancelled = true + } + }, [session]) - {currentSetting === 'short' ? ( - error ? ( - {`${error}`} - ) : loading ? ( - Generating short URL... - ) : ( - { - const target = event.target as HTMLTextAreaElement - target.select() - }} - data-testid="share-url-field" - /> - ) + return ( + <> + + + + Copy the URL below to share your current JBrowse session. + setSettingsDialogOpen(true)}> + + + + + {currentSetting === 'short' ? ( + error ? ( + {`${error}`} + ) : loading ? ( + Generating short URL... ) : ( - )} - - - - - - - + variant="filled" + style={{ width: '100%' }} + onClick={event => { + const target = event.target as HTMLTextAreaElement + target.select() + }} + /> + )} + + + - { - setSettingsDialogOpen(false) - }} - currentSetting={currentSetting} - /> - - ) - }, -) + + + -const ShareButton = observer( - (props: { session: AbstractSessionModel & { shareURL: string } }) => { - const [open, setOpen] = useState(false) + { + setSettingsDialogOpen(false) + }} + currentSetting={currentSetting} + /> + + ) +}) - const { session } = props - const { classes } = useStyles() +const ShareButton = observer(function (props: { + session: AbstractSessionModel & { shareURL: string } +}) { + const [open, setOpen] = useState(false) - const handleClose = () => { - setOpen(false) - } + const { session } = props + const { classes } = useStyles() - return ( -
    - - {open ? ( - - ) : null} -
    - ) - }, -) + return ( +
    + + {open ? ( + setOpen(false)} session={session} /> + ) : null} +
    + ) +}) export default ShareButton diff --git a/products/jbrowse-web/src/StartScreen.tsx b/products/jbrowse-web/src/StartScreen.tsx index 29d661cb14..0f0dcd95fd 100644 --- a/products/jbrowse-web/src/StartScreen.tsx +++ b/products/jbrowse-web/src/StartScreen.tsx @@ -58,6 +58,7 @@ const DeleteSessionDialog = ({ }) => { const [deleteSession, setDeleteSession] = useState(false) useEffect(() => { + // eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { try { if (deleteSession) { @@ -118,6 +119,7 @@ export default function StartScreen({ const [reset, setReset] = useState(false) useEffect(() => { + // eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { try { if (sessionToLoad) { @@ -130,6 +132,7 @@ export default function StartScreen({ }, [rootModel, sessionToLoad]) useEffect(() => { + // eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { try { if (updateSessionsList) { diff --git a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap index 74d9149c09..7ac2ee0d02 100644 --- a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap +++ b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap @@ -1,40 +1,40 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`JBrowse model creates with empty snapshot 1`] = ` -Object { - "aggregateTextSearchAdapters": Array [], - "assemblies": Array [], - "configuration": Object {}, - "connections": Array [], - "defaultSession": Object { +{ + "aggregateTextSearchAdapters": [], + "assemblies": [], + "configuration": {}, + "connections": [], + "defaultSession": { "name": "New session", }, - "internetAccounts": Array [], - "plugins": Array [], - "tracks": Array [], + "internetAccounts": [], + "plugins": [], + "tracks": [], } `; exports[`JBrowse model creates with non-empty snapshot 1`] = ` -Object { - "aggregateTextSearchAdapters": Array [ - Object { - "assemblyNames": Array [ +{ + "aggregateTextSearchAdapters": [ + { + "assemblyNames": [ "volvox", ], - "ixFilePath": Object { + "ixFilePath": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "trix/volvox.ix", }, - "ixxFilePath": Object { + "ixxFilePath": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "trix/volvox.ixx", }, - "metaFilePath": Object { + "metaFilePath": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -43,27 +43,52 @@ Object { "textSearchAdapterId": "volvox-index", "type": "TrixTextSearchAdapter", }, + { + "assemblyNames": [ + "volvox-rev-del", + ], + "ixFilePath": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "trix/volvox-rev-del.ix", + }, + "ixxFilePath": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "trix/volvox-rev-del.ixx", + }, + "metaFilePath": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "trix/volvox-rev-del_meta.json", + }, + "textSearchAdapterId": "volvox-rev-del-index", + "type": "TrixTextSearchAdapter", + }, ], - "assemblies": Array [ - Object { - "aliases": Array [ + "assemblies": [ + { + "aliases": [ "vvx", ], "name": "volvox", - "refNameAliases": Object { - "adapter": Object { + "refNameAliases": { + "adapter": { "adapterId": "W6DyPGJ0UU", - "features": Array [ - Object { - "aliases": Array [ + "features": [ + { + "aliases": [ "A", "contigA", ], "refName": "ctgA", "uniqueId": "alias1", }, - Object { - "aliases": Array [ + { + "aliases": [ "B", "contigB", ], @@ -74,15 +99,15 @@ Object { "type": "FromConfigAdapter", }, }, - "sequence": Object { - "adapter": Object { - "chromSizesLocation": Object { + "sequence": { + "adapter": { + "chromSizesLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "/path/to/default.chrom.sizes", }, - "twoBitLocation": Object { + "twoBitLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -90,34 +115,38 @@ Object { }, "type": "TwoBitAdapter", }, - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_refseq-LinearReferenceSequenceDisplay", "type": "LinearReferenceSequenceDisplay", }, + { + "displayId": "volvox_refseq-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, ], - "formatAbout": Object { + "formatAbout": { "config": "jexl:{extraField:'important data'}", "hideUris": true, }, - "metadata": Object { + "metadata": { "date": "2020-08-20", }, "trackId": "volvox_refseq", "type": "ReferenceSequenceTrack", }, }, - Object { + { "name": "volvox2", - "sequence": Object { - "adapter": Object { - "chromSizesLocation": Object { + "sequence": { + "adapter": { + "chromSizesLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "/path/to/default.chrom.sizes", }, - "twoBitLocation": Object { + "twoBitLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -125,27 +154,31 @@ Object { }, "type": "TwoBitAdapter", }, - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_refseq2-LinearReferenceSequenceDisplay", "type": "LinearReferenceSequenceDisplay", }, + { + "displayId": "volvox_refseq2-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, ], "trackId": "volvox_refseq2", "type": "ReferenceSequenceTrack", }, }, - Object { + { "name": "volvox404", - "sequence": Object { - "adapter": Object { - "chromSizesLocation": Object { + "sequence": { + "adapter": { + "chromSizesLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "/path/to/default.chrom.sizes", }, - "twoBitLocation": Object { + "twoBitLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -153,33 +186,75 @@ Object { }, "type": "TwoBitAdapter", }, - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_refseq404-LinearReferenceSequenceDisplay", "type": "LinearReferenceSequenceDisplay", }, + { + "displayId": "volvox_refseq404-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, ], "trackId": "volvox_refseq404", "type": "ReferenceSequenceTrack", }, }, - Object { + { + "name": "misc", + "sequence": { + "adapter": { + "faiLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "misc.fa.fai", + }, + "fastaLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "misc.fa", + }, + "metadataLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml", + }, + "type": "IndexedFastaAdapter", + }, + "displays": [ + { + "displayId": "misc_asm-LinearReferenceSequenceDisplay", + "type": "LinearReferenceSequenceDisplay", + }, + { + "displayId": "misc_asm-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, + ], + "trackId": "misc_asm", + "type": "ReferenceSequenceTrack", + }, + }, + { "name": "volvox_del", - "sequence": Object { - "adapter": Object { - "faiLocation": Object { + "sequence": { + "adapter": { + "faiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox_del.fa.fai", }, - "fastaLocation": Object { + "fastaLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox_del.fa", }, - "metadataLocation": Object { + "metadataLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -187,33 +262,37 @@ Object { }, "type": "IndexedFastaAdapter", }, - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_del-ReferenceSequenceTrack-LinearReferenceSequenceDisplay", "type": "LinearReferenceSequenceDisplay", }, + { + "displayId": "volvox_del-ReferenceSequenceTrack-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, ], "trackId": "volvox_del-ReferenceSequenceTrack", "type": "ReferenceSequenceTrack", }, }, - Object { + { "name": "volvox_ins", - "sequence": Object { - "adapter": Object { - "faiLocation": Object { + "sequence": { + "adapter": { + "faiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox_ins.fa.fai", }, - "fastaLocation": Object { + "fastaLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox_ins.fa", }, - "metadataLocation": Object { + "metadataLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -221,29 +300,147 @@ Object { }, "type": "IndexedFastaAdapter", }, - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_ins-ReferenceSequenceTrack-LinearReferenceSequenceDisplay", "type": "LinearReferenceSequenceDisplay", }, + { + "displayId": "volvox_ins-ReferenceSequenceTrack-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, ], "trackId": "volvox_ins-ReferenceSequenceTrack", "type": "ReferenceSequenceTrack", }, }, + { + "name": "volvox-rev-del", + "sequence": { + "adapter": { + "faiLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-rev-del.fa.fai", + }, + "fastaLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-rev-del.fa", + }, + "metadataLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml", + }, + "type": "IndexedFastaAdapter", + }, + "displays": [ + { + "displayId": "volvox-rev-del-ReferenceSequenceTrack-LinearReferenceSequenceDisplay", + "type": "LinearReferenceSequenceDisplay", + }, + { + "displayId": "volvox-rev-del-ReferenceSequenceTrack-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, + ], + "trackId": "volvox-rev-del-ReferenceSequenceTrack", + "type": "ReferenceSequenceTrack", + }, + }, + { + "name": "volvox-simple-inv", + "sequence": { + "adapter": { + "faiLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv.fa.fai", + }, + "fastaLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv.fa", + }, + "metadataLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml", + }, + "type": "IndexedFastaAdapter", + }, + "displays": [ + { + "displayId": "volvox-simple-inv-ReferenceSequenceTrack-LinearReferenceSequenceDisplay", + "type": "LinearReferenceSequenceDisplay", + }, + { + "displayId": "volvox-simple-inv-ReferenceSequenceTrack-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, + ], + "trackId": "volvox-simple-inv-ReferenceSequenceTrack", + "type": "ReferenceSequenceTrack", + }, + }, + { + "name": "volvox_random_inv", + "sequence": { + "adapter": { + "faiLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "output_prefix3.simseq.genome.fa.fai", + }, + "fastaLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "output_prefix3.simseq.genome.fa", + }, + "metadataLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml", + }, + "type": "IndexedFastaAdapter", + }, + "displays": [ + { + "displayId": "volvox_random_inv-ReferenceSequenceTrack-LinearReferenceSequenceDisplay", + "type": "LinearReferenceSequenceDisplay", + }, + { + "displayId": "volvox_random_inv-ReferenceSequenceTrack-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, + ], + "trackId": "volvox_random_inv-ReferenceSequenceTrack", + "type": "ReferenceSequenceTrack", + }, + }, ], - "configuration": Object {}, - "connections": Array [], - "defaultSession": Object { - "activeWidgets": Object { + "configuration": {}, + "connections": [], + "defaultSession": { + "activeWidgets": { "hierarchicalTrackSelector": "hierarchicalTrackSelector", }, "name": "Integration test example", - "views": Array [ - Object { + "views": [ + { "bpPerPx": 0.05, - "displayedRegions": Array [ - Object { + "displayedRegions": [ + { "assemblyName": "volvox", "end": 50001, "refName": "ctgA", @@ -255,8 +452,8 @@ Object { "type": "LinearGenomeView", }, ], - "widgets": Object { - "hierarchicalTrackSelector": Object { + "widgets": { + "hierarchicalTrackSelector": { "filterText": "", "id": "hierarchicalTrackSelector", "type": "HierarchicalTrackSelectorWidget", @@ -264,15 +461,15 @@ Object { }, }, }, - "internetAccounts": Array [ - Object { + "internetAccounts": [ + { "clientId": "50knr6xrjfc39sk", "description": "Account to access Dropbox files", "internetAccountId": "dropboxOAuth", "name": "Dropbox", "type": "DropboxOAuthInternetAccount", }, - Object { + { "clientId": "109518325434-udfch80a0v70mgu65d5fejqsq5kvhm1b.apps.googleusercontent.com", "description": "Account to access Google Drive files", "internetAccountId": "googleOAuth", @@ -280,23 +477,23 @@ Object { "type": "GoogleDriveOAuthInternetAccount", }, ], - "plugins": Array [ - Object { + "plugins": [ + { "name": "UMDLocPlugin", - "umdLoc": Object { + "umdLoc": { "uri": "umd_plugin.js", }, }, - Object { + { "name": "UMDUrlPlugin", "umdUrl": "umd_plugin.js", }, ], - "tracks": Array [ - Object { - "adapter": Object { - "index": Object { - "location": Object { + "tracks": [ + { + "adapter": { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -304,25 +501,25 @@ Object { }, }, "type": "VcfTabixAdapter", - "vcfGzLocation": Object { + "vcfGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.dup.vcf.gz", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_sv_test-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "volvox_sv_test-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -331,10 +528,10 @@ Object { "trackId": "volvox_sv_test", "type": "VariantTrack", }, - Object { - "adapter": Object { - "index": Object { - "location": Object { + { + "adapter": { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -342,25 +539,25 @@ Object { }, }, "type": "VcfTabixAdapter", - "vcfGzLocation": Object { + "vcfGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.dup.renamed.vcf.gz", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_sv_test_renamed-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "volvox_sv_test_renamed-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -369,22 +566,22 @@ Object { "trackId": "volvox_sv_test_renamed", "type": "VariantTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -392,47 +589,55 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_cram_alignments-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_cram_alignments-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_cram_alignments-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_cram_alignments-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_cram_alignments-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.cram (contigA, default display)", "trackId": "volvox_cram_alignments", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.cram", }, "fetchSizeLimit": 1000, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -440,49 +645,57 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_cram_pileup_pileup", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_cram_pileup-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_cram_pileup-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_cram_pileup-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_cram_pileup-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], - "metadata": Object { + "metadata": { "source": "We generated 150bp paired end reads from a Volvox mythicus, an imaginary species, for this jbrowse demo", }, "name": "volvox-sorted.cram (contigA, LinearPileupDisplay)", "trackId": "volvox_cram_pileup", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -490,46 +703,54 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_cram_snpcoverage_snpcoverage", "type": "LinearSNPCoverageDisplay", }, - Object { + { "displayId": "volvox_cram_snpcoverage-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_cram_snpcoverage-LinearPileupDisplay", "type": "LinearPileupDisplay", }, + { + "displayId": "volvox_cram_snpcoverage-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_cram_snpcoverage-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.cram (contigA, LinearSNPCoverageDisplay)", "trackId": "volvox_cram_snpcoverage", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -537,46 +758,54 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_cram_alignments_ctga-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_cram_alignments_ctga-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_cram_alignments_ctga-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_cram_alignments_ctga-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_cram_alignments_ctga-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.cram (ctgA, default display)", "trackId": "volvox_cram_alignments_ctga", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -584,46 +813,54 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_cram_pileup_ctga_pileup", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_cram_pileup_ctga-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_cram_pileup_ctga-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_cram_pileup_ctga-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_cram_pileup_ctga-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.cram (ctgA, LinearPileupDisplay)", "trackId": "volvox_cram_pileup_ctga", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -631,40 +868,48 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_cram_pileup_ctga_snpcoverage", "type": "LinearSNPCoverageDisplay", }, - Object { + { "displayId": "volvox_cram_snpcoverage_ctga-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_cram_snpcoverage_ctga-LinearPileupDisplay", "type": "LinearPileupDisplay", }, + { + "displayId": "volvox_cram_snpcoverage_ctga-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_cram_snpcoverage_ctga-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.cram (ctgA, LinearSNPCoverageDisplay)", "trackId": "volvox_cram_snpcoverage_ctga", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -673,45 +918,53 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", "volvox2", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_alignments_alignments", - "pileupDisplay": Object { + "pileupDisplay": { "displayId": "volvox_bam_altname_alignments_pileup", "type": "LinearPileupDisplay", }, "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_alignments-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_alignments-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_alignments-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_alignments-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (ctgA)", "trackId": "volvox_alignments", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -720,40 +973,48 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_bam_snpcoverage_snpcoverage", "type": "LinearSNPCoverageDisplay", }, - Object { + { "displayId": "volvox_bam_snpcoverage-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_bam_snpcoverage-LinearPileupDisplay", "type": "LinearPileupDisplay", }, + { + "displayId": "volvox_bam_snpcoverage-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_bam_snpcoverage-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (contigA LinearSNPCoverageDisplay)", "trackId": "volvox_bam_snpcoverage", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -762,40 +1023,48 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_bam_pileup_pileup", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_bam_pileup-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_bam_pileup-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_bam_pileup-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_bam_pileup-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (contigA LinearPileupDisplay)", "trackId": "volvox_bam_pileup", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -804,40 +1073,48 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_alignments_pileup_coverage-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_alignments_pileup_coverage-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_alignments_pileup_coverage-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_alignments_pileup_coverage-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_alignments_pileup_coverage-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (ctgA, canvas)", "trackId": "volvox_alignments_pileup_coverage", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted-altname.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -846,40 +1123,48 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_bam_altname-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_bam_altname-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_bam_altname-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_bam_altname-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_bam_altname-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (contigA)", "trackId": "volvox_bam_altname", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -888,19 +1173,19 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_bam_small_max_height_alignments", - "pileupDisplay": Object { + "pileupDisplay": { "displayId": "volvox_bam_small_max_height_alignments_pileup", - "renderers": Object { - "PileupRenderer": Object { + "renderers": { + "PileupRenderer": { "maxHeight": 10, "type": "PileupRenderer", }, @@ -909,23 +1194,31 @@ Object { }, "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_bam_small_max_height-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_bam_small_max_height-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_bam_small_max_height-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_bam_small_max_height-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (small max height)", "trackId": "volvox_bam_small_max_height", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "index": Object { - "location": Object { + { + "adapter": { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -933,25 +1226,25 @@ Object { }, }, "type": "VcfTabixAdapter", - "vcfGzLocation": Object { + "vcfGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.test.vcf.gz", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_test_vcf-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "volvox_test_vcf-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -960,9 +1253,9 @@ Object { "trackId": "volvox_test_vcf", "type": "VariantTrack", }, - Object { - "adapter": Object { - "rootUrlTemplate": Object { + { + "adapter": { + "rootUrlTemplate": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -970,18 +1263,18 @@ Object { }, "type": "NCListAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "nclist_long_names-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "nclist_long_names-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -990,16 +1283,16 @@ Object { "trackId": "nclist_long_names", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.bam.nonexist", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1008,40 +1301,48 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_alignments_bam_nonexist-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_alignments_bam_nonexist-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_alignments_bam_nonexist-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_alignments_bam_nonexist-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_alignments_bam_nonexist-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (bam nonexist 404)", "trackId": "volvox_alignments_bam_nonexist", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1050,33 +1351,41 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_alignments_bai_nonexist-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_alignments_bai_nonexist-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_alignments_bai_nonexist-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_alignments_bai_nonexist-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_alignments_bai_nonexist-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam (bai nonexist 404)", "trackId": "volvox_alignments_bai_nonexist", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1084,15 +1393,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", "Wiggle", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_bigwig_nonexist-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -1101,34 +1410,34 @@ Object { "trackId": "volvox_bigwig_nonexist", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "subadapters": Array [ - Object { - "bigWigLocation": Object { + { + "adapter": { + "subadapters": [ + { + "bigWigLocation": { "uri": "v1.cram.bw", }, "name": "k1", "source": "j1", "type": "BigWigAdapter", }, - Object { - "bigWigLocation": Object { + { + "bigWigLocation": { "uri": "v2.cram.bw", }, "name": "k2", "source": "j2", "type": "BigWigAdapter", }, - Object { - "bigWigLocation": Object { + { + "bigWigLocation": { "uri": "v3.cram.bw", }, "name": "k3", "type": "BigWigAdapter", }, - Object { - "bigWigLocation": Object { + { + "bigWigLocation": { "uri": "v4.cram.bw", }, "name": "k4", @@ -1137,11 +1446,11 @@ Object { ], "type": "MultiWiggleAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_microarray_multi-MultiLinearWiggleDisplay", "type": "MultiLinearWiggleDisplay", }, @@ -1150,9 +1459,9 @@ Object { "trackId": "volvox_microarray_multi", "type": "MultiQuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1160,15 +1469,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", "Wiggle", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_microarray-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -1177,9 +1486,9 @@ Object { "trackId": "volvox_microarray", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": "dropboxOAuth", "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1187,14 +1496,14 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Authentication", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "dropbox_bigwig-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -1203,9 +1512,9 @@ Object { "trackId": "dropbox_bigwig", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": "googleOAuth", "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1213,14 +1522,14 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Authentication", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "google_bigwig-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -1229,9 +1538,9 @@ Object { "trackId": "google_bigwig", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1239,15 +1548,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", "Wiggle", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "line", "displayId": "volvox_microarray_line_line", "type": "LinearWiggleDisplay", @@ -1257,9 +1566,9 @@ Object { "trackId": "volvox_microarray_line", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1267,15 +1576,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", "Wiggle", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "density", "displayId": "volvox_microarray_density_density", "type": "LinearWiggleDisplay", @@ -1285,9 +1594,9 @@ Object { "trackId": "volvox_microarray_density", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1295,15 +1604,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", "Wiggle", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_microarray_density_altname-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -1312,11 +1621,11 @@ Object { "trackId": "volvox_microarray_density_altname", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { + { + "adapter": { "adapterId": "Xvg1McRUAP", - "features": Array [ - Object { + "features": [ + { "end": 191, "name": "Boris", "note": "note for boris", @@ -1326,7 +1635,7 @@ Object { "type": "foo", "uniqueId": "one", }, - Object { + { "end": 192, "name": "Theresa", "note": "note for theresa", @@ -1336,7 +1645,7 @@ Object { "type": "bar", "uniqueId": "two", }, - Object { + { "end": 211, "name": "Nigel", "note": "note for nigel", @@ -1346,7 +1655,7 @@ Object { "type": "baz", "uniqueId": "three", }, - Object { + { "end": 221, "name": "Geoffray", "note": "note for geoffray", @@ -1359,22 +1668,22 @@ Object { ], "type": "FromConfigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "lollipop_track_linear", "type": "LinearLollipopDisplay", }, - Object { + { "displayId": "lollipop_track-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "lollipop_track-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -1383,16 +1692,16 @@ Object { "trackId": "lollipop_track", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-long-reads-sv.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1401,46 +1710,54 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox-long-reads-sv-bam-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox-long-reads-sv-bam-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox-long-reads-sv-bam-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox-long-reads-sv-bam-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-long-reads-sv-bam-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-long reads with SV", "trackId": "volvox-long-reads-sv-bam", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-long-reads-sv.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-long-reads-sv.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -1448,46 +1765,54 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox-long-reads-sv-cram-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox-long-reads-sv-cram-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox-long-reads-sv-cram-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox-long-reads-sv-cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-long-reads-sv-cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-long reads with SV (cram)", "trackId": "volvox-long-reads-sv-cram", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-long-reads.fastq.sorted.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-long-reads.fastq.sorted.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -1495,40 +1820,48 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox-long-reads-cram-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox-long-reads-cram-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox-long-reads-cram-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox-long-reads-cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-long-reads-cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-long reads (cram)", "trackId": "volvox-long-reads-cram", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-long-reads.fastq.sorted.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1537,46 +1870,54 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox-long-reads-bam-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox-long-reads-bam-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox-long-reads-bam-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox-long-reads-bam-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-long-reads-bam-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-long reads", "trackId": "volvox-long-reads-bam", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-samspec.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-samspec.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -1584,40 +1925,48 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_samspec_cram-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_samspec_cram-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_samspec_cram-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_samspec_cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_samspec_cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-samspec (cram)", "trackId": "volvox_samspec_cram", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-samspec.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1626,46 +1975,54 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_samspec-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_samspec-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_samspec-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_samspec-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_samspec-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-samspec", "trackId": "volvox_samspec", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sv.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sv.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -1673,40 +2030,48 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_sv_cram-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_sv_cram-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_sv_cram-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_sv_cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_sv_cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sv (cram)", "trackId": "volvox_sv_cram", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sv.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1715,40 +2080,48 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_sv-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_sv-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_sv-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_sv-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_sv-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sv", "trackId": "volvox_sv", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "gffGzLocation": Object { + { + "adapter": { + "gffGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.sort.gff3.gz", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1757,45 +2130,45 @@ Object { }, "type": "Gff3TabixAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "gff3tabix_genes-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "gff3tabix_genes-LinearArcDisplay", "type": "LinearArcDisplay", }, ], - "formatDetails": Object { + "formatDetails": { "feature": "jexl:{name:''+feature.name+'',extrafield:'Field added with custom callback:' + feature.name,phase:undefined,type:undefined}", }, "name": "GFF3Tabix genes", "trackId": "gff3tabix_genes", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -1803,40 +2176,48 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_cram-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_cram-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_cram-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.cram", "trackId": "volvox_cram", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-sorted.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1845,34 +2226,42 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_bam-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox_bam-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox_bam-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox_bam-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox_bam-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-sorted.bam", "trackId": "volvox_bam", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "index": Object { - "location": Object { + { + "adapter": { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1880,25 +2269,25 @@ Object { }, }, "type": "VcfTabixAdapter", - "vcfGzLocation": Object { + "vcfGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.filtered.vcf.gz", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_filtered_vcf-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "volvox_filtered_vcf-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -1907,10 +2296,10 @@ Object { "trackId": "volvox_filtered_vcf", "type": "VariantTrack", }, - Object { - "adapter": Object { - "index": Object { - "location": Object { + { + "adapter": { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1918,25 +2307,25 @@ Object { }, }, "type": "VcfTabixAdapter", - "vcfGzLocation": Object { + "vcfGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.filtered.vcf.gz", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "vvx", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_filtered_vcf_assembly_alias-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "volvox_filtered_vcf_assembly_alias-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -1945,9 +2334,9 @@ Object { "trackId": "volvox_filtered_vcf_assembly_alias", "type": "VariantTrack", }, - Object { - "adapter": Object { - "bigBedLocation": Object { + { + "adapter": { + "bigBedLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1955,18 +2344,18 @@ Object { }, "type": "BigBedAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "bigbed_genes-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "bigbed_genes-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -1975,16 +2364,16 @@ Object { "trackId": "bigbed_genes", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "bedGzLocation": Object { + { + "adapter": { + "bedGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-bed12.bed.gz", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -1993,18 +2382,18 @@ Object { }, "type": "BedTabixAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "bedtabix_genes-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "bedtabix_genes-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -2013,9 +2402,9 @@ Object { "trackId": "bedtabix_genes", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "bedLocation": Object { + { + "adapter": { + "bedLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2023,18 +2412,18 @@ Object { }, "type": "BedAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "bed_genes-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "bed_genes-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -2043,9 +2432,9 @@ Object { "trackId": "bed_genes", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2053,15 +2442,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "Line", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "line", "displayId": "LrM3WWJR0tj_line", "type": "LinearWiggleDisplay", @@ -2071,9 +2460,9 @@ Object { "trackId": "LrM3WWJR0tj", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "rootUrlTemplate": Object { + { + "adapter": { + "rootUrlTemplate": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2081,18 +2470,18 @@ Object { }, "type": "NCListAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "Genes-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "Genes-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -2101,9 +2490,9 @@ Object { "trackId": "Genes", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2111,15 +2500,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "Density", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "density", "displayId": "VUyE25kYsQo_density", "type": "LinearWiggleDisplay", @@ -2129,9 +2518,9 @@ Object { "trackId": "VUyE25kYsQo", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2139,15 +2528,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "XYPlot", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "24eGIUSM86l-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -2156,9 +2545,9 @@ Object { "trackId": "24eGIUSM86l", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2166,15 +2555,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "Density", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "density", "displayId": "oMVFQozR9NO_density", "type": "LinearWiggleDisplay", @@ -2184,9 +2573,9 @@ Object { "trackId": "oMVFQozR9NO", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2194,15 +2583,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "XYPlot", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "1at1sLO1Gsl-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -2211,9 +2600,9 @@ Object { "trackId": "1at1sLO1Gsl", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2221,15 +2610,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "Line", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "line", "displayId": "wiggle_track_posneg_line", "type": "LinearWiggleDisplay", @@ -2239,9 +2628,9 @@ Object { "trackId": "wiggle_track_posneg", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2249,15 +2638,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "Line", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "line", "displayId": "wiggle_track_fractional_posneg_line", "type": "LinearWiggleDisplay", @@ -2267,9 +2656,9 @@ Object { "trackId": "wiggle_track_fractional_posneg", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2277,15 +2666,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "XYPlot", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "jdYHuGnpAc_-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -2294,9 +2683,9 @@ Object { "trackId": "jdYHuGnpAc_", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2304,15 +2693,15 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", "Line", ], - "displays": Array [ - Object { + "displays": [ + { "defaultRendering": "line", "displayId": "p7FU-K6WqS__line", "type": "LinearWiggleDisplay", @@ -2322,9 +2711,9 @@ Object { "trackId": "p7FU-K6WqS_", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2332,14 +2721,14 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "BigWig", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "pOOtg9wxcUC-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -2348,13 +2737,13 @@ Object { "trackId": "pOOtg9wxcUC", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "assemblyNames": Array [ + { + "adapter": { + "assemblyNames": [ "volvox", "volvox", ], - "pafLocation": Object { + "pafLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2362,35 +2751,42 @@ Object { }, "type": "PAFAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", "volvox", ], - "displays": Array [ - Object { + "category": [ + "Synteny", + ], + "displays": [ + { "displayId": "volvox_fake_synteny_alt-DotplotDisplay", "type": "DotplotDisplay", }, - Object { + { "displayId": "volvox_fake_synteny_alt-LinearComparativeDisplay", "type": "LinearComparativeDisplay", }, - Object { + { "displayId": "volvox_fake_synteny_alt-LinearSyntenyDisplay", "type": "LinearSyntenyDisplay", }, + { + "displayId": "volvox_fake_synteny_alt-LGVSyntenyDisplay", + "type": "LGVSyntenyDisplay", + }, ], "name": "volvox_fake_synteny_alt", "trackId": "volvox_fake_synteny_alt", "type": "SyntenyTrack", }, - Object { - "adapter": Object { - "assemblyNames": Array [ + { + "adapter": { + "assemblyNames": [ "volvox", "volvox", ], - "pafLocation": Object { + "pafLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2398,46 +2794,53 @@ Object { }, "type": "PAFAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", "volvox", ], - "displays": Array [ - Object { + "category": [ + "Synteny", + ], + "displays": [ + { "displayId": "volvox_fake_synteny-DotplotDisplay", "type": "DotplotDisplay", }, - Object { + { "displayId": "volvox_fake_synteny-LinearComparativeDisplay", "type": "LinearComparativeDisplay", }, - Object { + { "displayId": "volvox_fake_synteny-LinearSyntenyDisplay", "type": "LinearSyntenyDisplay", }, + { + "displayId": "volvox_fake_synteny-LGVSyntenyDisplay", + "type": "LGVSyntenyDisplay", + }, ], "name": "volvox_fake_synteny", "trackId": "volvox_fake_synteny", "type": "SyntenyTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-rg.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-rg.bam.bai", }, }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -2445,46 +2848,54 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox-rg-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox-rg-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox-rg-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox-rg-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-rg-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-rg (read groups, bam)", "trackId": "volvox-rg", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-rg.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox-rg.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -2492,33 +2903,41 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox-rg-cram-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "volvox-rg-cram-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "volvox-rg-cram-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "volvox-rg-cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-rg-cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-rg (read groups, cram)", "trackId": "volvox-rg-cram", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bigWigLocation": Object { + { + "adapter": { + "bigWigLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2526,14 +2945,14 @@ Object { }, "type": "BigWigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "wombat", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_wrong_assembly-LinearWiggleDisplay", "type": "LinearWiggleDisplay", }, @@ -2542,10 +2961,10 @@ Object { "trackId": "volvox_wrong_assembly", "type": "QuantitativeTrack", }, - Object { - "adapter": Object { - "index": Object { - "location": Object { + { + "adapter": { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2553,28 +2972,28 @@ Object { }, }, "type": "VcfTabixAdapter", - "vcfGzLocation": Object { + "vcfGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.filtered.vcf.gz", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox_filtered_vcf_color-ChordVariantDisplay", "type": "ChordVariantDisplay", }, - Object { + { "displayId": "volvox_filtered_vcf_color-LinearVariantDisplay", "maxFeatureScreenDensity": 0.0006, - "renderer": Object { + "renderer": { "color1": "jexl:get(feature,'type')=='SNV'?'green':'purple'", "type": "SvgFeatureRenderer", }, @@ -2585,24 +3004,24 @@ Object { "trackId": "variant_colors", "type": "VariantTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-chebi-volvox.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-chebi-volvox.bam.bai", }, }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -2610,48 +3029,56 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Methylation", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "MM-chebi-volvox-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "MM-chebi-volvox-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "MM-chebi-volvox-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "MM-chebi-volvox-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "MM-chebi-volvox-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "MM-chebi-volvox", "trackId": "MM-chebi-volvox", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-double-volvox.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-double-volvox.bam.bai", }, }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -2659,48 +3086,56 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Methylation", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "MM-double-volvox-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "MM-double-volvox-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "MM-double-volvox-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "MM-double-volvox-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "MM-double-volvox-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "MM-double-volvox", "trackId": "MM-double-volvox", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-multi-volvox.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-multi-volvox.bam.bai", }, }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -2708,48 +3143,56 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Methylation", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "MM-multi-volvox-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "MM-multi-volvox-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "MM-multi-volvox-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "MM-multi-volvox-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "MM-multi-volvox-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "MM-multi-volvox", "trackId": "MM-multi-volvox", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-orient-volvox.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "MM-orient-volvox.bam.bai", }, }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -2757,40 +3200,48 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Methylation", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "MM-orient-volvox-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "MM-orient-volvox-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "MM-orient-volvox-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "MM-orient-volvox-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "MM-orient-volvox-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "MM-orient-volvox", "trackId": "MM-orient-volvox", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { - "gffGzLocation": Object { + { + "adapter": { + "gffGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "single_exon_gene.sorted.gff.gz", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2799,18 +3250,18 @@ Object { }, "type": "Gff3TabixAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "single_exon_gene-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "single_exon_gene-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -2819,9 +3270,9 @@ Object { "trackId": "single_exon_gene", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "gtfLocation": Object { + { + "adapter": { + "gtfLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2829,35 +3280,35 @@ Object { }, "type": "GtfAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "gtf_plain_text_test-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "gtf_plain_text_test-LinearArcDisplay", "type": "LinearArcDisplay", }, ], "name": "GTF - volvox.sorted.gtf", - "textSearching": Object { - "indexingAttributes": Array [ + "textSearching": { + "indexingAttributes": [ "gene_id", ], }, "trackId": "gtf_plain_text_test", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "index": Object { - "location": Object { + { + "adapter": { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -2865,25 +3316,25 @@ Object { }, }, "type": "VcfTabixAdapter", - "vcfGzLocation": Object { + "vcfGzLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.inv.vcf.gz", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox.inv.vcf-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "volvox.inv.vcf-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -2892,22 +3343,22 @@ Object { "trackId": "volvox.inv.vcf", "type": "VariantTrack", }, - Object { - "adapter": Object { - "craiLocation": Object { + { + "adapter": { + "craiLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "deep_sequencing.cram.crai", }, - "cramLocation": Object { + "cramLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "deep_sequencing.cram", }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -2915,19 +3366,19 @@ Object { }, "type": "CramAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "deep_seq_alignments", - "pileupDisplay": Object { + "pileupDisplay": { "displayId": "deep_seq_pileup", - "renderers": Object { - "PileupRenderer": Object { + "renderers": { + "PileupRenderer": { "maxHeight": 10000, "type": "PileupRenderer", }, @@ -2936,24 +3387,32 @@ Object { }, "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "Deep sequencing-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "Deep sequencing-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "Deep sequencing-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "Deep sequencing-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "Deep sequencing", "trackId": "Deep sequencing", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { + { + "adapter": { "adapterId": "Y4yJ6gAC2E", - "features": Array [ - Object { + "features": [ + { "end": 200, "name": "SE_001", "refName": "ctgA", @@ -2962,7 +3421,7 @@ Object { "type": "foo", "uniqueId": "arc-one", }, - Object { + { "end": 192, "name": "SE_002", "refName": "ctgA", @@ -2971,7 +3430,7 @@ Object { "type": "bar", "uniqueId": "arc-two", }, - Object { + { "end": 290, "name": "SE_003", "refName": "ctgA", @@ -2980,7 +3439,7 @@ Object { "type": "baz", "uniqueId": "arc-three", }, - Object { + { "end": 189, "name": "SE_004, and some other characters that make the name extra long", "refName": "ctgA", @@ -2992,18 +3451,18 @@ Object { ], "type": "FromConfigAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Miscellaneous", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "arc_track_linear", "type": "LinearArcDisplay", }, - Object { + { "displayId": "arc_track-LinearBasicDisplay", "type": "LinearBasicDisplay", }, @@ -3012,24 +3471,24 @@ Object { "trackId": "arc_track", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "bamLocation": Object { + { + "adapter": { + "bamLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "spliced.bam", }, - "index": Object { - "location": Object { + "index": { + "location": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "spliced.bam.bai", }, }, - "sequenceAdapter": Object { - "twoBitLocation": Object { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", "uri": "volvox.2bit", }, @@ -3037,52 +3496,60 @@ Object { }, "type": "BamAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Alignments", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "spliced-LinearAlignmentsDisplay", "type": "LinearAlignmentsDisplay", }, - Object { + { "displayId": "spliced-LinearPileupDisplay", "type": "LinearPileupDisplay", }, - Object { + { "displayId": "spliced-LinearSNPCoverageDisplay", "type": "LinearSNPCoverageDisplay", }, + { + "displayId": "spliced-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "spliced-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, ], "name": "volvox-rnaseq demo", "trackId": "spliced", "type": "AlignmentsTrack", }, - Object { - "adapter": Object { + { + "adapter": { "type": "VcfAdapter", - "vcfLocation": Object { + "vcfLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox.filtered.lowercase.vcf", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "Integration test", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "volvox.filtered.lowercase-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "volvox.filtered.lowercase-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -3091,9 +3558,9 @@ Object { "trackId": "volvox.filtered.lowercase", "type": "FeatureTrack", }, - Object { - "adapter": Object { - "pafLocation": Object { + { + "adapter": { + "pafLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -3103,50 +3570,98 @@ Object { "targetAssembly": "volvox", "type": "PAFAdapter", }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", "volvox_del", ], - "displays": Array [ - Object { + "category": [ + "Synteny", + ], + "displays": [ + { "displayId": "volvox_del.paf-1658813720770-DotplotDisplay", "type": "DotplotDisplay", }, - Object { + { "displayId": "volvox_del.paf-1658813720770-LinearComparativeDisplay", "type": "LinearComparativeDisplay", }, - Object { + { "displayId": "volvox_del.paf-1658813720770-LinearSyntenyDisplay", "type": "LinearSyntenyDisplay", }, + { + "displayId": "volvox_del.paf-1658813720770-LGVSyntenyDisplay", + "type": "LGVSyntenyDisplay", + }, ], "name": "volvox_del.paf", "trackId": "volvox_del.paf-1658813720770", "type": "SyntenyTrack", }, - Object { - "adapter": Object { + { + "adapter": { + "pafLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox_ins.paf", + }, + "queryAssembly": "volvox_ins", + "targetAssembly": "volvox", + "type": "PAFAdapter", + }, + "assemblyNames": [ + "volvox", + "volvox_ins", + ], + "category": [ + "Synteny", + ], + "displays": [ + { + "displayId": "volvox_ins.paf-1658813720770-DotplotDisplay", + "type": "DotplotDisplay", + }, + { + "displayId": "volvox_ins.paf-1658813720770-LinearComparativeDisplay", + "type": "LinearComparativeDisplay", + }, + { + "displayId": "volvox_ins.paf-1658813720770-LinearSyntenyDisplay", + "type": "LinearSyntenyDisplay", + }, + { + "displayId": "volvox_ins.paf-1658813720770-LGVSyntenyDisplay", + "type": "LGVSyntenyDisplay", + }, + ], + "name": "volvox_ins.paf", + "trackId": "volvox_ins.paf-1658813720770", + "type": "SyntenyTrack", + }, + { + "adapter": { "type": "VcfAdapter", - "vcfLocation": Object { + "vcfLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "variant_effect_demo_data.vcf", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "variant_effect_demo_data-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "variant_effect_demo_data-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -3155,28 +3670,28 @@ Object { "trackId": "variant_effect_demo_data", "type": "VariantTrack", }, - Object { - "adapter": Object { + { + "adapter": { "type": "VcfAdapter", - "vcfLocation": Object { + "vcfLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", "uri": "volvox_vcf_jannovar.vcf", }, }, - "assemblyNames": Array [ + "assemblyNames": [ "volvox", ], - "category": Array [ + "category": [ "VCF", ], - "displays": Array [ - Object { + "displays": [ + { "displayId": "variant_effect_demo_jannovar-LinearVariantDisplay", "type": "LinearVariantDisplay", }, - Object { + { "displayId": "variant_effect_demo_jannovar-ChordVariantDisplay", "type": "ChordVariantDisplay", }, @@ -3185,6 +3700,343 @@ Object { "trackId": "variant_effect_demo_jannovar", "type": "VariantTrack", }, + { + "adapter": { + "assemblyNames": [ + "volvox-rev-del", + "volvox", + ], + "pafLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-rev-del.paf", + }, + "type": "PAFAdapter", + }, + "assemblyNames": [ + "volvox-rev-del", + "volvox", + ], + "category": [ + "Synteny", + ], + "displays": [ + { + "displayId": "volvox-rev-del-DotplotDisplay", + "type": "DotplotDisplay", + }, + { + "displayId": "volvox-rev-del-LinearComparativeDisplay", + "type": "LinearComparativeDisplay", + }, + { + "displayId": "volvox-rev-del-LinearSyntenyDisplay", + "type": "LinearSyntenyDisplay", + }, + { + "displayId": "volvox-rev-del-LGVSyntenyDisplay", + "type": "LGVSyntenyDisplay", + }, + ], + "name": "volvox-rev-del", + "trackId": "volvox-rev-del", + "type": "SyntenyTrack", + }, + { + "adapter": { + "gffLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-rev-del.gff", + }, + "type": "Gff3Adapter", + }, + "assemblyNames": [ + "volvox-rev-del", + ], + "displays": [ + { + "displayId": "volvox-rev-del-annotations-LinearBasicDisplay", + "type": "LinearBasicDisplay", + }, + { + "displayId": "volvox-rev-del-annotations-LinearArcDisplay", + "type": "LinearArcDisplay", + }, + ], + "name": "volvox-rev-del-annotations", + "trackId": "volvox-rev-del-annotations", + "type": "FeatureTrack", + }, + { + "adapter": { + "bamLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv.bam", + }, + "index": { + "location": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv.bam.bai", + }, + }, + "sequenceAdapter": { + "twoBitLocation": { + "locationType": "UriLocation", + "uri": "volvox.2bit", + }, + "type": "TwoBitAdapter", + }, + "type": "BamAdapter", + }, + "assemblyNames": [ + "volvox", + ], + "category": [ + "Alignments", + ], + "displays": [ + { + "displayId": "volvox-simple-inv.bam-LinearAlignmentsDisplay", + "type": "LinearAlignmentsDisplay", + }, + { + "displayId": "volvox-simple-inv.bam-LinearPileupDisplay", + "type": "LinearPileupDisplay", + }, + { + "displayId": "volvox-simple-inv.bam-LinearSNPCoverageDisplay", + "type": "LinearSNPCoverageDisplay", + }, + { + "displayId": "volvox-simple-inv.bam-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-simple-inv.bam-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, + ], + "name": "volvox-simple-inv.bam", + "trackId": "volvox-simple-inv.bam", + "type": "AlignmentsTrack", + }, + { + "adapter": { + "craiLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv.cram.crai", + }, + "cramLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv.cram", + }, + "sequenceAdapter": { + "twoBitLocation": { + "locationType": "UriLocation", + "uri": "volvox.2bit", + }, + "type": "TwoBitAdapter", + }, + "type": "CramAdapter", + }, + "assemblyNames": [ + "volvox", + ], + "category": [ + "Alignments", + ], + "displays": [ + { + "displayId": "volvox-simple-inv.cram-LinearAlignmentsDisplay", + "type": "LinearAlignmentsDisplay", + }, + { + "displayId": "volvox-simple-inv.cram-LinearPileupDisplay", + "type": "LinearPileupDisplay", + }, + { + "displayId": "volvox-simple-inv.cram-LinearSNPCoverageDisplay", + "type": "LinearSNPCoverageDisplay", + }, + { + "displayId": "volvox-simple-inv.cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-simple-inv.cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, + ], + "name": "volvox-simple-inv.cram", + "trackId": "volvox-simple-inv.cram", + "type": "AlignmentsTrack", + }, + { + "adapter": { + "craiLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv-paired.cram.crai", + }, + "cramLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv-paired.cram", + }, + "sequenceAdapter": { + "twoBitLocation": { + "locationType": "UriLocation", + "uri": "volvox.2bit", + }, + "type": "TwoBitAdapter", + }, + "type": "CramAdapter", + }, + "assemblyNames": [ + "volvox", + ], + "category": [ + "Alignments", + ], + "displays": [ + { + "displayId": "volvox-simple-inv-paired.cram-LinearAlignmentsDisplay", + "type": "LinearAlignmentsDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.cram-LinearPileupDisplay", + "type": "LinearPileupDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.cram-LinearSNPCoverageDisplay", + "type": "LinearSNPCoverageDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.cram-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.cram-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, + ], + "name": "volvox-simple-inv-paired.cram", + "trackId": "volvox-simple-inv-paired.cram", + "type": "AlignmentsTrack", + }, + { + "adapter": { + "bamLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv-paired.bam", + }, + "index": { + "location": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox-simple-inv-paired.bam.bai", + }, + }, + "sequenceAdapter": { + "twoBitLocation": { + "locationType": "UriLocation", + "uri": "volvox.2bit", + }, + "type": "TwoBitAdapter", + }, + "type": "BamAdapter", + }, + "assemblyNames": [ + "volvox", + ], + "category": [ + "Alignments", + ], + "displays": [ + { + "displayId": "volvox-simple-inv-paired.bam-LinearAlignmentsDisplay", + "type": "LinearAlignmentsDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.bam-LinearPileupDisplay", + "type": "LinearPileupDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.bam-LinearSNPCoverageDisplay", + "type": "LinearSNPCoverageDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.bam-LinearReadArcsDisplay", + "type": "LinearReadArcsDisplay", + }, + { + "displayId": "volvox-simple-inv-paired.bam-LinearReadCloudDisplay", + "type": "LinearReadCloudDisplay", + }, + ], + "name": "volvox-simple-inv-paired.bam", + "trackId": "volvox-simple-inv-paired.bam", + "type": "AlignmentsTrack", + }, + { + "adapter": { + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "pafLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox_inv_indels.paf", + }, + "type": "PAFAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "category": [ + "Synteny", + ], + "displays": [ + { + "displayId": "volvox_inv_indels-DotplotDisplay", + "type": "DotplotDisplay", + }, + { + "displayId": "volvox_inv_indels-LinearComparativeDisplay", + "type": "LinearComparativeDisplay", + }, + { + "displayId": "volvox_inv_indels-LinearSyntenyDisplay", + "type": "LinearSyntenyDisplay", + }, + { + "displayId": "volvox_inv_indels-LGVSyntenyDisplay", + "type": "LGVSyntenyDisplay", + }, + ], + "name": "volvox_inv_indels", + "trackId": "volvox_inv_indels", + "type": "SyntenyTrack", + }, ], } `; diff --git a/products/jbrowse-web/src/__snapshots__/rootModel.test.js.snap b/products/jbrowse-web/src/__snapshots__/rootModel.test.js.snap index ef16325af4..bb5e662c01 100644 --- a/products/jbrowse-web/src/__snapshots__/rootModel.test.js.snap +++ b/products/jbrowse-web/src/__snapshots__/rootModel.test.js.snap @@ -1,15 +1,15 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`Root MST model adds menus 1`] = ` -Array [ - Object { +[ + { "label": "File", - "menuItems": Array [ - Object { - "icon": Object { + "menuItems": [ + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -17,11 +17,11 @@ Array [ "label": "New session", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -29,11 +29,11 @@ Array [ "label": "Import session…", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -41,11 +41,11 @@ Array [ "label": "Export session", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -53,11 +53,11 @@ Array [ "label": "Open session…", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -65,11 +65,11 @@ Array [ "label": "Save session", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -77,14 +77,14 @@ Array [ "label": "Duplicate session", "onClick": [Function], }, - Object { + { "type": "divider", }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -92,19 +92,19 @@ Array [ "label": "Open track...", "onClick": [Function], }, - Object { + { "icon": [Function], "label": "Open connection...", "onClick": [Function], }, - Object { + { "type": "divider", }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -114,19 +114,18 @@ Array [ }, ], }, - Object { + { "label": "Add", - "menuItems": Array [], + "menuItems": [], }, - Object { + { "label": "Tools", - "menuItems": Array [ - Object { - "disabled": false, - "icon": Object { + "menuItems": [ + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -134,12 +133,11 @@ Array [ "label": "Undo", "onClick": [Function], }, - Object { - "disabled": false, - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -147,14 +145,14 @@ Array [ "label": "Redo", "onClick": [Function], }, - Object { + { "type": "divider", }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -168,15 +166,15 @@ Array [ `; exports[`Root MST model adds menus 2`] = ` -Array [ - Object { +[ + { "label": "File", - "menuItems": Array [ - Object { - "icon": Object { + "menuItems": [ + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -184,11 +182,11 @@ Array [ "label": "New session", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -196,11 +194,11 @@ Array [ "label": "Import session…", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -208,11 +206,11 @@ Array [ "label": "Export session", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -220,11 +218,11 @@ Array [ "label": "Open session…", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -232,11 +230,11 @@ Array [ "label": "Save session", "onClick": [Function], }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -244,14 +242,14 @@ Array [ "label": "Duplicate session", "onClick": [Function], }, - Object { + { "type": "divider", }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -259,19 +257,19 @@ Array [ "label": "Open track...", "onClick": [Function], }, - Object { + { "icon": [Function], "label": "Open connection...", "onClick": [Function], }, - Object { + { "type": "divider", }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -281,19 +279,18 @@ Array [ }, ], }, - Object { + { "label": "Add", - "menuItems": Array [], + "menuItems": [], }, - Object { + { "label": "Tools", - "menuItems": Array [ - Object { - "disabled": false, - "icon": Object { + "menuItems": [ + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -301,12 +298,11 @@ Array [ "label": "Undo", "onClick": [Function], }, - Object { - "disabled": false, - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -314,14 +310,14 @@ Array [ "label": "Redo", "onClick": [Function], }, - Object { + { "type": "divider", }, - Object { - "icon": Object { + { + "icon": { "$$typeof": Symbol(react.memo), "compare": null, - "type": Object { + "type": { "$$typeof": Symbol(react.forward_ref), "render": [Function], }, @@ -331,25 +327,25 @@ Array [ }, ], }, - Object { + { "label": "Second Menu", - "menuItems": Array [ - Object { + "menuItems": [ + { "label": "First Menu Item", "onClick": [Function], }, - Object { + { "label": "Second Menu Item", "onClick": [Function], }, - Object { + { "label": "First Sub Menu", - "subMenu": Array [ - Object { + "subMenu": [ + { "label": "First Sub Menu Item", "onClick": [Function], }, - Object { + { "label": "Second Sub Menu Item", "onClick": [Function], }, @@ -357,24 +353,24 @@ Array [ }, ], }, - Object { + { "label": "Third Menu", - "menuItems": Array [], + "menuItems": [], }, ] `; exports[`Root MST model adds track and connection configs to an assembly 1`] = ` -Object { - "aliases": Array [ +{ + "aliases": [ "assemblyA", ], "name": "assembly1", - "sequence": Object { - "adapter": Object { + "sequence": { + "adapter": { "adapterId": "sequenceConfigAdapterId", - "features": Array [ - Object { + "features": [ + { "end": 10, "refName": "ctgA", "seq": "cattgttgcg", @@ -384,11 +380,15 @@ Object { ], "type": "FromConfigSequenceAdapter", }, - "displays": Array [ - Object { + "displays": [ + { "displayId": "sequenceConfigId-LinearReferenceSequenceDisplay", "type": "LinearReferenceSequenceDisplay", }, + { + "displayId": "sequenceConfigId-LinearGCContentDisplay", + "type": "LinearGCContentDisplay", + }, ], "trackId": "sequenceConfigId", "type": "ReferenceSequenceTrack", @@ -397,13 +397,13 @@ Object { `; exports[`Root MST model adds track and connection configs to an assembly 2`] = ` -Object { - "displays": Array [ - Object { +{ + "displays": [ + { "displayId": "trackId0-LinearBasicDisplay", "type": "LinearBasicDisplay", }, - Object { + { "displayId": "trackId0-LinearArcDisplay", "type": "LinearArcDisplay", }, @@ -414,9 +414,9 @@ Object { `; exports[`Root MST model adds track and connection configs to an assembly 3`] = ` -Object { +{ "connectionId": "connectionId0", - "dataDirLocation": Object { + "dataDirLocation": { "internetAccountId": undefined, "internetAccountPreAuthorization": undefined, "locationType": "UriLocation", @@ -426,4 +426,4 @@ Object { } `; -exports[`Root MST model creates with defaults 1`] = `Object {}`; +exports[`Root MST model creates with defaults 1`] = `{}`; diff --git a/products/jbrowse-web/src/__snapshots__/sessionModelFactory.test.js.snap b/products/jbrowse-web/src/__snapshots__/sessionModelFactory.test.js.snap index a006d7e955..32615c7812 100644 --- a/products/jbrowse-web/src/__snapshots__/sessionModelFactory.test.js.snap +++ b/products/jbrowse-web/src/__snapshots__/sessionModelFactory.test.js.snap @@ -1,20 +1,20 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`JBrowseWebSessionModel creates with no parent and just a name 1`] = ` -Object { - "activeWidgets": Object {}, - "connectionInstances": Array [], +{ + "activeWidgets": {}, + "connectionInstances": [], "drawerPosition": "right", "drawerWidth": 384, "margin": 0, "minimized": false, "name": "testSession", - "sessionAssemblies": Array [], - "sessionConnections": Array [], - "sessionPlugins": Array [], - "sessionTracks": Array [], - "temporaryAssemblies": Array [], - "views": Array [], - "widgets": Object {}, + "sessionAssemblies": [], + "sessionConnections": [], + "sessionPlugins": [], + "sessionTracks": [], + "temporaryAssemblies": [], + "views": [], + "widgets": {}, } `; diff --git a/products/jbrowse-web/src/corePlugins.ts b/products/jbrowse-web/src/corePlugins.ts index 1afed6d6e6..788fcf19f8 100644 --- a/products/jbrowse-web/src/corePlugins.ts +++ b/products/jbrowse-web/src/corePlugins.ts @@ -19,9 +19,9 @@ import RDF from '@jbrowse/plugin-rdf' import Sequence from '@jbrowse/plugin-sequence' import SVG from '@jbrowse/plugin-svg' import Canvas from '@jbrowse/plugin-canvas' -import TrackHubRegistry from '@jbrowse/plugin-trackhub-registry' import Variants from '@jbrowse/plugin-variants' import Wiggle from '@jbrowse/plugin-wiggle' +import GCContent from '@jbrowse/plugin-gccontent' import SpreadsheetViewPlugin from '@jbrowse/plugin-spreadsheet-view' import SvInspectorPlugin from '@jbrowse/plugin-sv-inspector' import HicPlugin from '@jbrowse/plugin-hic' @@ -48,9 +48,9 @@ const corePlugins = [ Menus, RDF, Sequence, - TrackHubRegistry, Variants, Wiggle, + GCContent, SpreadsheetViewPlugin, SvInspectorPlugin, BreakpointSplitView, diff --git a/products/jbrowse-web/src/rootModel.ts b/products/jbrowse-web/src/rootModel.ts index 44fc962304..a7cea2a030 100644 --- a/products/jbrowse-web/src/rootModel.ts +++ b/products/jbrowse-web/src/rootModel.ts @@ -3,11 +3,9 @@ import { cast, getSnapshot, getType, - resolveIdentifier, types, IAnyStateTreeNode, SnapshotIn, - IAnyModelType, } from 'mobx-state-tree' import { saveAs } from 'file-saver' @@ -43,6 +41,7 @@ import corePlugins from './corePlugins' import jbrowseWebFactory from './jbrowseModel' import sessionModelFactory from './sessionModelFactory' import { filterSessionInPlace } from './util' +import { AnyConfigurationModel } from '@jbrowse/core/configuration' interface Menu { label: string @@ -157,7 +156,8 @@ export default function RootModel( ) { self.history.redo() } - } else if (self.history.canUndo) { + } + if (self.history.canUndo) { // ctrl+z or cmd+z if (cm && !e.shiftKey && e.code === 'KeyZ') { self.history.undo() @@ -241,7 +241,7 @@ export default function RootModel( self, autorun(() => { self.jbrowse.internetAccounts.forEach(account => { - this.initializeInternetAccount(account.internetAccountId) + this.initializeInternetAccount(account) }) }), ) @@ -261,28 +261,22 @@ export default function RootModel( } }, initializeInternetAccount( - internetAccountId: string, + internetAccountConfig: AnyConfigurationModel, initialSnapshot = {}, ) { - const internetAccountConfigSchema = - pluginManager.pluggableConfigSchemaType('internet account') - const configuration = resolveIdentifier( - internetAccountConfigSchema as IAnyModelType, - self, - internetAccountId, - ) - const internetAccountType = pluginManager.getInternetAccountType( - configuration.type, + internetAccountConfig.type, ) if (!internetAccountType) { - throw new Error(`unknown internet account type ${configuration.type}`) + throw new Error( + `unknown internet account type ${internetAccountConfig.type}`, + ) } const length = self.internetAccounts.push({ ...initialSnapshot, - type: configuration.type, - configuration, + type: internetAccountConfig.type, + configuration: internetAccountConfig, }) return self.internetAccounts[length - 1] }, @@ -568,18 +562,20 @@ export default function RootModel( menuItems: [ { label: 'Undo', - disabled: self.history.canUndo, icon: UndoIcon, onClick: () => { - self.history.undo() + if (self.history.canUndo) { + self.history.undo() + } }, }, { label: 'Redo', - disabled: self.history.canRedo, icon: RedoIcon, onClick: () => { - self.history.redo() + if (self.history.canRedo) { + self.history.redo() + } }, }, { type: 'divider' }, diff --git a/products/jbrowse-web/src/sessionModelFactory.ts b/products/jbrowse-web/src/sessionModelFactory.ts index 3dd9cf1830..6ed97612b9 100644 --- a/products/jbrowse-web/src/sessionModelFactory.ts +++ b/products/jbrowse-web/src/sessionModelFactory.ts @@ -64,6 +64,7 @@ type AnyConfiguration = /** * #stateModel JBrowseWebSessionModel + * inherits SnackbarModel */ export default function sessionModelFactory( pluginManager: PluginManager, @@ -343,6 +344,33 @@ export default function sessionModelFactory( }, })) .actions(self => ({ + /** + * #action + */ + moveViewUp(id: string) { + const idx = self.views.findIndex(v => v.id === id) + + if (idx === -1) { + return + } + if (idx > 0) { + self.views.splice(idx - 1, 2, self.views[idx], self.views[idx - 1]) + } + }, + /** + * #action + */ + moveViewDown(id: string) { + const idx = self.views.findIndex(v => v.id === id) + + if (idx === -1) { + return + } + + if (idx < self.views.length - 1) { + self.views.splice(idx, 2, self.views[idx + 1], self.views[idx]) + } + }, /** * #action */ diff --git a/products/jbrowse-web/src/tests/AdminComponent.test.tsx b/products/jbrowse-web/src/tests/AdminComponent.test.tsx index 4db64e3c74..a5effd625d 100644 --- a/products/jbrowse-web/src/tests/AdminComponent.test.tsx +++ b/products/jbrowse-web/src/tests/AdminComponent.test.tsx @@ -2,10 +2,8 @@ import React from 'react' import { render } from '@testing-library/react' import { JBrowse, getPluginManager } from './util' -describe('', () => { - it('renders when in admin mode', async () => { - const pluginManager = getPluginManager({}, true) - const { findByText } = render() - expect(await findByText('Admin')).toBeTruthy() - }) +test('renders when in admin mode', async () => { + const pluginManager = getPluginManager({}, true) + const { findByText } = render() + expect(await findByText('Admin')).toBeTruthy() }) diff --git a/products/jbrowse-web/src/tests/Alignments.test.tsx b/products/jbrowse-web/src/tests/Alignments.test.tsx index 8d24abd83f..13704dce5a 100644 --- a/products/jbrowse-web/src/tests/Alignments.test.tsx +++ b/products/jbrowse-web/src/tests/Alignments.test.tsx @@ -17,24 +17,25 @@ beforeEach(() => { }) const delay = { timeout: 20000 } +const opts = [{}, delay] test('opens an alignments track', async () => { const { view, findByTestId, findByText, findAllByTestId } = createView() await findByText('Help') view.setNewView(5, 100) fireEvent.click( - await findByTestId(hts('volvox_alignments_pileup_coverage'), {}, delay), + await findByTestId(hts('volvox_alignments_pileup_coverage'), ...opts), ) const { findByTestId: f1 } = within( - await findByTestId('Blockset-pileup', {}, delay), + await findByTestId('Blockset-pileup', ...opts), ) - expectCanvasMatch(await f1(pc('{volvox}ctgA:1..4,000-0'), {}, delay)) + expectCanvasMatch(await f1(pc('{volvox}ctgA:1..4000-0'), ...opts)) const { findByTestId: f2 } = within( - await findByTestId('Blockset-snpcoverage', {}, delay), + await findByTestId('Blockset-snpcoverage', ...opts), ) - expectCanvasMatch(await f2(pc('{volvox}ctgA:1..4,000-0'), {}, delay)) + expectCanvasMatch(await f2(pc('{volvox}ctgA:1..4000-0'), ...opts)) const track = await findAllByTestId('pileup_overlay_canvas') fireEvent.mouseMove(track[0], { clientX: 200, clientY: 20 }) @@ -45,29 +46,27 @@ test('opens an alignments track', async () => { fireEvent.mouseMove(track[0], { clientX: -100, clientY: -100 }) // this is to confirm a alignment detail widget opened - await findByTestId('alignment-side-drawer') + await findByTestId('alignment-side-drawer', ...opts) }, 20000) test('test that bam with small max height displays message', async () => { const { findByTestId, findAllByText } = createView() fireEvent.click( - await findByTestId(hts('volvox_bam_small_max_height'), {}, delay), + await findByTestId(hts('volvox_bam_small_max_height'), ...opts), ) - await findAllByText('Max height reached', {}, delay) + await findAllByText('Max height reached', ...opts) }, 30000) test('test snpcoverage doesnt count snpcoverage', async () => { const { view, findByTestId, findByText } = createView() await findByText('Help') view.setNewView(0.03932, 67884.16536402702) - fireEvent.click( - await findByTestId(hts('volvox-long-reads-sv-cram'), {}, delay), - ) + fireEvent.click(await findByTestId(hts('volvox-long-reads-sv-cram'), ...opts)) const { findByTestId: f1 } = within( - await findByTestId('Blockset-snpcoverage', {}, delay), + await findByTestId('Blockset-snpcoverage', ...opts), ) - expectCanvasMatch(await f1(pc('{volvox}ctgA:2,657..2,688-0'), {}, delay)) - expectCanvasMatch(await f1(pc('{volvox}ctgA:2,689..2,720-0'), {}, delay)) + expectCanvasMatch(await f1(pc('{volvox}ctgA:2657..2688-0'), ...opts)) + expectCanvasMatch(await f1(pc('{volvox}ctgA:2689..2720-0'), ...opts)) }, 30000) diff --git a/products/jbrowse-web/src/tests/AlignmentsFeatures.test.tsx b/products/jbrowse-web/src/tests/AlignmentsFeatures.test.tsx index bd28c02663..2064245fb8 100644 --- a/products/jbrowse-web/src/tests/AlignmentsFeatures.test.tsx +++ b/products/jbrowse-web/src/tests/AlignmentsFeatures.test.tsx @@ -17,98 +17,64 @@ beforeEach(() => { }) const delay = { timeout: 20000 } +const opts = [{}, delay] test('opens the track menu and enables soft clipping', async () => { - console.error = jest.fn() const { view, findByTestId, findByText } = createView() await findByText('Help') view.setNewView(0.02, 142956) // load track - fireEvent.click( - await findByTestId(hts('volvox-long-reads-sv-bam'), {}, delay), - ) - await findByTestId( - 'display-volvox-long-reads-sv-bam-LinearAlignmentsDisplay', - {}, - delay, - ) - expect(view.tracks[0]).toBeTruthy() + fireEvent.click(await findByTestId(hts('volvox-long-reads-sv-bam'), ...opts)) // opens the track menu - fireEvent.click(await findByTestId('track_menu_icon')) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) fireEvent.click(await findByText('Show soft clipping')) // wait for block to rerender const { findByTestId: f0 } = within(await findByTestId('Blockset-pileup')) + // slightly higher threshold for fonts expectCanvasMatch( - await f0(pc('softclipped_{volvox}ctgA:2,849..2,864-0'), {}, delay), + await f0(pc('softclipped_{volvox}ctgA:2849..2864-0'), ...opts), + 0.05, ) }, 30000) -test('selects a sort, sort by strand', async () => { - console.error = jest.fn() +test('selects a sort, sort by base pair', async () => { const { view, findByTestId, findByText, findAllByTestId } = createView() await findByText('Help') - view.setNewView(0.02, 2086500) + view.setNewView(0.043688891869634636, 301762) + const track = 'volvox_cram_alignments_ctga' // load track - fireEvent.click(await findByTestId(hts('volvox-long-reads-cram'), {}, delay)) - await findByTestId( - 'display-volvox-long-reads-cram-LinearAlignmentsDisplay', - {}, - delay, - ) - expect(view.tracks[0]).toBeTruthy() + fireEvent.click(await findByTestId(hts(track), ...opts)) - fireEvent.click(await findByTestId('track_menu_icon')) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) fireEvent.click(await findByText('Sort by')) - fireEvent.click(await findByText('Read strand')) + fireEvent.click(await findByText('Base pair')) // wait for pileup track to render with sort - await findAllByTestId('pileup-Read strand', {}, delay) + await findAllByTestId('pileup-Base pair', ...opts) const { findByTestId: find1 } = within(await findByTestId('Blockset-pileup')) - expectCanvasMatch(await find1(pc('{volvox}ctgA:41,729..41,744-0'), {}, delay)) -}, 35000) + expectCanvasMatch(await find1(pc('{volvox}ctgA:13196..13230-0'), ...opts)) -test('color by strand', async () => { - console.error = jest.fn() - const { view, findByTestId, findByText, findAllByTestId } = createView() - await findByText('Help') - view.setNewView(0.02, 2086500) - - // load track - fireEvent.click(await findByTestId(hts('volvox-long-reads-cram'), {}, delay)) - await findByTestId( - 'display-volvox-long-reads-cram-LinearAlignmentsDisplay', - {}, - delay, - ) - - fireEvent.click(await findByTestId('track_menu_icon')) - fireEvent.click(await findByText('Color scheme')) - fireEvent.click(await findByText('Strand')) - - // wait for pileup track to render with color - await findAllByTestId('pileup-strand', {}, delay) - const { findByTestId: find1 } = within(await findByTestId('Blockset-pileup')) - expectCanvasMatch(await find1(pc('{volvox}ctgA:41,729..41,744-0'), {}, delay)) -}, 30000) + fireEvent.click(await findByTestId('zoom_out')) + await findAllByTestId('pileup-Base pair', ...opts) + const { findByTestId: find2 } = within(await findByTestId('Blockset-pileup')) + expectCanvasMatch(await find2(pc('{volvox}ctgA:13161..13230-0'), ...opts)) +}, 35000) test('color by tag', async () => { - console.error = jest.fn() const { view, findByTestId, findByText, findAllByTestId } = createView() await findByText('Help') view.setNewView(0.465, 85055) // load track - fireEvent.click(await findByTestId(hts('volvox_cram'), {}, delay)) - await findByTestId('display-volvox_cram-LinearAlignmentsDisplay', {}, delay) - expect(view.tracks[0]).toBeTruthy() + fireEvent.click(await findByTestId(hts('volvox_cram'), ...opts)) // colors by HP tag - fireEvent.click(await findByTestId('track_menu_icon')) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) fireEvent.click(await findByText('Color scheme')) fireEvent.click(await findByText('Color by tag...')) fireEvent.change(await findByTestId('color-tag-name-input'), { @@ -116,7 +82,79 @@ test('color by tag', async () => { }) fireEvent.click(await findByText('Submit')) // wait for pileup track to render with color - await findAllByTestId('pileup-tagHP', {}, delay) + await findAllByTestId('pileup-tagHP', ...opts) const { findByTestId: find1 } = within(await findByTestId('Blockset-pileup')) - expectCanvasMatch(await find1(pc('{volvox}ctgA:39,805..40,176-0'), {}, delay)) + expectCanvasMatch(await find1(pc('{volvox}ctgA:39805..40176-0'), ...opts)) +}, 30000) + +test('toggle short-read arc display', async () => { + console.warn = jest.fn() + const { view, findByTestId, findAllByText, findByText } = createView() + await findByText('Help') + await view.navToLocString('ctgA:1-50000') + fireEvent.click(await findByTestId(hts('volvox_sv_cram'), ...opts)) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Replace lower panel with...')) + fireEvent.click((await findAllByText('Arc display'))[0]) + expectCanvasMatch(await findByTestId('Arc-display-true', ...opts)) +}, 30000) + +test('toggle short-read cloud display', async () => { + console.warn = jest.fn() + const { view, findByTestId, findAllByText, findByText } = createView() + await findByText('Help') + await view.navToLocString('ctgA:1-50000') + fireEvent.click(await findByTestId(hts('volvox_sv_cram'), ...opts)) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Replace lower panel with...')) + fireEvent.click((await findAllByText('Read cloud display'))[0]) + expectCanvasMatch(await findByTestId('ReadCloud-display-true', ...opts)) +}, 30000) + +test('toggle long-read cloud display', async () => { + console.warn = jest.fn() + const { view, findByTestId, findAllByText, findByText } = createView() + await findByText('Help') + await view.navToLocString('ctgA:19,101..32,027') + fireEvent.click(await findByTestId(hts('volvox-simple-inv.bam'), ...opts)) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Replace lower panel with...')) + fireEvent.click((await findAllByText('Read cloud display'))[0]) + expectCanvasMatch(await findByTestId('ReadCloud-display-true', ...opts)) +}, 30000) + +test('toggle long-read arc display', async () => { + console.warn = jest.fn() + const { view, findByTestId, findAllByText, findByText } = createView() + await findByText('Help') + await view.navToLocString('ctgA:19,101..32,027') + fireEvent.click(await findByTestId(hts('volvox-simple-inv.bam'), ...opts)) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Replace lower panel with...')) + fireEvent.click((await findAllByText('Arc display'))[0]) + expectCanvasMatch(await findByTestId('Arc-display-true', ...opts)) +}, 30000) + +test('toggle long-read arc display, use out of view pairing', async () => { + console.warn = jest.fn() + const { view, findByTestId, findAllByText, findByText } = createView() + await findByText('Help') + await view.navToLocString('ctgA:478..6,191') + fireEvent.click(await findByTestId(hts('volvox-long-reads-sv-cram'), ...opts)) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Replace lower panel with...')) + fireEvent.click((await findAllByText('Arc display'))[0]) + expectCanvasMatch(await findByTestId('Arc-display-true', ...opts)) +}, 30000) + +test('toggle short-read arc display, use out of view pairing', async () => { + console.warn = jest.fn() + const { view, findByTestId, findAllByText, findByText } = createView() + await findByText('Help') + await view.navToLocString('ctgA:478..6,191') + fireEvent.click(await findByTestId(hts('volvox_sv_cram'), ...opts)) + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Replace lower panel with...')) + fireEvent.click((await findAllByText('Arc display'))[0]) + expectCanvasMatch(await findByTestId('Arc-display-true', ...opts)) }, 30000) diff --git a/products/jbrowse-web/src/tests/AssemblySelectorImportForm.test.tsx b/products/jbrowse-web/src/tests/AssemblySelectorImportForm.test.tsx new file mode 100644 index 0000000000..9ec57fcf67 --- /dev/null +++ b/products/jbrowse-web/src/tests/AssemblySelectorImportForm.test.tsx @@ -0,0 +1,35 @@ +import { waitFor, fireEvent } from '@testing-library/react' + +// locals +import { setup, doSetupForImportForm, doBeforeEach } from './util' + +setup() + +beforeEach(() => { + doBeforeEach() +}) + +const delay = { timeout: 10000 } + +test('nav to volvox2', async () => { + const { getInputValue, findByText } = await doSetupForImportForm() + fireEvent.mouseDown(await findByText('volvox')) + fireEvent.click(await findByText('volvox2')) + await waitFor(() => expect(getInputValue()).toBe('ctgA')) + fireEvent.click(await findByText('Open')) + await waitFor(() => expect(getInputValue()).toBe('ctgA:1..50,001'), delay) +}, 30000) + +test('select volvox404', async () => { + const { findByText } = await doSetupForImportForm() + fireEvent.mouseDown(await findByText('volvox')) + fireEvent.click(await findByText('volvox404')) + await findByText(/HTTP 404/) +}, 30000) + +test('select misc', async () => { + const { getInputValue, findByText } = await doSetupForImportForm() + fireEvent.mouseDown(await findByText('volvox')) + fireEvent.click(await findByText('misc')) + await waitFor(() => expect(getInputValue()).toBe('t1')) +}, 30000) diff --git a/products/jbrowse-web/src/tests/Authentication.test.tsx b/products/jbrowse-web/src/tests/Authentication.test.tsx index bf08d234b6..f0d3ad0f67 100644 --- a/products/jbrowse-web/src/tests/Authentication.test.tsx +++ b/products/jbrowse-web/src/tests/Authentication.test.tsx @@ -59,9 +59,7 @@ test('open a bigwig track that needs oauth authentication and has existing token fireEvent.click( await findByTestId(hts('volvox_microarray_dropbox'), {}, delay), ) - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..4,000-0'), {}, delay), - ) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..4000-0'), {}, delay)) }, 25000) test('opens a bigwig track that needs external token authentication', async () => { @@ -109,9 +107,7 @@ test('opens a bigwig track that needs external token authentication', async () = expect(Object.keys(sessionStorage)).toContain('ExternalTokenTest-token') expect(Object.values(sessionStorage)).toContain('testentry') - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..4,000-0'), {}, delay), - ) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..4000-0'), {}, delay)) }, 25000) test('opens a bigwig track that needs httpbasic authentication', async () => { @@ -155,7 +151,5 @@ test('opens a bigwig track that needs httpbasic authentication', async () => { sessionStorage.getItem('HTTPBasicInternetAccount-HTTPBasicTest-token'), ).toContain(btoa(`username:password`)) - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..4,000-0'), {}, delay), - ) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..4000-0'), {}, delay)) }, 25000) diff --git a/products/jbrowse-web/src/tests/BasicLinearGenomeView.test.tsx b/products/jbrowse-web/src/tests/BasicLinearGenomeView.test.tsx index 7268268e4f..335b280e46 100644 --- a/products/jbrowse-web/src/tests/BasicLinearGenomeView.test.tsx +++ b/products/jbrowse-web/src/tests/BasicLinearGenomeView.test.tsx @@ -7,6 +7,7 @@ beforeEach(() => { }) const delay = { timeout: 20000 } +const opts = [{}, delay] test('access about menu', async () => { const { findByText, findAllByText } = createView() @@ -14,18 +15,18 @@ test('access about menu', async () => { fireEvent.click(await findByText('Help')) fireEvent.click(await findByText('About')) - await findByText(/The Evolutionary Software Foundation/, {}, delay) + await findByText(/The Evolutionary Software Foundation/, ...opts) // wait for ctgA because otherwise can give 'import a file after jest // environment has been torn down' - await findAllByText('ctgA', {}, delay) + await findAllByText('ctgA', ...opts) }, 30000) test('click and drag to move sideways', async () => { const { view, findByTestId, findAllByText } = createView() - await findAllByText('ctgA', {}, delay) + await findAllByText('ctgA', ...opts) const start = view.offsetPx - const track = await findByTestId('trackContainer', {}, delay) + const track = await findByTestId('trackContainer', ...opts) fireEvent.mouseDown(track, { clientX: 250, clientY: 20 }) fireEvent.mouseMove(track, { clientX: 100, clientY: 20 }) fireEvent.mouseUp(track, { clientX: 100, clientY: 20 }) @@ -34,7 +35,7 @@ test('click and drag to move sideways', async () => { test('click and drag to rubberband', async () => { const { view, findByTestId, findByText } = createView() - const track = await findByTestId('rubberBand_controls', {}, delay) + const track = await findByTestId('rubberband_controls', ...opts) expect(view.bpPerPx).toEqual(0.05) fireEvent.mouseDown(track, { clientX: 100, clientY: 0 }) fireEvent.mouseMove(track, { clientX: 250, clientY: 0 }) @@ -43,9 +44,9 @@ test('click and drag to rubberband', async () => { expect(view.bpPerPx).toEqual(0.02) }, 30000) -test('click and drag rubberBand, click get sequence to open sequenceDialog', async () => { +test('click and drag rubberband, click get sequence to open sequenceDialog', async () => { const { view, findByTestId, findByText } = createView() - const rubberband = await findByTestId('rubberBand_controls', {}, delay) + const rubberband = await findByTestId('rubberband_controls', ...opts) expect(view.bpPerPx).toEqual(0.05) fireEvent.mouseDown(rubberband, { clientX: 100, clientY: 0 }) fireEvent.mouseMove(rubberband, { clientX: 250, clientY: 0 }) @@ -57,8 +58,8 @@ test('click and drag rubberBand, click get sequence to open sequenceDialog', asy test('click and drag to reorder tracks', async () => { const { view, findByTestId } = createView() - fireEvent.click(await findByTestId(hts('bigbed_genes'), {}, delay)) - fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), {}, delay)) + fireEvent.click(await findByTestId(hts('bigbed_genes'), ...opts)) + fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), ...opts)) const trackId1 = view.tracks[1].id const dragHandle0 = await findByTestId( @@ -66,7 +67,7 @@ test('click and drag to reorder tracks', async () => { {}, delay, ) - const trackRenderingContainer1 = await findByTestId( + const container1 = await findByTestId( 'trackRenderingContainer-integration_test-volvox_filtered_vcf', {}, delay, @@ -79,7 +80,7 @@ test('click and drag to reorder tracks', async () => { fireEvent.mouseDown(dragHandle0, { clientX: 10, clientY: 100 }) fireEvent(dragHandle0, dragStartEvent) fireEvent.mouseMove(dragHandle0, { clientX: 10, clientY: 220 }) - fireEvent.dragEnter(trackRenderingContainer1) + fireEvent.dragEnter(container1) fireEvent.dragEnd(dragHandle0, { clientX: 10, clientY: 220 }) fireEvent.mouseUp(dragHandle0, { clientX: 10, clientY: 220 }) await waitFor(() => expect(view.tracks[0].id).toBe(trackId1)) @@ -87,7 +88,7 @@ test('click and drag to reorder tracks', async () => { test('click and zoom in and back out', async () => { const { view, findByTestId, findAllByText } = createView() - await findAllByText('ctgA', {}, delay) + await findAllByText('ctgA', ...opts) const before = view.bpPerPx fireEvent.click(await findByTestId('zoom_in')) await waitFor(() => expect(view.bpPerPx).toBe(before / 2), delay) @@ -97,16 +98,16 @@ test('click and zoom in and back out', async () => { test('opens track selector', async () => { const { view, findByTestId, findAllByText } = createView() - await findAllByText('ctgA', {}, delay) - await findByTestId(hts('bigbed_genes'), {}, delay) + await findAllByText('ctgA', ...opts) + await findByTestId(hts('bigbed_genes'), ...opts) expect(view.tracks.length).toBe(0) - fireEvent.click(await findByTestId(hts('bigbed_genes'), {}, delay)) + fireEvent.click(await findByTestId(hts('bigbed_genes'), ...opts)) expect(view.tracks.length).toBe(1) }, 30000) test('opens reference sequence track and expects zoom in message', async () => { const { view, findByTestId, findAllByText } = createView() - fireEvent.click(await findByTestId(hts('volvox_refseq'), {}, delay)) + fireEvent.click(await findByTestId(hts('volvox_refseq'), ...opts)) view.setNewView(20, 0) await findByTestId( 'display-volvox_refseq-LinearReferenceSequenceDisplay', @@ -118,8 +119,8 @@ test('opens reference sequence track and expects zoom in message', async () => { test('click to display center line with correct value', async () => { const { view, findAllByText, findByTestId, findByText } = createView() - await findAllByText('ctgA', {}, delay) - fireEvent.click(await findByTestId(hts('bigbed_genes'), {}, delay)) + await findAllByText('ctgA', ...opts) + fireEvent.click(await findByTestId(hts('bigbed_genes'), ...opts)) // opens the view menu and selects show center line fireEvent.click(await findByTestId('view_menu_icon')) @@ -131,36 +132,23 @@ test('click to display center line with correct value', async () => { test('test choose option from dropdown refName autocomplete', async () => { const { - view, findByText, findByTestId, - getByPlaceholderText, findAllByText, findByPlaceholderText, + getByPlaceholderText, } = createView() - await findAllByText('ctgA', {}, delay) + await findAllByText('ctgA', ...opts) fireEvent.click(await findByText('Help')) - // need this to complete before we can try to search - // fireEvent.click(await findByTestId(hts('bigbed_genes'), {}, delay)) - + fireEvent.click(await findByPlaceholderText('Search for location')) const autocomplete = await findByTestId('autocomplete') - const inputBox = await findByPlaceholderText('Search for location') - await waitFor(() => - expect(view.coarseDynamicBlocks.length).toBeGreaterThan(0), - ) - fireEvent.mouseDown(inputBox) autocomplete.focus() fireEvent.keyDown(autocomplete, { key: 'ArrowDown' }) fireEvent.keyDown(autocomplete, { key: 'ArrowDown' }) fireEvent.click((await screen.findAllByText('ctgB'))[0]) fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) - await waitFor( - () => expect(view.displayedRegions[0].refName).toEqual('ctgB'), - delay, - ) - await waitFor(() => { const n = getByPlaceholderText('Search for location') as HTMLInputElement expect(n.value).toEqual(expect.stringContaining('ctgB')) diff --git a/products/jbrowse-web/src/tests/BigWig.test.tsx b/products/jbrowse-web/src/tests/BigWig.test.tsx index 969297fe39..fd0e175a9e 100644 --- a/products/jbrowse-web/src/tests/BigWig.test.tsx +++ b/products/jbrowse-web/src/tests/BigWig.test.tsx @@ -16,35 +16,28 @@ beforeEach(() => { }) const delay = { timeout: 10000 } +const opts = [{}, delay] test('open a bigwig track', async () => { const { view, findByTestId, findByText } = createView() await findByText('Help') view.setNewView(5, 0) - fireEvent.click(await findByTestId(hts('volvox_microarray'), {}, delay)) - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..4,000-0'), {}, delay), - ) + fireEvent.click(await findByTestId(hts('volvox_microarray'), ...opts)) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..4000-0'), ...opts)) }, 15000) test('open a bigwig line track 2', async () => { const { view, findByTestId, findByText } = createView() await findByText('Help') view.setNewView(10, 0) - fireEvent.click(await findByTestId(hts('volvox_microarray_line'), {}, delay)) - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..8,000-0'), {}, delay), - ) + fireEvent.click(await findByTestId(hts('volvox_microarray_line'), ...opts)) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..8000-0'), ...opts)) }, 15000) test('open a bigwig density track', async () => { const { view, findByTestId, findByText } = createView() await findByText('Help') view.setNewView(5, 0) - fireEvent.click( - await findByTestId(hts('volvox_microarray_density'), {}, delay), - ) - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..4,000-0'), {}, delay), - ) + fireEvent.click(await findByTestId(hts('volvox_microarray_density'), ...opts)) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..4000-0'), ...opts)) }, 15000) diff --git a/products/jbrowse-web/src/tests/BookmarkWidget.test.tsx b/products/jbrowse-web/src/tests/BookmarkWidget.test.tsx index 6233b57b92..a33a998229 100644 --- a/products/jbrowse-web/src/tests/BookmarkWidget.test.tsx +++ b/products/jbrowse-web/src/tests/BookmarkWidget.test.tsx @@ -10,16 +10,15 @@ beforeEach(() => { const delay = { timeout: 15000 } -test('click and drag rubberBand, bookmarks region', async () => { +test('click and drag rubberband, bookmarks region', async () => { const { session, view, findByTestId, findByText } = createView() - const rubberband = await findByTestId('rubberBand_controls', {}, delay) + const rubberband = await findByTestId('rubberband_controls', {}, delay) expect(view.bpPerPx).toEqual(0.05) fireEvent.mouseDown(rubberband, { clientX: 100, clientY: 0 }) fireEvent.mouseMove(rubberband, { clientX: 250, clientY: 0 }) fireEvent.mouseUp(rubberband, { clientX: 250, clientY: 0 }) - const bookmarkMenuItem = await findByText('Bookmark region') - fireEvent.click(bookmarkMenuItem) + fireEvent.click(await findByText('Bookmark region')) // @ts-ignore const { widgets } = session @@ -51,8 +50,7 @@ test('navigates to bookmarked region from widget', async () => { delay, ) - const viewMenu = await findByTestId('view_menu_icon') - fireEvent.click(viewMenu) + fireEvent.click(await findByTestId('view_menu_icon')) fireEvent.click(await findByText('Open bookmark widget')) // @ts-ignore diff --git a/products/jbrowse-web/src/tests/Connection.test.tsx b/products/jbrowse-web/src/tests/Connection.test.tsx new file mode 100644 index 0000000000..c889a5a7e6 --- /dev/null +++ b/products/jbrowse-web/src/tests/Connection.test.tsx @@ -0,0 +1,45 @@ +import { fireEvent } from '@testing-library/react' +import { LocalFile } from 'generic-filehandle' + +import { createView, generateReadBuffer, doBeforeEach } from './util' +jest.mock('../makeWorkerInstance', () => () => {}) + +beforeEach(() => { + doBeforeEach() +}) + +const readBuffer = generateReadBuffer( + url => new LocalFile(require.resolve(`../../test_data/volvox/${url}`)), +) + +const readBuffer2 = generateReadBuffer( + url => + new LocalFile(require.resolve(`../../test_data/volvoxhub/hub1/${url}`)), +) + +const delay = 20000 +const opts = [{}, delay] +const root = 'https://jbrowse.org/volvoxhub/' + +test('Open up a UCSC trackhub connection', async () => { + // @ts-ignore + fetch.mockResponse(async request => { + if (request.url.startsWith(root)) { + const str = request.url.replace(root, '') + // @ts-ignore + return readBuffer2({ url: str, headers: new Map() }) + } + return readBuffer(request) + }) + + const { findByTestId, findByText } = createView() + + fireEvent.click(await findByText('File')) + fireEvent.click(await findByText(/Open connection/)) + fireEvent.click(await findByText('Next')) + fireEvent.change(await findByTestId('urlInput'), { + target: { value: 'https://jbrowse.org/volvoxhub/hub.txt' }, + }) + fireEvent.click(await findByText('Connect')) + await findByText('CRAM - Volvox Sorted', ...opts) +}, 40000) diff --git a/products/jbrowse-web/src/tests/CopyAndDelete.test.tsx b/products/jbrowse-web/src/tests/CopyAndDelete.test.tsx index 48640bad40..9991981325 100644 --- a/products/jbrowse-web/src/tests/CopyAndDelete.test.tsx +++ b/products/jbrowse-web/src/tests/CopyAndDelete.test.tsx @@ -51,7 +51,7 @@ test('copy and delete reference sequence track disabled', async () => { // @ts-ignore const trackMenuItems = session.getTrackActionMenuItems(trackConf) - // copy ref seq track disbaled + // copy ref seq track disabled fireEvent.click( await findByTestId('htsTrackEntryMenu-volvox_refseq', {}, delay), ) diff --git a/products/jbrowse-web/src/tests/Dotplot.test.tsx b/products/jbrowse-web/src/tests/Dotplot.test.tsx index 6d11b0167e..f71e99374f 100644 --- a/products/jbrowse-web/src/tests/Dotplot.test.tsx +++ b/products/jbrowse-web/src/tests/Dotplot.test.tsx @@ -1,6 +1,4 @@ import { fireEvent } from '@testing-library/react' -import { toMatchImageSnapshot } from 'jest-image-snapshot' -import { TextEncoder, TextDecoder } from 'web-encoding' import path from 'path' // locals @@ -9,16 +7,9 @@ import dotplotSession from './dotplot_inverted_test.json' import dotplotSessionFlipAxes from './dotplot_inverted_flipaxes.json' import { setup, doBeforeEach, expectCanvasMatch, createView } from './util' -if (!window.TextEncoder) { - window.TextEncoder = TextEncoder -} -if (!window.TextDecoder) { - window.TextDecoder = TextDecoder -} - const delay = { timeout: 25000 } +const opts = [{}, delay] -expect.extend({ toMatchImageSnapshot }) setup() beforeEach(() => { @@ -27,8 +18,8 @@ beforeEach(() => { test('open a dotplot view', async () => { const { findByTestId } = createView(config) - expectCanvasMatch(await findByTestId('prerendered_canvas_done', {}, delay)) -}, 20000) + expectCanvasMatch(await findByTestId('prerendered_canvas_done', ...opts)) +}, 30000) test('open a dotplot view with import form', async () => { const { findByTestId, findAllByTestId, findByText } = createView(config) @@ -43,14 +34,15 @@ test('open a dotplot view with import form', async () => { value: 'peach', }, }) - fireEvent.change(await findByTestId('urlInput', {}, delay), { + fireEvent.click(await findByText('New track', ...opts)) + fireEvent.change(await findByTestId('urlInput', ...opts), { target: { value: 'peach_grape_small.paf.gz', }, }) - fireEvent.click(await findByTestId('submitDotplot')) + fireEvent.click(await findByText('Launch')) - expectCanvasMatch(await findByTestId('prerendered_canvas_done', {}, delay)) + expectCanvasMatch(await findByTestId('prerendered_canvas_done', ...opts)) }, 30000) test('inverted dotplot', async () => { @@ -58,7 +50,7 @@ test('inverted dotplot', async () => { ...config, defaultSession: dotplotSession.session, }) - expectCanvasMatch(await findByTestId('prerendered_canvas_done', {}, delay), 0) + expectCanvasMatch(await findByTestId('prerendered_canvas_done', ...opts), 0) }, 30000) test('inverted dotplot flip axes', async () => { @@ -66,7 +58,7 @@ test('inverted dotplot flip axes', async () => { ...config, defaultSession: dotplotSessionFlipAxes.session, }) - expectCanvasMatch(await findByTestId('prerendered_canvas_done', {}, delay), 0) + expectCanvasMatch(await findByTestId('prerendered_canvas_done', ...opts), 0) }, 30000) // session with dotplots and linear synteny views with both orientations tested diff --git a/products/jbrowse-web/src/tests/DrawerWidget.test.tsx b/products/jbrowse-web/src/tests/DrawerWidget.test.tsx index 4f3edc640d..d78f10f52c 100644 --- a/products/jbrowse-web/src/tests/DrawerWidget.test.tsx +++ b/products/jbrowse-web/src/tests/DrawerWidget.test.tsx @@ -9,21 +9,33 @@ beforeEach(() => { doBeforeEach() }) -test('variant track test - opens feature detail view', async () => { +test('opens feature detail from left click', async () => { const { view, findByTestId, findAllByTestId, findByText } = createView() await findByText('Help') view.setNewView(0.05, 5000) fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), {}, delay)) + view.tracks[0].displays[0].setFeatureIdUnderMouse('test-vcf-604452') - const feats1 = await findAllByTestId('test-vcf-604452', {}, delay) - fireEvent.click(feats1[0]) + fireEvent.click((await findAllByTestId('test-vcf-604452', {}, delay))[0]) + expect( + await findByTestId('variant-side-drawer', {}, delay), + ).toBeInTheDocument() +}, 20000) - // this text is to confirm a feature detail drawer opened - expect(await findByTestId('variant-side-drawer')).toBeInTheDocument() - const feats2 = await findAllByTestId('test-vcf-604452', {}, delay) - fireEvent.contextMenu(feats2[0]) +test('open feature detail from right click', async () => { + const { view, findByTestId, findAllByTestId, findByText } = createView() + await findByText('Help') + view.setNewView(0.05, 5000) + fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), {}, delay)) + view.tracks[0].displays[0].setFeatureIdUnderMouse('test-vcf-604452') + + fireEvent.contextMenu( + (await findAllByTestId('test-vcf-604452', {}, delay))[0], + ) fireEvent.click(await findByText('Open feature details')) - expect(await findByTestId('variant-side-drawer')).toBeInTheDocument() + expect( + await findByTestId('variant-side-drawer', {}, delay), + ).toBeInTheDocument() }, 20000) test('widget drawer navigation', async () => { diff --git a/products/jbrowse-web/src/tests/ExportSvg.test.tsx b/products/jbrowse-web/src/tests/ExportSvg.test.tsx index 2550176432..1227cf74d2 100644 --- a/products/jbrowse-web/src/tests/ExportSvg.test.tsx +++ b/products/jbrowse-web/src/tests/ExportSvg.test.tsx @@ -1,5 +1,4 @@ import { fireEvent, waitFor } from '@testing-library/react' -import { TextEncoder } from 'web-encoding' import fs from 'fs' import path from 'path' import FileSaver from 'file-saver' @@ -7,8 +6,6 @@ import FileSaver from 'file-saver' // locals import { hts, createView, setup, doBeforeEach } from './util' -window.TextEncoder = TextEncoder - // mock from https://stackoverflow.com/questions/44686077 jest.mock('file-saver', () => ({ saveAs: jest.fn() })) @@ -32,7 +29,7 @@ test('export svg', async () => { fireEvent.click( await findByTestId(hts('volvox_alignments_pileup_coverage'), {}, delay), ) - view.exportSvg() + await view.exportSvg() await waitFor(() => expect(FileSaver.saveAs).toHaveBeenCalled(), delay) // @ts-ignore diff --git a/products/jbrowse-web/src/tests/Hic.test.tsx b/products/jbrowse-web/src/tests/Hic.test.tsx index c0f8837198..0e36ad0a6b 100644 --- a/products/jbrowse-web/src/tests/Hic.test.tsx +++ b/products/jbrowse-web/src/tests/Hic.test.tsx @@ -25,5 +25,5 @@ test('hic', async () => { view.setNewView(5000, 0) fireEvent.click(await findByTestId(hts('hic_test'), {}, delay)) - expectCanvasMatch(await findByTestId(pc('{hg19}1:1..4,000,000-0'), {}, delay)) + expectCanvasMatch(await findByTestId(pc('{hg19}1:1..4000000-0'), {}, delay)) }, 25000) diff --git a/products/jbrowse-web/src/tests/JBrowse.test.tsx b/products/jbrowse-web/src/tests/JBrowse.test.tsx index df1e96a21a..6cb245c802 100644 --- a/products/jbrowse-web/src/tests/JBrowse.test.tsx +++ b/products/jbrowse-web/src/tests/JBrowse.test.tsx @@ -1,7 +1,6 @@ import '@testing-library/jest-dom/extend-expect' import { fireEvent } from '@testing-library/react' -import { TextEncoder } from 'web-encoding' import { readConfObject, getConf } from '@jbrowse/core/configuration' import PluginManager from '@jbrowse/core/PluginManager' @@ -15,7 +14,6 @@ import TestPlugin from './TestPlugin' jest.mock('../makeWorkerInstance', () => () => {}) -window.TextEncoder = TextEncoder setup() const delay = { timeout: 15000 } @@ -41,13 +39,12 @@ test('lollipop track test', async () => { await findByTestId('display-lollipop_track_linear', {}, delay) await findByTestId('three', {}, delay) -}, 10000) +}, 30000) test('toplevel configuration', () => { const pm = new PluginManager([...corePlugins, TestPlugin].map(P => new P())) pm.createPluggableElements() - const JBrowseRootModel = JBrowseRootModelFactory(pm, true) - const rootModel = JBrowseRootModel.create({ + const rootModel = JBrowseRootModelFactory(pm, true).create({ jbrowse: volvoxConfigSnapshot, assemblyManager: {}, }) @@ -97,15 +94,12 @@ test('test sharing', async () => { }, password: '123', }) - const { findByTestId, findByText } = createView() - await findByText('Help') + const { findByLabelText, findByText } = createView() fireEvent.click(await findByText('Share')) - - // check the share dialog has the above session shared - await findByTestId('share-dialog') - const url = (await findByTestId('share-url-text')) as HTMLInputElement - expect(url.value).toBe('http://localhost/?session=share-abc&password=123') -}) + expect(((await findByLabelText('URL')) as HTMLInputElement).value).toBe( + 'http://localhost/?session=share-abc&password=123', + ) +}, 15000) test('looks at about this track dialog', async () => { const { findByTestId, findAllByText, findByText } = createView() diff --git a/products/jbrowse-web/src/tests/Loader.test.tsx b/products/jbrowse-web/src/tests/Loader.test.tsx index 69aaa260dc..ac4e7a287f 100644 --- a/products/jbrowse-web/src/tests/Loader.test.tsx +++ b/products/jbrowse-web/src/tests/Loader.test.tsx @@ -1,31 +1,22 @@ -// we use mainthread rpc so we mock the makeWorkerInstance to an empty file import React from 'react' import { render, waitFor } from '@testing-library/react' -import { TextEncoder, TextDecoder } from 'web-encoding' + +import { toMatchImageSnapshot } from 'jest-image-snapshot' import { LocalFile } from 'generic-filehandle' import rangeParser from 'range-parser' + +// local +import { App } from './loaderUtil' + import { Image, createCanvas } from 'canvas' -import { QueryParamProvider } from 'use-query-params' -import { WindowHistoryAdapter } from 'use-query-params/adapters/window' -import { Loader } from '../Loader' +jest.mock('../makeWorkerInstance', () => () => {}) // @ts-ignore global.nodeImage = Image // @ts-ignore global.nodeCreateCanvas = createCanvas -jest.mock('../makeWorkerInstance', () => () => {}) - -const delay = { timeout: 20000 } - -if (!window.TextEncoder) { - window.TextEncoder = TextEncoder -} -if (!window.TextDecoder) { - window.TextDecoder = TextDecoder -} - const getFile = (url: string) => new LocalFile( require.resolve(`../../${url.replace(/http:\/\/localhost\//, '')}`), @@ -103,29 +94,20 @@ const readBuffer = async (url: string, args: RequestInit) => { } } +jest.mock('../makeWorkerInstance', () => () => {}) + +expect.extend({ toMatchImageSnapshot }) + +const delay = { timeout: 20000 } + // @ts-ignore jest.spyOn(global, 'fetch').mockImplementation(readBuffer) -function App({ search }: { search: string }) { - const location = { - ...window.location, - search, - } - Object.defineProperty(window, 'location', { - writable: true, - value: location, - }) - return ( - - - - ) -} - afterEach(() => { localStorage.clear() sessionStorage.clear() }) + test('errors with config in URL that does not exist', async () => { console.error = jest.fn() const { findByText } = render() @@ -150,19 +132,19 @@ test('can use config from a url with shared session ', async () => { }, 20000) // minimal session with plugin in our plugins.json -// {"session":{"id":"xSHu7qGJN","name":"test","sessionPlugins":[{"url":"https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js"}]}} -test('can warn of callbacks in json session', async () => { +test('approves sessionPlugins from plugin list', async () => { + expect(sessionStorage.length).toBe(0) render( - , + , ) await waitFor(() => expect(sessionStorage.length).toBeGreaterThan(0), { - timeout: 30000, + timeout: 50000, }) -}, 30000) +}, 50000) // minimal session, // {"session":{"id":"xSHu7qGJN","name":"test","sessionPlugins":[{"url":"https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js"}]}} -test('pops up a warning for evil plugin', async () => { +test('pops up a warning for evil plugin in sessionPlugins', async () => { const { findByTestId } = render( , ) @@ -196,23 +178,6 @@ test('can use a spec url for lgv', async () => { ) }, 40000) -test('can use a spec url for dotplot view', async () => { - const { findByTestId } = render( - , - ) - - await findByTestId('prerendered_canvas_done', {}, delay) -}, 40000) - -test('can use a spec url for synteny view', async () => { - console.warn = jest.fn() - const { findByTestId } = render( - , - ) - - await findByTestId('synteny_canvas', {}, delay) -}, 40000) - test('can use a spec url for spreadsheet view', async () => { console.warn = jest.fn() const { findByText } = render( @@ -230,3 +195,11 @@ test('can use a spec url for sv inspector view', async () => { await findByText('ctgB:1982..1983', {}, delay) }, 40000) + +test('can use a spec url for dotplot view', async () => { + const { findByTestId } = render( + , + ) + + await findByTestId('prerendered_canvas_done', {}, delay) +}, 40000) diff --git a/products/jbrowse-web/src/tests/ReadVsRef.test.tsx b/products/jbrowse-web/src/tests/ReadVsRef.test.tsx index 0c2850b02b..cd725e040f 100644 --- a/products/jbrowse-web/src/tests/ReadVsRef.test.tsx +++ b/products/jbrowse-web/src/tests/ReadVsRef.test.tsx @@ -38,7 +38,7 @@ test('launch read vs ref panel', async () => { expect(session.views[1].type).toBe('LinearSyntenyView') expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) -}, 20000) +}, 40000) test('launch read vs ref dotplot', async () => { console.warn = jest.fn() @@ -59,4 +59,4 @@ test('launch read vs ref dotplot', async () => { expect(session.views[1].type).toBe('DotplotView') expectCanvasMatch(await findByTestId('prerendered_canvas_done', {}, delay)) -}, 20000) +}, 40000) diff --git a/products/jbrowse-web/src/tests/Reload.test.tsx b/products/jbrowse-web/src/tests/Reload.test.tsx index c85f7b6b0d..f1140c5c23 100644 --- a/products/jbrowse-web/src/tests/Reload.test.tsx +++ b/products/jbrowse-web/src/tests/Reload.test.tsx @@ -21,6 +21,7 @@ beforeEach(() => { }) const delay = { timeout: 10000 } +const opts = [{}, delay] // this tests reloading after an initial track error // it performs a full image snapshot test to ensure that the features are rendered and not @@ -40,14 +41,14 @@ test('reloads alignments track (CRAI 404)', async () => { createView() await findByText('Help') view.setNewView(0.5, 0) - fireEvent.click(await findByTestId(hts('volvox_cram_pileup'), {}, delay)) - await findAllByText(/HTTP 404/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_cram_pileup'), ...opts)) + await findAllByText(/HTTP 404/, ...opts) // @ts-ignore fetch.mockResponse(readBuffer) const buttons = await findAllByTestId('reload_button') fireEvent.click(buttons[0]) - expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), {}, delay)) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), ...opts)) }, 20000) test('reloads alignments track (CRAM 404)', async () => { @@ -67,13 +68,13 @@ test('reloads alignments track (CRAM 404)', async () => { createView() await findByText('Help') view.setNewView(0.5, 0) - fireEvent.click(await findByTestId(hts('volvox_cram_snpcoverage'), {}, delay)) - await findAllByText(/HTTP 404/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_cram_snpcoverage'), ...opts)) + await findAllByText(/HTTP 404/, ...opts) // @ts-ignore fetch.mockResponse(readBuffer) const buttons = await findAllByTestId('reload_button') fireEvent.click(buttons[0]) - expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), {}, delay)) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), ...opts)) }, 20000) test('reloads alignments track (BAI 404)', async () => { // @ts-ignore @@ -88,13 +89,13 @@ test('reloads alignments track (BAI 404)', async () => { createView() await findByText('Help') view.setNewView(0.5, 0) - fireEvent.click(await findByTestId(hts('volvox_bam_snpcoverage'), {}, delay)) - await findAllByText(/HTTP 404/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_bam_snpcoverage'), ...opts)) + await findAllByText(/HTTP 404/, ...opts) // @ts-ignore fetch.mockResponse(readBuffer) const buttons = await findAllByTestId('reload_button') fireEvent.click(buttons[0]) - expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), {}, delay)) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), ...opts)) }, 20000) test('reloads alignments track (BAM 404)', async () => { // @ts-ignore @@ -109,14 +110,14 @@ test('reloads alignments track (BAM 404)', async () => { createView() await findByText('Help') view.setNewView(0.5, 0) - fireEvent.click(await findByTestId(hts('volvox_bam_pileup'), {}, delay)) - await findAllByText(/HTTP 404/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_bam_pileup'), ...opts)) + await findAllByText(/HTTP 404/, ...opts) // @ts-ignore fetch.mockResponse(readBuffer) const buttons = await findAllByTestId('reload_button') fireEvent.click(buttons[0]) - expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), {}, delay)) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..400-0'), ...opts)) }, 20000) test('reloads bigwig (BW 404)', async () => { @@ -134,15 +135,13 @@ test('reloads bigwig (BW 404)', async () => { createView() await findByText('Help') view.setNewView(10, 0) - fireEvent.click(await findByTestId(hts('volvox_microarray'), {}, delay)) - await findAllByText(/HTTP 404/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_microarray'), ...opts)) + await findAllByText(/HTTP 404/, ...opts) // @ts-ignore fetch.mockResponse(readBuffer) const buttons = await findAllByTestId('reload_button') fireEvent.click(buttons[0]) - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..8,000-0'), {}, delay), - ) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..8000-0'), ...opts)) }, 20000) test('reloads vcf (VCF.GZ 404)', async () => { @@ -160,15 +159,15 @@ test('reloads vcf (VCF.GZ 404)', async () => { createView() await findByText('Help') view.setNewView(0.05, 5000) - fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), {}, delay)) - await findAllByText(/HTTP 404/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), ...opts)) + await findAllByText(/HTTP 404/, ...opts) // @ts-ignore fetch.mockResponse(readBuffer) const buttons = await findAllByTestId('reload_button') fireEvent.click(buttons[0]) - await findAllByTestId('box-test-vcf-604452', {}, delay) + await findAllByTestId('box-test-vcf-604452', ...opts) }, 20000) test('reloads vcf (VCF.GZ.TBI 404)', async () => { @@ -185,12 +184,12 @@ test('reloads vcf (VCF.GZ.TBI 404)', async () => { createView() await findByText('Help') view.setNewView(0.05, 5000) - fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), {}, delay)) - await findAllByText(/HTTP 404/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_filtered_vcf'), ...opts)) + await findAllByText(/HTTP 404/, ...opts) // @ts-ignore fetch.mockResponse(readBuffer) const buttons = await findAllByTestId('reload_button') fireEvent.click(buttons[0]) - await findAllByTestId('box-test-vcf-604452', {}, delay) + await findAllByTestId('box-test-vcf-604452', ...opts) }, 20000) diff --git a/products/jbrowse-web/src/tests/2.SVInspector.test.tsx b/products/jbrowse-web/src/tests/SVInspector.test.tsx similarity index 89% rename from products/jbrowse-web/src/tests/2.SVInspector.test.tsx rename to products/jbrowse-web/src/tests/SVInspector.test.tsx index 021bf70c8d..4480356273 100644 --- a/products/jbrowse-web/src/tests/2.SVInspector.test.tsx +++ b/products/jbrowse-web/src/tests/SVInspector.test.tsx @@ -1,12 +1,7 @@ import '@testing-library/jest-dom/extend-expect' import { fireEvent, waitFor } from '@testing-library/react' -import { TextEncoder, TextDecoder } from 'web-encoding' - import { doBeforeEach, createView, setup } from './util' -window.TextEncoder = TextEncoder -window.TextDecoder = TextDecoder - setup() beforeEach(() => { diff --git a/products/jbrowse-web/src/tests/1.Spreadsheet.test.tsx b/products/jbrowse-web/src/tests/Spreadsheet.test.tsx similarity index 92% rename from products/jbrowse-web/src/tests/1.Spreadsheet.test.tsx rename to products/jbrowse-web/src/tests/Spreadsheet.test.tsx index 267f7e6958..07ab2af60f 100644 --- a/products/jbrowse-web/src/tests/1.Spreadsheet.test.tsx +++ b/products/jbrowse-web/src/tests/Spreadsheet.test.tsx @@ -1,12 +1,8 @@ import '@testing-library/jest-dom/extend-expect' import { fireEvent, waitFor } from '@testing-library/react' -import { TextEncoder, TextDecoder } from 'web-encoding' import { createView, setup, doBeforeEach } from './util' -window.TextEncoder = TextEncoder -window.TextDecoder = TextDecoder - setup() beforeEach(() => { diff --git a/products/jbrowse-web/src/tests/StatsEstimation.test.tsx b/products/jbrowse-web/src/tests/StatsEstimation.test.tsx index d141a2efc4..749648d332 100644 --- a/products/jbrowse-web/src/tests/StatsEstimation.test.tsx +++ b/products/jbrowse-web/src/tests/StatsEstimation.test.tsx @@ -19,24 +19,20 @@ beforeEach(() => { }) const delay = { timeout: 20000 } +const o = [{}, delay] test('test stats estimation pileup, zoom in to see', async () => { const { view, findByText, findAllByText, findByTestId } = createView() await findByText('Help') view.setNewView(30, 183) - - fireEvent.click(await findByTestId(hts('volvox_cram_pileup'), {}, delay)) - - await findAllByText(/Requested too much data/, {}, delay) + fireEvent.click(await findByTestId(hts('volvox_cram_pileup'), ...o)) + await findAllByText(/Requested too much data/, ...o) const before = view.bpPerPx fireEvent.click(await findByTestId('zoom_in')) // found it helps avoid flaky test to check that it is zoomed in before // checking snapshot (even though it seems like it is unneeded) #2673 await waitFor(() => expect(view.bpPerPx).toBe(before / 2), delay) - - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..12,000-0'), {}, delay), - ) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..12000-0'), ...o)) }, 30000) test('test stats estimation pileup, force load to see', async () => { @@ -44,17 +40,13 @@ test('test stats estimation pileup, force load to see', async () => { await findByText('Help') view.setNewView(25.07852564102564, 283) - fireEvent.click( - await findByTestId('htsTrackEntry-volvox_cram_pileup', {}, delay), - ) + fireEvent.click(await findByTestId('htsTrackEntry-volvox_cram_pileup', ...o)) - await findAllByText(/Requested too much data/, {}, delay) - const buttons = await findAllByText(/Force load/, {}, delay) + await findAllByText(/Requested too much data/, ...o) + const buttons = await findAllByText(/Force load/, ...o) fireEvent.click(buttons[0]) - expectCanvasMatch( - await findByTestId(pc('{volvox}ctgA:1..20,063-0'), {}, delay), - ) + expectCanvasMatch(await findByTestId(pc('{volvox}ctgA:1..20063-0'), ...o)) }, 30000) test('test stats estimation on vcf track, zoom in to see', async () => { @@ -62,29 +54,22 @@ test('test stats estimation on vcf track, zoom in to see', async () => { createView() await findByText('Help') view.setNewView(34, 5) - - fireEvent.click(await findByTestId('htsTrackEntry-variant_colors', {}, delay)) - - await findAllByText(/Zoom in to see features/, {}, delay) + fireEvent.click(await findByTestId('htsTrackEntry-variant_colors', ...o)) + await findAllByText(/Zoom in to see features/, ...o) const before = view.bpPerPx fireEvent.click(await findByTestId('zoom_in')) // found it helps avoid flaky test to check that it is zoomed in before // checking snapshot (even though it seems like it is unneeded) #2673 await waitFor(() => expect(view.bpPerPx).toBe(before / 2), delay) - - await findAllByTestId('box-test-vcf-605560', {}, delay) + await findAllByTestId('box-test-vcf-605560', ...o) }, 30000) test('test stats estimation on vcf track, force load to see', async () => { const { view, findByText, findAllByText, findByTestId } = createView() await findByText('Help') view.setNewView(34, 5) - await findAllByText('ctgA', {}, delay) - - fireEvent.click(await findByTestId('htsTrackEntry-variant_colors', {}, delay)) - - await findAllByText(/Zoom in to see features/, {}, delay) - const buttons = await findAllByText(/Force load/, {}, delay) - fireEvent.click(buttons[0]) - await findByTestId('box-test-vcf-605223', {}, delay) + await findAllByText('ctgA', ...o) + fireEvent.click(await findByTestId('htsTrackEntry-variant_colors', ...o)) + fireEvent.click((await findAllByText(/Force load/, ...o))[0]) + await findByTestId('box-test-vcf-605223', ...o) }, 30000) diff --git a/products/jbrowse-web/src/tests/Synteny.test.tsx b/products/jbrowse-web/src/tests/Synteny.test.tsx new file mode 100644 index 0000000000..df4eb3b289 --- /dev/null +++ b/products/jbrowse-web/src/tests/Synteny.test.tsx @@ -0,0 +1,225 @@ +import React from 'react' +import { render } from '@testing-library/react' + +import { toMatchImageSnapshot } from 'jest-image-snapshot' +import { LocalFile } from 'generic-filehandle' +import rangeParser from 'range-parser' + +// local +import { App } from './loaderUtil' +import { expectCanvasMatch } from './util' + +const getFile = (url: string) => + new LocalFile( + require.resolve(`../../${url.replace(/http:\/\/localhost\//, '')}`), + ) + +const readBuffer = async (url: string, args: RequestInit) => { + // this is the analytics + if (url.match(/jb2=true/)) { + return { + ok: true, + async json() { + return {} + }, + } + } + try { + const file = getFile(url) + const maxRangeRequest = 2000000 // kind of arbitrary, part of the rangeParser + if (args.headers && 'range' in args.headers) { + const range = rangeParser(maxRangeRequest, args.headers.range) + if (range === -2 || range === -1) { + throw new Error(`Error parsing range "${args.headers.range}"`) + } + const { start, end } = range[0] + const len = end - start + 1 + const buf = Buffer.alloc(len) + const { bytesRead } = await file.read(buf, 0, len, start) + const stat = await file.stat() + return new Response(buf.slice(0, bytesRead), { + status: 206, + headers: [['content-range', `${start}-${end}/${stat.size}`]], + }) + } + const body = await file.readFile() + return new Response(body, { status: 200 }) + } catch (e) { + console.error(e) + return new Response(undefined, { status: 404 }) + } +} + +jest.mock('../makeWorkerInstance', () => () => {}) + +expect.extend({ toMatchImageSnapshot }) + +const delay = { timeout: 20000 } + +// @ts-ignore +jest.spyOn(global, 'fetch').mockImplementation(readBuffer) + +afterEach(() => { + localStorage.clear() + sessionStorage.clear() +}) + +test('horizontally flipped inverted alignment', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'Pp01:28,845,211..28,845,272[rev]', assembly: 'peach' }, + { loc: 'chr1:316,306..316,364', assembly: 'grape' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) + +test('regular orientation inverted alignment', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'Pp01:28,845,211..28,845,272', assembly: 'peach' }, + { loc: 'chr1:316,306..316,364', assembly: 'grape' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) + +test('regular orientation inverted alignment bottom', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'Pp01:28,845,211..28,845,272', assembly: 'peach' }, + { loc: 'chr1:316,306..316,364[rev]', assembly: 'grape' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) + +test('regular orientation both horizontally flipped', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'Pp01:28,845,211..28,845,272[rev]', assembly: 'peach' }, + { loc: 'chr1:316,306..316,364[rev]', assembly: 'grape' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) + +test('switch rows regular orientation both horizontally flipped', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'chr1:316,306..316,364', assembly: 'grape' }, + { loc: 'Pp01:28,845,211..28,845,272', assembly: 'peach' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) + +test('switch rows regular orientation both horizontally flipped rev 1', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'chr1:316,306..316,364[rev]', assembly: 'grape' }, + { loc: 'Pp01:28,845,211..28,845,272', assembly: 'peach' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) + +test('switch rows regular orientation both horizontally flipped rev2', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'chr1:316,306..316,364', assembly: 'grape' }, + { loc: 'Pp01:28,845,211..28,845,272[rev]', assembly: 'peach' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) + +test('switch rows regular orientation both horizontally flipped both rev', async () => { + console.warn = jest.fn() + const str = `?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=spec-${JSON.stringify( + { + views: [ + { + type: 'LinearSyntenyView', + tracks: ['subset'], + views: [ + { loc: 'chr1:316,306..316,364[rev]', assembly: 'grape' }, + { loc: 'Pp01:28,845,211..28,845,272[rev]', assembly: 'peach' }, + ], + }, + ], + }, + )}` + const { findByTestId } = render() + expectCanvasMatch(await findByTestId('synteny_canvas', {}, delay)) +}, 40000) diff --git a/products/jbrowse-web/src/tests/TextSearching.test.tsx b/products/jbrowse-web/src/tests/TextSearching.test.tsx index 3229dcc92b..205e39396c 100644 --- a/products/jbrowse-web/src/tests/TextSearching.test.tsx +++ b/products/jbrowse-web/src/tests/TextSearching.test.tsx @@ -1,4 +1,4 @@ -import { screen, waitFor, fireEvent } from '@testing-library/react' +import { waitFor, fireEvent } from '@testing-library/react' // locals import { setup, doBeforeEach, createView } from './util' @@ -11,12 +11,13 @@ beforeEach(() => { }) const delay = { timeout: 10000 } +const opts = [{}, delay] async function doSetup(val?: unknown) { const args = createView(val) const { findByTestId, findByPlaceholderText } = args - const autocomplete = await findByTestId('autocomplete', {}, delay) + const autocomplete = await findByTestId('autocomplete', ...opts) const input = (await findByPlaceholderText( 'Search for location', )) as HTMLInputElement @@ -35,19 +36,19 @@ test('single result, searching: eden.1', async () => { }, 30000) test('dialog with multiple results, searching seg02', async () => { - const { input, view, autocomplete } = await doSetup() + const { input, view, findByText, autocomplete } = await doSetup() fireEvent.change(input, { target: { value: 'seg02' } }) fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) - await screen.findByText('Search results', {}, delay) + await findByText('Search results', ...opts) await waitFor(() => expect(view.searchResults?.length).toBeGreaterThan(0)) }, 30000) test('dialog with multiple results with jb1 config, searching: eden.1', async () => { - const { input, view, autocomplete } = await doSetup(jb1_config) + const { input, view, findByText, autocomplete } = await doSetup(jb1_config) fireEvent.change(input, { target: { value: 'eden.1' } }) fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) - await screen.findByText('Search results', {}, delay) + await findByText('Search results', ...opts) expect(view.searchResults?.length).toBeGreaterThan(0) }, 30000) @@ -88,13 +89,20 @@ test('nav lower case refnames, searching: contigb:1-100', async () => { }, 30000) test('description of gene, searching: kinase', async () => { - console.warn = jest.fn() - const { input, autocomplete } = await doSetup() + const { input, findByText, autocomplete } = await doSetup() - fireEvent.mouseDown(input) fireEvent.change(input, { target: { value: 'kinase' } }) - - fireEvent.click(await screen.findByText('EDEN (protein kinase)', {}, delay)) + fireEvent.click(await findByText('EDEN (protein kinase)', ...opts)) fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) await waitFor(() => expect(input.value).toBe('ctgA:1,055..9,005'), delay) }, 30000) + +test('search matches description for feature in two places', async () => { + const { view, input, findByText, autocomplete } = await doSetup() + + fireEvent.change(input, { target: { value: 'fingerprint' } }) + fireEvent.click(await findByText(/b101.2/, ...opts)) + fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) + await findByText('Search results', ...opts) + await waitFor(() => expect(view.searchResults?.length).toBeGreaterThan(0)) +}, 30000) diff --git a/products/jbrowse-web/src/tests/TextSearchingImportForm.test.tsx b/products/jbrowse-web/src/tests/TextSearchingImportForm.test.tsx index 01d0ded6cb..2936fdc1fb 100644 --- a/products/jbrowse-web/src/tests/TextSearchingImportForm.test.tsx +++ b/products/jbrowse-web/src/tests/TextSearchingImportForm.test.tsx @@ -1,7 +1,7 @@ -import { screen, waitFor, fireEvent } from '@testing-library/react' +import { waitFor, fireEvent } from '@testing-library/react' // locals -import { setup, createView, doBeforeEach } from './util' +import { setup, doSetupForImportForm, doBeforeEach } from './util' setup() @@ -10,60 +10,40 @@ beforeEach(() => { }) const delay = { timeout: 10000 } - -async function doSetup(val?: unknown) { - const args = createView(val) - const { view, findByTestId, getByPlaceholderText, findByPlaceholderText } = - args - - // clear view takes us to the import form - view.clearView() - - const autocomplete = await findByTestId('autocomplete') - const input = (await findByPlaceholderText( - 'Search for location', - )) as HTMLInputElement - - // this will be the input that is obtained after opening the LGV from the import form - const getInputValue = () => - (getByPlaceholderText('Search for location') as HTMLInputElement).value - - autocomplete.focus() - input.focus() - - return { - autocomplete, - input, - getInputValue, - ...args, - } -} +const opts = [{}, delay] test('search eden.1 and hit open', async () => { - console.warn = jest.fn() - const { input, getInputValue, findByText } = await doSetup() + const { input, getInputValue, findByText } = await doSetupForImportForm() + fireEvent.change(input, { target: { value: 'eden.1' } }) fireEvent.click(await findByText('Open')) await waitFor(() => expect(getInputValue()).toBe('ctgA:1,055..9,005'), delay) }, 30000) +test('dialog with multiple results, searching seg02', async () => { + const { input, view, findByText, autocomplete } = await doSetupForImportForm() + + fireEvent.change(input, { target: { value: 'seg02' } }) + fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) + fireEvent.click(await findByText('Open')) + await findByText('Search results', ...opts) + await waitFor(() => expect(view.searchResults?.length).toBeGreaterThan(0)) +}, 30000) + test('search eden.1 and hit enter', async () => { - console.warn = jest.fn() - const { input, findByText, autocomplete, getInputValue } = await doSetup() + const { input, findByText, autocomplete, getInputValue } = + await doSetupForImportForm() - fireEvent.mouseDown(input) fireEvent.change(input, { target: { value: 'eden.1' } }) fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) - fireEvent.click(await findByText('Open')) await waitFor(() => expect(getInputValue()).toBe('ctgA:1,055..9,005'), delay) }, 30000) test('lower case refname, searching: contigb', async () => { - console.warn = jest.fn() - const { input, autocomplete, findByText, getInputValue } = await doSetup() + const { input, autocomplete, findByText, getInputValue } = + await doSetupForImportForm() - fireEvent.mouseDown(input) fireEvent.change(input, { target: { value: 'contigb' } }) fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) fireEvent.click(await findByText('Open')) @@ -72,14 +52,24 @@ test('lower case refname, searching: contigb', async () => { }, 30000) test('description of gene, searching: kinase', async () => { - console.warn = jest.fn() - const { input, findByText, getInputValue, autocomplete } = await doSetup() + const { input, findByText, getInputValue, autocomplete } = + await doSetupForImportForm() - fireEvent.mouseDown(input) fireEvent.change(input, { target: { value: 'kinase' } }) fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) - fireEvent.click(await screen.findByText('EDEN (protein kinase)', {}, delay)) + fireEvent.click(await findByText('EDEN (protein kinase)', ...opts)) fireEvent.click(await findByText('Open')) await waitFor(() => expect(getInputValue()).toBe('ctgA:1,055..9,005'), delay) }, 30000) + +test('search matches description for feature in two places', async () => { + const { view, input, findByText, autocomplete } = await doSetupForImportForm() + + fireEvent.change(input, { target: { value: 'fingerprint' } }) + fireEvent.click(await findByText(/b101.2/, ...opts)) + fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' }) + fireEvent.click(await findByText('Open')) + await findByText('Search results', ...opts) + await waitFor(() => expect(view.searchResults?.length).toBeGreaterThan(0)) +}, 30000) diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/alignments-features-test-tsx-color-by-strand-1-snap.png b/products/jbrowse-web/src/tests/__image_snapshots__/alignments-features-test-tsx-color-by-strand-1-snap.png deleted file mode 100644 index 6dfe5b1c3d..0000000000 Binary files a/products/jbrowse-web/src/tests/__image_snapshots__/alignments-features-test-tsx-color-by-strand-1-snap.png and /dev/null differ diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/alignments-features-test-tsx-selects-a-sort-sort-by-base-pair-1-snap.png b/products/jbrowse-web/src/tests/__image_snapshots__/alignments-features-test-tsx-selects-a-sort-sort-by-base-pair-1-snap.png new file mode 100644 index 0000000000..f2b2ffea08 Binary files /dev/null and b/products/jbrowse-web/src/tests/__image_snapshots__/alignments-features-test-tsx-selects-a-sort-sort-by-base-pair-1-snap.png differ diff --git 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a/products/jbrowse-web/src/tests/__image_snapshots__/snapshot.svg +++ b/products/jbrowse-web/src/tests/__image_snapshots__/snapshot.svg @@ -1 +1 @@ -volvox80bpctgA020406080volvox-sorted.bam (ctgA, canvas)001111GTACAGAGTGACGCTCAAAGC \ No newline at end of file +volvox80bpctgA020406080volvox-sorted.bam (ctgA, canvas)001111GTACAGAGTGACGCTCAAAGC \ No newline at end of file diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/stats-estimation-test-tsx-test-stats-estimation-pileup-force-load-to-see-1-snap.png b/products/jbrowse-web/src/tests/__image_snapshots__/stats-estimation-test-tsx-test-stats-estimation-pileup-force-load-to-see-1-snap.png index d53ce4ac44..91b4da81e5 100644 Binary files a/products/jbrowse-web/src/tests/__image_snapshots__/stats-estimation-test-tsx-test-stats-estimation-pileup-force-load-to-see-1-snap.png and b/products/jbrowse-web/src/tests/__image_snapshots__/stats-estimation-test-tsx-test-stats-estimation-pileup-force-load-to-see-1-snap.png differ diff 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100644 index 0000000000..038be94030 Binary files /dev/null and b/products/jbrowse-web/src/tests/__image_snapshots__/synteny-test-tsx-switch-rows-regular-orientation-both-horizontally-flipped-rev-1-1-snap.png differ diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/synteny-test-tsx-switch-rows-regular-orientation-both-horizontally-flipped-rev-2-1-snap.png b/products/jbrowse-web/src/tests/__image_snapshots__/synteny-test-tsx-switch-rows-regular-orientation-both-horizontally-flipped-rev-2-1-snap.png new file mode 100644 index 0000000000..52dc216a52 Binary files /dev/null and b/products/jbrowse-web/src/tests/__image_snapshots__/synteny-test-tsx-switch-rows-regular-orientation-both-horizontally-flipped-rev-2-1-snap.png differ diff --git a/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap b/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap index 14e2c9693b..6504beaf88 100644 --- a/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap +++ b/products/jbrowse-web/src/tests/__snapshots__/ExportSvg.test.tsx.snap @@ -1,3 +1,3 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`export svg 1`] = `"volvox80bpctgA020406080volvox-sorted.bam (ctgA, canvas)001111GTACAGAGTGACGCTCAAAGC"`; +exports[`export svg 1`] = `"volvox80bpctgA020406080volvox-sorted.bam (ctgA, canvas)001111GTACAGAGTGACGCTCAAAGC"`; diff --git a/products/jbrowse-web/src/tests/loaderUtil.tsx b/products/jbrowse-web/src/tests/loaderUtil.tsx new file mode 100644 index 0000000000..4de45354ec --- /dev/null +++ b/products/jbrowse-web/src/tests/loaderUtil.tsx @@ -0,0 +1,24 @@ +// we use mainthread rpc so we mock the makeWorkerInstance to an empty file +import React from 'react' +import { QueryParamProvider } from 'use-query-params' +import { WindowHistoryAdapter } from 'use-query-params/adapters/window' + +import { Loader } from '../Loader' + +jest.mock('../makeWorkerInstance', () => () => {}) + +export function App({ search }: { search: string }) { + const location = { + ...window.location, + search, + } + Object.defineProperty(window, 'location', { + writable: true, + value: location, + }) + return ( + + + + ) +} diff --git a/products/jbrowse-web/src/tests/util.tsx b/products/jbrowse-web/src/tests/util.tsx index fe6dfaf3a0..7200d64c8f 100644 --- a/products/jbrowse-web/src/tests/util.tsx +++ b/products/jbrowse-web/src/tests/util.tsx @@ -68,12 +68,10 @@ export function getPluginManager(initialState?: any, adminMode = true) { return pluginManager } -export function generateReadBuffer( - getFileFunction: (str: string) => GenericFilehandle, -) { +export function generateReadBuffer(getFile: (s: string) => GenericFilehandle) { return async (request: Request) => { try { - const file = getFileFunction(request.url) + const file = getFile(request.url) const maxRangeRequest = 10000000 // kind of arbitrary, part of the rangeParser const r = request.headers.get('range') if (r) { @@ -126,7 +124,7 @@ export function canvasToBuffer(canvas: HTMLCanvasElement) { export function expectCanvasMatch( canvas: HTMLElement, - failureThreshold = 0.05, + failureThreshold = 0.01, ) { expect(canvasToBuffer(canvas as HTMLCanvasElement)).toMatchImageSnapshot({ failureThreshold, @@ -171,3 +169,31 @@ export function doBeforeEach( // @ts-ignore fetch.mockResponse(generateReadBuffer(url => new LocalFile(cb(url)))) } + +export async function doSetupForImportForm(val?: unknown) { + const args = createView(val) + const { view, findByTestId, getByPlaceholderText, findByPlaceholderText } = + args + + // clear view takes us to the import form + view.clearView() + + const autocomplete = await findByTestId('autocomplete') + const input = (await findByPlaceholderText( + 'Search for location', + )) as HTMLInputElement + + // this will be the input that is obtained after opening the LGV from the import form + const getInputValue = () => + (getByPlaceholderText('Search for location') as HTMLInputElement).value + + autocomplete.focus() + input.focus() + + return { + autocomplete, + input, + getInputValue, + ...args, + } +} diff --git a/scripts/getSuggestions.js b/scripts/getSuggestions.js index 8e842dfc1d..5e2973f87f 100755 --- a/scripts/getSuggestions.js +++ b/scripts/getSuggestions.js @@ -44,7 +44,8 @@ async function getFiles(dir) { .reduce((all, folderContents) => all.concat(folderContents), []) } -async function main() { +// eslint-disable-next-line @typescript-eslint/no-floating-promises +;(async () => { const child = cp.spawn('yarn', ['tsserver']) const files = await getFiles('.') @@ -99,6 +100,4 @@ async function main() { }) }) child.stdin.end() -} - -main() +})() diff --git a/scripts/release.sh b/scripts/release.sh index 18169e47d2..da681d973d 100755 --- a/scripts/release.sh +++ b/scripts/release.sh @@ -27,7 +27,7 @@ LOCAL_CHANGES=$(git status --short) yarn # make sure the tests are passing -yarn test --runInBand +yarn test # Get the version before release from lerna.json PREVIOUS_VERSION=$(node --print "const lernaJson = require('./lerna.json'); lernaJson.version") diff --git a/test_data/config_demo.json b/test_data/config_demo.json index 973d4c8b3c..09c7836ca7 100644 --- a/test_data/config_demo.json +++ b/test_data/config_demo.json @@ -427,13 +427,7 @@ "displays": [ { "type": "LinearBasicDisplay", - "displayId": "gencode_nclist_hg38_linear", - "renderer": { - "type": "SvgFeatureRenderer", - "labels": { - "description": "jexl:get(feature,'gene_name')" - } - } + "displayId": "gencode_nclist_hg38_linear" } ] }, @@ -603,7 +597,7 @@ }, { "type": "AlignmentsTrack", - "trackId": "nanopore_targetted_alignments_0.1", + "trackId": "nanopore_targeted_alignments_0.1", "name": "Nanopore amplicon alignments 0.1x (chr7:55,000,000-56,000,000)", "description": "Source http://bioinformatics.uni-muenster.de/share/NanoPipe_test_data/?lang=en", "assemblyNames": ["hg38"], @@ -637,7 +631,7 @@ }, { "type": "AlignmentsTrack", - "trackId": "nanopore_targetted_alignments", + "trackId": "nanopore_targeted_alignments", "name": "Nanopore amplicon (chr7:55,000,000-56,000,000) [causes out-of-memory]", "description": "Source http://bioinformatics.uni-muenster.de/share/NanoPipe_test_data/?lang=en", "assemblyNames": ["hg38"], @@ -1022,6 +1016,36 @@ } } }, + { + "type": "AlignmentsTrack", + "trackId": "NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome", + "name": "NA12878 Exome", + "assemblyNames": ["GRCh38"], + "category": ["1000 Genomes", "Alignments"], + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "locationType": "UriLocation", + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram" + }, + "craiLocation": { + "locationType": "UriLocation", + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai" + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" + }, + "faiLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai" + }, + "gziLocation": { + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi" + } + } + } + }, { "type": "AlignmentsTrack", "trackId": "chm1_pacbio", @@ -1344,6 +1368,19 @@ } } }, + { + "type": "FeatureTrack", + "trackId": "skbr3_bedpe", + "name": "SKBR3 BEDPE", + "assemblyNames": ["hg19"], + "category": ["SKBR3"], + "adapter": { + "type": "BedpeAdapter", + "bedpeLocation": { + "uri": "reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.bedpe" + } + } + }, { "type": "FeatureTrack", "trackId": "variants_hg002_ncbi", diff --git a/test_data/config_dotplot.json b/test_data/config_dotplot.json index 245a5b8d17..7fe31cc164 100644 --- a/test_data/config_dotplot.json +++ b/test_data/config_dotplot.json @@ -147,6 +147,41 @@ }, "assemblyNames": ["peach", "grape"] } + }, + + { + "type": "FeatureTrack", + "trackId": "grape_genes", + "name": "Vvinifera_457_v2.1.gene.sorted.gff", + "adapter": { + "type": "Gff3TabixAdapter", + "gffGzLocation": { + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz" + }, + "index": { + "location": { + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz.tbi" + } + } + }, + "assemblyNames": ["grape"] + }, + { + "type": "FeatureTrack", + "trackId": "peach_genes", + "name": "Ppersica_298_v2.1.gene.sorted.gff3", + "adapter": { + "type": "Gff3TabixAdapter", + "gffGzLocation": { + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz" + }, + "index": { + "location": { + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz.tbi" + } + } + }, + "assemblyNames": ["peach"] } ], "defaultSession": { diff --git a/test_data/config_human_dotplot.json b/test_data/config_human_dotplot.json index 8a8ef4600d..e54da949ea 100644 --- a/test_data/config_human_dotplot.json +++ b/test_data/config_human_dotplot.json @@ -29,7 +29,22 @@ } } ], - "tracks": [], + "tracks": [ + { + "type": "SyntenyTrack", + "trackId": "hg19ToHg38.over.chain.gz-1645073157673", + "name": "hg19ToHg38.over.chain.gz", + "assemblyNames": ["hg38", "hg19"], + "adapter": { + "type": "ChainAdapter", + "assemblyNames": ["hg38", "hg19"], + "chainLocation": { + "locationType": "UriLocation", + "uri": "https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz" + } + } + } + ], "defaultSession": { "name": "hg19 vs hg38", "width": 1850, diff --git a/test_data/config_synteny_grape_peach.json b/test_data/config_synteny_grape_peach.json index dd065f292a..47fed0b8cf 100644 --- a/test_data/config_synteny_grape_peach.json +++ b/test_data/config_synteny_grape_peach.json @@ -1818,29 +1818,15 @@ "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { - "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz", - "locationType": "UriLocation" + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz" }, "index": { "location": { - "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz.tbi", - "locationType": "UriLocation" - }, - "indexType": "TBI" + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_457_v2.1.gene.sorted.gff.gz.tbi" + } } }, - "assemblyNames": ["grape"], - - "displays": [ - { - "type": "LinearBasicDisplay", - "displayId": "grape_genes_linear" - }, - { - "type": "LinearLollipopDisplay", - "displayId": "grape_genes-LinearLollipopDisplay" - } - ] + "assemblyNames": ["grape"] }, { "type": "FeatureTrack", @@ -1849,29 +1835,15 @@ "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { - "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz", - "locationType": "UriLocation" + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz" }, "index": { "location": { - "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz.tbi", - "locationType": "UriLocation" - }, - "indexType": "TBI" + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.1.gene.sorted.gff3.gz.tbi" + } } }, - "assemblyNames": ["peach"], - - "displays": [ - { - "type": "LinearBasicDisplay", - "displayId": "peach_genes_linear" - }, - { - "type": "LinearLollipopDisplay", - "displayId": "peach_genes-LinearLollipopDisplay" - } - ] + "assemblyNames": ["peach"] }, { "type": "SyntenyTrack", diff --git a/test_data/config_wormbase.json b/test_data/config_wormbase.json index 3262a6f74c..5047f10d62 100644 --- a/test_data/config_wormbase.json +++ b/test_data/config_wormbase.json @@ -1,5 +1,34 @@ { "assemblies": [ + { + "name": "c_brenneri_PRJNA20035", + "sequence": { + "displays": [ + { + "displayId": "c_brenneri_PRJNA20035-LinearReferenceSequenceDisplay", + "type": "LinearReferenceSequenceDisplay" + } + ], + "trackId": "c_brenneri_PRJNA20035-1646426635733", + "type": "ReferenceSequenceTrack", + "adapter": { + "fastaLocation": { + "uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz", + "locationType": "UriLocation" + }, + "faiLocation": { + "locationType": "UriLocation", + "uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai" + }, + "type": "BgzipFastaAdapter", + "gziLocation": { + "uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi", + "locationType": "UriLocation" + } + } + }, + "displayName": "c_brenneri_PRJNA20035" + }, { "name": "C. elegans (N2)", "sequence": { diff --git a/test_data/grape_peach_synteny/config.json b/test_data/grape_peach_synteny/config.json new file mode 100644 index 0000000000..7f54b0aed4 --- /dev/null +++ b/test_data/grape_peach_synteny/config.json @@ -0,0 +1,57 @@ +{ + "configuration": { + "rpc": { + "defaultDriver": "MainThreadRpcDriver" + } + }, + "assemblies": [ + { + "name": "grape", + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "grape-ReferenceSequenceTrack", + "adapter": { + "type": "ChromSizesAdapter", + "chromSizesLocation": { + "uri": "grape.chrom.sizes", + "locationType": "UriLocation" + } + } + } + }, + { + "name": "peach", + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "peach-ReferenceSequenceTrack", + "adapter": { + "type": "ChromSizesAdapter", + "chromSizesLocation": { + "uri": "peach.chrom.sizes", + "locationType": "UriLocation" + } + } + } + } + ], + "connections": [], + "defaultSession": { + "name": "New Session" + }, + "tracks": [ + { + "type": "SyntenyTrack", + "trackId": "subset", + "name": "subset", + "adapter": { + "type": "PAFAdapter", + "pafLocation": { + "uri": "subset.paf", + "locationType": "UriLocation" + }, + "assemblyNames": ["peach", "grape"] + }, + "assemblyNames": ["peach", "grape"] + } + ] +} diff --git a/test_data/peach.chrom.sizes b/test_data/grape_peach_synteny/peach.chrom.sizes similarity index 100% rename from test_data/peach.chrom.sizes rename to test_data/grape_peach_synteny/peach.chrom.sizes diff --git a/test_data/grape_peach_synteny/subset.paf b/test_data/grape_peach_synteny/subset.paf new file mode 100644 index 0000000000..8a17a1e5c7 --- /dev/null +++ b/test_data/grape_peach_synteny/subset.paf @@ -0,0 +1 @@ +Pp01 47851208 28845209 28845603 - chr1 23037639 315959 316369 330 413 2 NM:i:83 ms:i:328 AS:i:328 nn:i:0 tp:A:P cm:i:6 s1:i:46 s2:i:0 de:f:0.1791 rl:i:921840 cg:Z:145M2D3M3D1M3D5M2D6M2D7M1D6M2D12M2I9M1D2M1I160M3D35M diff --git a/test_data/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.bedpe b/test_data/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.bedpe new file mode 100644 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115881_1 , + + INV +X 148736231 148736231 X 148830362 148830362 115885_0 , + + INV +X 148762214 148762214 X 148804389 148804389 115887 , - - INV +X 149570438 149570438 X 149586202 149586202 115897 , + + INV +X 152410968 152410968 X 152519872 152519872 115958 , - - INV +X 153819591 153819591 X 153841359 153841359 115981 , + + INV +X 154566439 154566439 X 154733777 154733777 115991 , - - INV +X 154790191 154790191 X 154803272 154803272 116002_1 , + - DEL +X 155032961 155032961 X 155216352 155216352 116009_1 , - + DUP +X 155033487 155033487 X 155214085 155214085 116007_2 , + - DEL diff --git a/test_data/volvox/config.json b/test_data/volvox/config.json index ae156fa1e6..acd6aad470 100644 --- a/test_data/volvox/config.json +++ b/test_data/volvox/config.json @@ -1,8 +1,4 @@ { - "plugins": [ - { "name": "UMDLocPlugin", "umdLoc": { "uri": "umd_plugin.js" } }, - { "name": "UMDUrlPlugin", "umdUrl": "umd_plugin.js" } - ], "assemblies": [ { "name": "volvox", @@ -72,6 +68,22 @@ } } }, + { + "name": "misc", + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "misc_asm", + "adapter": { + "type": "IndexedFastaAdapter", + "fastaLocation": { + "uri": "misc.fa" + }, + "faiLocation": { + "uri": "misc.fa.fai" + } + } + } + }, { "name": "volvox_del", "sequence": { @@ -107,6 +119,60 @@ } } } + }, + { + "name": "volvox-rev-del", + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "volvox-rev-del-ReferenceSequenceTrack", + "adapter": { + "type": "IndexedFastaAdapter", + "fastaLocation": { + "uri": "volvox-rev-del.fa", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "volvox-rev-del.fa.fai", + "locationType": "UriLocation" + } + } + } + }, + { + "name": "volvox-simple-inv", + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "volvox-simple-inv-ReferenceSequenceTrack", + "adapter": { + "type": "IndexedFastaAdapter", + "fastaLocation": { + "uri": "volvox-simple-inv.fa", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "volvox-simple-inv.fa.fai", + "locationType": "UriLocation" + } + } + } + }, + { + "name": "volvox_random_inv", + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "volvox_random_inv-ReferenceSequenceTrack", + "adapter": { + "type": "IndexedFastaAdapter", + "fastaLocation": { + "uri": "output_prefix3.simseq.genome.fa", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "output_prefix3.simseq.genome.fa.fai", + "locationType": "UriLocation" + } + } + } } ], "configuration": {}, @@ -1342,6 +1408,7 @@ }, { "type": "SyntenyTrack", + "category": ["Synteny"], "trackId": "volvox_fake_synteny_alt", "name": "volvox_fake_synteny_alt", "assemblyNames": ["volvox", "volvox"], @@ -1356,6 +1423,7 @@ }, { "type": "SyntenyTrack", + "category": ["Synteny"], "trackId": "volvox_fake_synteny", "name": "volvox_fake_synteny", "assemblyNames": ["volvox", "volvox"], @@ -1786,6 +1854,7 @@ }, { "type": "SyntenyTrack", + "category": ["Synteny"], "trackId": "volvox_del.paf-1658813720770", "name": "volvox_del.paf", "assemblyNames": ["volvox", "volvox_del"], @@ -1798,6 +1867,21 @@ } } }, + { + "type": "SyntenyTrack", + "category": ["Synteny"], + "trackId": "volvox_ins.paf-1658813720770", + "name": "volvox_ins.paf", + "assemblyNames": ["volvox", "volvox_ins"], + "adapter": { + "type": "PAFAdapter", + "targetAssembly": "volvox", + "queryAssembly": "volvox_ins", + "pafLocation": { + "uri": "volvox_ins.paf" + } + } + }, { "type": "VariantTrack", "trackId": "variant_effect_demo_data", @@ -1825,6 +1909,168 @@ }, "category": ["VCF"], "assemblyNames": ["volvox"] + }, + { + "type": "SyntenyTrack", + "trackId": "volvox-rev-del", + "category": ["Synteny"], + "name": "volvox-rev-del", + "adapter": { + "type": "PAFAdapter", + "pafLocation": { + "uri": "volvox-rev-del.paf", + "locationType": "UriLocation" + }, + "assemblyNames": ["volvox-rev-del", "volvox"] + }, + "assemblyNames": ["volvox-rev-del", "volvox"] + }, + { + "type": "FeatureTrack", + "trackId": "volvox-rev-del-annotations", + "name": "volvox-rev-del-annotations", + "adapter": { + "type": "Gff3Adapter", + "gffLocation": { + "uri": "volvox-rev-del.gff", + "locationType": "UriLocation" + } + }, + "assemblyNames": ["volvox-rev-del"] + }, + { + "type": "AlignmentsTrack", + "category": ["Alignments"], + "trackId": "volvox-simple-inv.bam", + "name": "volvox-simple-inv.bam", + "adapter": { + "type": "BamAdapter", + "bamLocation": { + "uri": "volvox-simple-inv.bam", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "volvox-simple-inv.bam.bai", + "locationType": "UriLocation" + }, + "indexType": "BAI" + }, + "sequenceAdapter": { + "type": "TwoBitAdapter", + "twoBitLocation": { + "uri": "volvox.2bit", + "locationType": "UriLocation" + } + } + }, + "assemblyNames": ["volvox"] + }, + { + "type": "AlignmentsTrack", + "category": ["Alignments"], + "trackId": "volvox-simple-inv.cram", + "name": "volvox-simple-inv.cram", + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "uri": "volvox-simple-inv.cram", + "locationType": "UriLocation" + }, + "craiLocation": { + "uri": "volvox-simple-inv.cram.crai", + "locationType": "UriLocation" + }, + "sequenceAdapter": { + "type": "TwoBitAdapter", + "twoBitLocation": { + "uri": "volvox.2bit", + "locationType": "UriLocation" + } + } + }, + "assemblyNames": ["volvox"] + }, + { + "type": "AlignmentsTrack", + "category": ["Alignments"], + "trackId": "volvox-simple-inv-paired.cram", + "name": "volvox-simple-inv-paired.cram", + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "uri": "volvox-simple-inv-paired.cram", + "locationType": "UriLocation" + }, + "craiLocation": { + "uri": "volvox-simple-inv-paired.cram.crai", + "locationType": "UriLocation" + }, + "sequenceAdapter": { + "type": "TwoBitAdapter", + "twoBitLocation": { + "uri": "volvox.2bit", + "locationType": "UriLocation" + } + } + }, + "assemblyNames": ["volvox"] + }, + { + "type": "AlignmentsTrack", + "category": ["Alignments"], + "trackId": "volvox-simple-inv-paired.bam", + "name": "volvox-simple-inv-paired.bam", + "adapter": { + "type": "BamAdapter", + "bamLocation": { + "uri": "volvox-simple-inv-paired.bam", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "volvox-simple-inv-paired.bam.bai", + "locationType": "UriLocation" + }, + "indexType": "BAI" + }, + "sequenceAdapter": { + "type": "TwoBitAdapter", + "twoBitLocation": { + "uri": "volvox.2bit", + "locationType": "UriLocation" + } + } + }, + "assemblyNames": ["volvox"] + }, + + { + "type": "SyntenyTrack", + "trackId": "volvox_inv_indels", + "name": "volvox_inv_indels", + "category": ["Synteny"], + "adapter": { + "type": "PAFAdapter", + "pafLocation": { + "uri": "volvox_inv_indels.paf", + "locationType": "UriLocation" + }, + "assemblyNames": ["volvox_random_inv", "volvox"] + }, + "assemblyNames": ["volvox_random_inv", "volvox"] + } + ], + "plugins": [ + { + "name": "UMDLocPlugin", + "umdLoc": { + "uri": "umd_plugin.js" + } + }, + { + "name": "UMDUrlPlugin", + "umdUrl": "umd_plugin.js" } ], "aggregateTextSearchAdapters": [ @@ -1844,6 +2090,23 @@ "locationType": "UriLocation" }, "assemblyNames": ["volvox"] + }, + { + "type": "TrixTextSearchAdapter", + "textSearchAdapterId": "volvox-rev-del-index", + "ixFilePath": { + "uri": "trix/volvox-rev-del.ix", + "locationType": "UriLocation" + }, + "ixxFilePath": { + "uri": "trix/volvox-rev-del.ixx", + "locationType": "UriLocation" + }, + "metaFilePath": { + "uri": "trix/volvox-rev-del_meta.json", + "locationType": "UriLocation" + }, + "assemblyNames": ["volvox-rev-del"] } ], "internetAccounts": [ diff --git a/test_data/volvox/misc.fa b/test_data/volvox/misc.fa new file mode 100644 index 0000000000..4b3898cdda --- /dev/null +++ b/test_data/volvox/misc.fa @@ -0,0 +1,18 @@ +>t1 +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +>t2 +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +>t3 +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT +ACGTACGTACGT diff --git a/test_data/volvox/misc.fa.fai b/test_data/volvox/misc.fa.fai new file mode 100644 index 0000000000..d87e965901 --- /dev/null +++ b/test_data/volvox/misc.fa.fai @@ -0,0 +1,3 @@ +t1 60 4 12 13 +t2 60 73 12 13 +t3 60 142 12 13 diff --git a/test_data/volvox/output_prefix3.simseq.genome.fa b/test_data/volvox/output_prefix3.simseq.genome.fa new file mode 100644 index 0000000000..8cfeff68c1 --- /dev/null +++ b/test_data/volvox/output_prefix3.simseq.genome.fa @@ -0,0 +1,2 @@ +>ctgA +CGGCATTGGTTGCGGAGTTGAACATACGGCGCGATTAGGAACACTTCCGTCTCTCACTTTTATACGTTATGATTGGTTCTGCCTTGGTTAGATTGGTAGTAGTAGCGGCGCTTAAATGCTATACCAAATTGAGAACTCGAGCGCCTAGGCAAATCAGAAGCGGTTAGTTATGAGGGATTTAGGCGCTGCGGCCAAAGGTACTTCTTATGACACGTTGGACAAGCGGTTAGAAGACCAACCTGACCACCAAACCGTCCATATTAAACCGGTTATCTTCTCGAACGGCGGCTGTGGTCTCACCATGCAATTTAAACAGGTGAGAAAGATTGCTACAAATACGAGACGCTGTCACCGATGCTGTTCAGTCTGTTGCTCCTGGTCGCTCCGTTGTACCCAGGCTACTTATGAAAGAGCGCAGATACTGTAGGACGGTATCGATCATGGTAGCATAGCATTCTGATAACATGTATGGAGTTATCCGTCGCTGGGGCCGGACGGTCCGTTTATTTTGACCCTTCTGAAATGATTAGCATGCAAAGATTGCGACTAGTACAATACGGTACATCGGTGATTCTACATCTGGGTACCATAAACAAATGTGACGGACCGAATTTGGACGGTGCGTTCTCAAGCTGGTTGACGCCTCAGCAACATAGGCTTCCTTTCCCACGCATCTGCGAGAAAAGCAACTCAATTAACCCCTTGGTACCGTGGGCAGCATTCTGTCACGGTGAAGCCCAGTTCATCCTGAATCGCCGAATGGGACTATAAAAGTTAGCTTTATCTTGCAGGCTGCCGCGAGTGGGATGGGTTGGTCACAGGAATCAAAGCGGAGGCACTACATGCAGCTTATTTACGACGGTATTCTTAAAGTTTTTAAGACTAATGTATTTCATGGGTAGTTCGGTTTGTTTTATTGCTACTACGGCTATCTTGTAGACGACACCTACTTTTAGCACTACGCCGAGCGCAATAACCCCCCGGAAAGCAACTTGCTACTGGGAGGGGGTTTATCATCCATTACGGCTAGATAGGGGTTATCAGTACTACCAAGAAGTATTCGCTAGGAGGGTGGATATTAACAGTGAGAAAAAGTTCGGACTGGGCATGAAACGTGTGTCAGACGGAGCTTGAGGGACTGAATGGGTTCCCAGGCCCTTGAGGTGGATGTCACCTCGGGTTACGTGCCTCTATTACAGAGGTATCTTAATGGCCGCATCCAGCCTTGTGGCTGGGTCTACGTACGCGTGGGCACCATACGTATGTCTGGCAGGAAAGGTCAATCATGCTTGTTTCTCGTCGCAGAAACGTTCACATACTATTGGCTCGCGGGATCGAACGGGCCTGATTATTTTTCCAGCTCCTGCGTTCCTATCACGCCAATCTGAATCGCTAAAAAATGTTATAGACATGCCCATTGCTAGCAAGGATGGAAAACCGCATTCTACAACACCCTAGAATTACTTCAGCACTAACTCTAAGATACCGGAAAACCGTAGGTGAACCACTTGTTGAAGGGCAATGCCTAGGTGCCTTGCACTGGCGATTCGTGGAGTAACCTTGCTACCATTTCACCTTTTCTAGGTATGTTACATGCGATCGCCGATTGTAGTCAGTCGTAACGCAGGAAGGAATCAATACATGACGGTTTACCGAAAGCTATGAGGGCGCATCATAACGTGCGCTCTTTACTAAGGACACGTGTAGTCGGCTGATTTCGCGCAGAACTATACTTTCGTCTCACCGGACAGTGACTGCTCCGAACTTGGGGGCACTAGTAGATTCTAGCTAGAGACCGCAAAGAAACGCGAAAATGCCGACTCGCTAGGTGGCTATGGCGTCCAGCTATAGCTTGTGAGTTTTATGTAACGACAGCGATTCCGCGAAGTTTTCCCACGACACGGAGTCGTGACAATCTATTGAGAGGAAATGTCAGACAAAGGCTACCTCGCTGATGAGAACGATCCGGCGACTTGAGGGAATTCTACGGGGAGATCAACCGTCTGTTACCAACGAAGACAGCTGGTGCGCTCGTTAGCATATGAAGGGTATTTCGCAGCCTAATATCTGTTCCGTTGCGCTAAAACGCATGCAACGGCCGCTTTTATCACCGGACTAGCTATGTGCGAGCATCTATGTTAACGTGAGATTGAAGGTTTGTGAACTTTGATGAAAGGTAGACTTCAATTACCGAGTTACAACGAATGTGGGGGCCTATTTACTACCCACAGGTATCATAATGAACATCTCTTCTGTGAAATACTGCCGGTACGCCGAGAAGATCCCCACATTGCGTGTCACCAAGACCCAGTGTATTGGGCGTCGCTGGTTATAGTATCGCGGAGGCACCCGATGTGCTGCTAATCGACTACAAACTCGCACCACAGAGGCGACCGGTGCGGGATAGGGGGAACGCGAAGCCACGTGGTGGTACCGCTCCTGATGATACGAGCATGTGCTGGCACGGCCTGCCCTATGTCCAGCTAACAGGTGTCACATAATATCGCATCTATAGTTGAGTATGCTTATCGCGTGAGCGTTACTTGTCGATTCTCGGGTAGAATCGTCGTAGCTCATTCTAGTCCTTAGCGTAAGCAACGATATCCCGGATATTATAGGGGCAATAGGTCCACCCACCACGAGGTGTGACGAATATTTAACGCCCTAAGTACTAGTTTAACGGAGACTATAAACAATTATGCACGTTGAAAGATTAGGGTACTGCACACGTGTCACGTTGACGATGTAAACACCATCAATAGGTTGTTCTTATGCGATGCCCATACCTGCGGTGCAACGTCCTAAACTTATGCGAAACTTCTAATTCAGCCGACGTTGAGAACGCCAGTTTTTCCACATAAACGGACGACCTATTATCTCTGTAGTACAAGGAAAGCCCAGATCAAAAAATTGGAGTCTTGTCCGTAGCTCTTGGGTGGAGAGTGTACCACGAAACCTATACTAGGACTCAATTTCTCGTTCCACGCCCGGACATAGCAGCCTAGTGTTGTAGGTAGGCGTACAGAGGGCTCTATCCGAATAGCACAAAGACTCACCTAGTGCGTATAGGTCGTGCTCTGCGGTTTACGGCTCCACAGAAGAAATACCCACTGTCAGCTTTGTCGTGGGGACTTAGCCAAAACCTGAACGCAAACCGCATGGAGCTCTGTTTTGGTGGCGTGGAGTGCCCGCCTTTATGCTGGGTCAAAAGTACGTATATGATTCGGGGTCGGGGCGAATTGGCTCTTATGGTTTAGTAACTAGTTATTGTGCATCAGAACCGACTTATGCCCCGATTTTGCACCTCCCGAGAGAAATGGTACTAGTCATTGTCTCGGGGTCATTTCAACTCAAGGGATAATCTGCCACGCGGTACCGCCGAAATCCATCCCGAACGGCTGGTACTCTATGTTCTGGAGACCGAAATGGAGCCAGCTGCTATCAACGGACGCAAACCCTCGCTCTTTTCTATTGGCCCGGAGCTATTCGACTAATACTTGCGATGGCTGGGTTCATCTCTCTGCTTCGGCCGCGATCCTGCTGCCTATGGCCACAACACGAAAGAGCTGGCACGATCTTGGATTAACGTCCTCCACCATAGTCCAACGGACAGTGAAATAGGAGAGCGCACGGATACGAGTACGACGGGCCGCCCAATTACGCTGGTCCTTGTGTTATACTGTTTACTTGCCCGGTAAGGTGTACAGCATTGTACCCACCGGTGGACGGACCTTAGCGTCGTCTCCGCAGGTGTGGAGATTTCGCTACCTGTTGCATTGGGGCCTCGCCTTACGTTTTTTTCGACGGAGCGACTGCGTGCCCGCCAGGCCAGACCCTCATCATGGGATTTTTACTGCCTTGGACGGCAGATTCTGATGCTGGTAACGCGCTTGGCACACACCCTGCGTCGTAATTACGTATATATACGCTATCACGCTCTATTTTACCAGGGCGGGCCCCGCCTCAACGATCGGTAGTCTCCGTTAGAACAGTTGCTCTCCGTTAGCACTCACAACTCGGAGAATGAGCTTACACAGTCGTATAGTTCACTTTTTCCGGGCGACTTACTCTCCACAGTTCCCTGGAATGCGTTCGTACAGGGAGCTCCTGGGTCTAATGTGCTACCGCCTAACTTCGTTAGTGGTAAGGTCTCGTGTGCACCTCCAAATTAATCGCTACCAGTTTTCTATTAACCCCGAAACGCGGTTTGCTACGGGTTGGAAGCGAGTACCGGTTAAGGGAAGTTACGTAAAACGCCAACATAGTGAGGATGCTTAAAACACTGCATGCGAACAACGACCGAACGAGGAGCCATAATAAACAAAATGGATGGTGGTTAGAAATCCGCGCACAAGTGTCGTGCCACTCTCGTAAAGAATGATTGCTTAGCTATCTATGAGAAACCTAATGGCACGCACTGTGTCGCCGAGGAAAAACCACCATCGACAAGACGCTGAAATCGAGAATAGACACAACGTGCAGCGCGCGTACTATTAAGCACGATACCAGCCATCTTGAGCGCAGACGATGATCAGCCTTACGGAGATTACTTCTAAAGCGGACACCTCACGTAGCTCTCTATCGATGCATTGCATGCGCATGGCTTGAGCGAACCACTGCTAACGCTTGGATGACGTTGTTAGTCGGATTCACTCCATACTGTCCTTGTTAATCATCATAACTTCCCGAATTAAAACTCATTTTTCCTACCCTCATTTGTTTCATGGCGGCTGATCGACAACAGGCTTGTAGCGCACGGCTCTTGCAGTAGAATAACCATAGTCTTATCGCAGCCGCAGGTCAGCCGACAACACGCTATATAATATATCCCAGACTTCCACTGCGGTATTTTGGATCGTGGCGTCTGGGACAGTCACACTACTTTAACGGGAGCGCCGTTCAATGTCACTGCGAATGAGTCCATCCGCAGTTCGGTTGCGATTTTATTCTTCCCTGCGCCATCTGTCCGGATTCCTTCTTCTTGTCGGAGAATCGCCACTGCTCGATCAACAACTCATCAGTACTTATTGACCGTTTCATGCTATTACACCGGTCACACTGATGATAACGCTGCGGTTTATCCCCCCCAATGACGCGCACATCAGCGTCTTCTTTCGGGTGCGTCCTGTCGTACCCCTATTGCTCATGCATCTCCCAGCCGAGCAATGCTTTGGACAGGATGGTAACCAAGCTGGAGTGGGTTCTAGCGTGGGTTCGACACAGCTCGGTTCGTATAACCAACCGCATGCGAACTGCGAGTGCCTCGCCCCGAGCGCCGCTGTCTACTTTGTTTAGAGGAAGAAGCAACAGCTGCACCAGCAATCCGCATCTGCATATAGGTGGCCGTCTCCTCCGTGGCGCGCCGCTACGTTTAGCGCACGTGCAAAAGGCTTGTTACTATAGTGCGTCACACGTTGGTTCGGAGACGGTTCACCTCGAGCGCGCTATGTCGGATCTGCGCCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAACACCTGGGAAGACTACGGTTATATATGATGGAACCCTCACAGCATTCTAAAGGTTTGACAAACTTAAAAATGTGGGCCGCGGCCTGCTGTGAATCCCGGACGGTTTGGCCAATATAGCCTAGGAGTCTTTGGAAGGTAAGCTTTTCCTAGATCACCATACTATCGTTGTCAGTGGCCAACGGTTTCGTTAACTCTCGTCGCGTACCCAGTATCGGCGCAATAGGCCTTTTGTAACCCTTGGAAGATTAGTCGATCGTAACGTTCAACCCAGGTGAGGGCAAACGCTTCCGTCGAGTTCTTCACTTTCAGGTACGTGCCACTTATCTATACCGGACACTTGTTAAGCAGTGTTTGCGGATGTGGTTAAATTTGATGGCAGATTTCTGCAACCCACATATTGGGTGTTTTAGCTATAGCTGTTCCTTCGAGGTCGTCGTTTAACCCTCCTGTTGCTAGATCATATGTATCGTTGTTCGAGACGCTAGTAGTCGCTCCTGACCGAATCTTACAGGGTTCGATCTCTGCTCGGCTCGTACGACTTTGCCGCTGGGCCGGTGCTATAATTATAATGATAAAGGGAGTCGCACAACTGCAGATTACTGACACTTGAAAGACTTGAAGCATAGTGTTGAATAGAAAAGTATACTGTGACAAAAACAGGGGCCTGTGTCAGTGTCCTCAGTGATCTGGATATCAATCACAAGCCTTGTTAGCAGAGATGGTTTCTGCCGTTACGCATAGTGAATGGCCGGACTTTAATATTGCCCTGCTTGCGCTAGCTAGTACTGCGGGGGCTCTCTTTCCCCCTATTGATATTCTGAGCGGGCAGAATGCGGGTAGATCAGCATTCATGTCAGGCTTCTATCAACGTCTCATTCACCCTTGGAGTGTGACCTACGTGTTAACAGGCAATGTAGCCACCGAGAAGCCCGTTCAAAGACAAATAAGCCCGAAATTAAACAGACACGGTACTATGGAGTGTGGTACCAGTGTTTGGTTTCAGCCTGTCGGTTAACCTCGCAGGGCTAGGAGAATGAGCTGCAAGTAGGTGATTACACGAAGTCTTCCCCCCCAGAAAGGGAACAGTCTTATGAGAGTAGAGAATGTCGTCTTATTGAGTTTGTCTATGCACTCCTATTATTCAAGAGCATGCCCACCGAAGAGATGCGTCGCTCGTAGCGTAGACGTCGTAATGACCCAGTGGCGTTCGGCCTATTCGCGTCGGACGCGCGCGCTACTACAACGAGAGGGTTCTGAAAGTGCATGTACACTGAAAATTCTAATGTTGAGTAAACAACGCGCTGACCAATTGTTCCAGGCTTGTGACATTATGGCTGTCTGCGCCCGCTCAATGATCATCAAGACGTTCATTGTATGTTAACGCATATCAGGTTTAGTTATCCTATACTTTTTACGCCGCGCGCTTGGAACAGATAATTCTCCCAGCGACTCGCGGTTTCAAAAAGAACCATGTTATACCATCCTGTTCCCAATTCTGCCTGGTGTGCGGAGAAAAGACCGCCTCCTAGATAGCGTACCCGCTCGGTATTGGTAAGGTGGGGAAGCCAAGTCGAACGCATATTTCTTGGTTATATCACAGGCCACGTTCTATACGGAAGTGGCCGGATACGATTTGACGTTCTACCCCGAGAGCGCATTCTTGTTTGTTACCTATCCGAACGCGGCGCTTCTTATTCCAGATTACCCAGAGCCGGAATGTGCGGCAAGCTTTATCCATGAACAGATCTGGCGAGACTCCAGCAGTGCTTAGATGCAGGTAGTCCGGCCGGGAGAACGTCCGTTCAGTGAGTGCGGTGCTTTATTTCAATCTGGACCCGACTGCGCTCAAGGGTTGCAAGTTGTTGTGCGCCCAGTAATAGGCGACTCGTCGAATGGTCTGGTACATTGCATTTTCATCGGTACGGCGCTTAAATAAGGCATTTCTCACCCCAGTAAGTTTAAGGGGTATCAGGACCCGAAGCTTCTCTCCGCTGTCCATATTGGAGGTAGATCATTGTGGATGTTATGCAATGAAACTAAAAGTTATGGTGCTCCCACCGGGGCGCTCTAAAGAAGAGTGAGCTAAATTTGATACATTTAAATTGCTATTCCAACCCGGAGTCCTGAACCGGAACAGTAATGAAACTTCAACCATGCCGGGACAGACCTAGAAGAAGGGAAGTTGCTGTATATGGGAGTAAAGCATCAATGGATGTGGTCCGTAATGGTGCCGGAAGTGACTATAGATGACGCACCGGTGGCATGCTATAGTATGTCCTACGGCGCCGCCGGACCTCGAAGCTGAAATCTAGACACCGGCACACCACTAGCCGTAGCGACGGTGCGCGGCACGCTGCCCTGCGCGAAGGCCGGCTAACACGCATAAAACCCCCAAACACTCGAGCTACGCGGGAATTCACTCAGGCTGTGCTTCGAAAACGTGTAGTCTCATTACAATAATCATAATACCTCCAAGACTCTGGTATGACTCTCTTACCGTAGGGACATTTCGGGCACTAGGGAAACGGGCCTTAGAGCTGAGGACTTTGAAACGTCGATAAAACCATCGCGGAACTAGCTGCGTTAGAACTCCATACGGGTCGCAAGCTTGGGTCCTGTCCCGGCAGCTGCAAGTGCTACGGCAGGAGGGGATCTACCTACGGCAGAACGAGCCCCTGCCGTAATGAGGCGCGTCTCTAATTCGTCAGTAAGTTACTATGTCCGGAGGACGCCTCTACGAGTTGACACTCTGGCTAGGCCACCTGTCCGCCGCTCGGGTACCCCCATCTGCTATCACAACTCACCTCGCCTTACGGAATTCTTGGTTGCCAGTCATCCGAGTCACTTAAGCAGCGTGGTACATCGTAATACCGTTTCGGGCGCCAGCCATATTCCCAGCCCAAGCGGCTGCATAATTACAGCGCCTGGCACGCTAATCGATCCCACAAGCCTTGGTAGATGACCCTTAGCCCTAAAGCGCCCTCTGACCTAAATCTGCACGTGATACTTGATTATTTGTAAATGAGCAGGACAGGGTAGATGAACCAAAGATATCTCTAGGTTTGCACAATTGCAGACAAATACATCCGCGCAAGCCCGGACGGCTGTACTCACACAGACTAGTCCATCTCCCTCAGTCAGCACTAAGATTCCCACGTGACCAGGGCGACGGGCTGCAGCCAAACGTATCTTGATATCTACTTAAGTCAAGGTTGACTCCGAACCCTATGGGTCGGGCCACAGGTCTTATTCTCGGCGTTCCATGCTTTGTTTCAAACTCGCTGCTATAAGAGCGTGAAAGCGCTGGAGGGCATAGTTTATGCCCAAATTGCCGCGTAGATCCGTCGGGTATGTCGCTATAATAGGACTGCTCGAGGTAGGCGGTAACGGCGTCCCGCCTTCAGTAAAGCGCGCGGAACTCGAATCGAGTTACAGGACTTGACCGAGGTTCATATCCAAGTTTATGTTACCCCACGCGATCGGAGTCCGGGATGCTCGATCTGCGACGAGCGGAAGACGGACCGAAATATCGTCAACCGCGCGCAGAACCATTAGCATCTAACCTTTAGCCTGGGTGTTAACGGGTGGCTCACTCGGCGGTTCCAGTACTCTTTGTGTCAACTTTCCGACAGTAAGTTGCGAACATGATGCTCTTACGTGATTCCCACAGTTTCCACTCAGGCATGCTTTCTTTATACACCAATAGTTATGGCGGCACCTTCAGCGACTCCCACGAAGGACGGCTATGACGTTCACCATTCGCCGCAAAGGCTCGCTAACGAGTTCTGTAGTTTGTTCCGGGCCAGATCCGTGCAACAGACCCTCTACCGCTGTTATTAAGTTACCAGCGTTGTCCTTACGACATGGTCGTCGAGTACTCGCGTAGTCAAACGCCAGGACTAGCAGTCGACGAGCATTATTGTCCGATACTTACTACAATACTTACCGATATTGACGGATCAAACTCCCTCCACTCAGGTCCCTACGTCCGGGACCGCATTTTGCATATATTGGTTCCCAGAGCGTATCTAAGTTAGTCTTTGACCGGTTCACCGATGCCTCGCGTAGAACGATGCTTCTCGTTACCTCAATGATAGGCTGTAACGTAAGTGCATTCCCAATCTCACTCGTGCCTTGTCCACCTTCCGTGAAGCGAAGCAATACCGGAATACGTGGCTTCGTAATATTTTGAGATATGGGGCTTCGGGACGCTCAAGACTTCTCATGACAAACAAAGATGAAGAGACTGCACCCTATCCCAGAGTAGCTGATGGACTAACGCTAATTTGGTCAGGGCAGCTATCGCATCCCGCAGGTGTAGGCGGAGACTTTTTTTTTTGCGGTTGACAGGTAATCTCACGGGGTATAAGCACGGTTATTTACGCAAGCGACGTCCCTGGGAGAATCCGCCCAGAGGACGTAGGACCCCATAATCCATAAATACTGCGGTCGAAACTTCCTTCGTGACAGAAACGCTTCTAGGGGATGCGGTCCCCGCATTCAGAGTTCTACTTTGGCCAGCGTGAGACTTAACAACTCCCTGTACTTACGCGGTACATTGACGTCGTTCAGTTCCAGTGTGACCTGTTACCGAATAACGTGTTCTGGATGGGACGAATACGACTGAAGTCCACTCCAAAGCACCTTTTGGGACTTTCCAACGAGCCTGTTGGTCCGTTAAGCGGTATTTAGCAAATAGCATCACCCTTGTCGGTAACCGAACTACCCATTGGGATCATCGTGAGCTCGAAACACTAGAGCGGACCAATAAGACGAAGATAGGTAACCGGAGCCCGGATGGACATTTGATTCGGCTCTAAAGCTTGTCGCAGAGAAAACTGGGGGGAAAAGCGGGTTGTTTAGTCACACTCCTCATCGGCAATCTACGCTCGCGGGGAATTGACTTTAGCGGCCCGCTTAGACAGGTGTGGGACACTAGCTAGACACGACATAACAGCACCTTCCTGGCCAGCCAGAAATAGTCCTGGACCCTGACATCCAGCCTTCCGACGGACCATAATGTGAGCCGTAGCGCCCACGACGATCAACGGGAGAAATTTACAAAAGGCTGTGTGAATGCTACGCTCGGACTTAGTCTACCATTGCCAATCGAAACGAAAACGCAACGCACAGCATACAAACGTTGTACCATGCCGGAGCGGTTGATCAATTACAGAAACAGAGGTCGGTATGTAATTAAACTATGATCCGAACAAATGTAGGTTTACACAGCTACGCTCGTCCATTGGCGTACGTGCATCGCGTGCTAATACTACGTCATGCCGGCCCGCGATGCACGTACGAAAGGAATACCCTGTCTGCCCCCCGCGCGAGTTACGCTGTCTACGGACGCACATACCGAGCACTGTCGTTCGAAGCCTATTGAGCCCAGCCGAGCTCCTTATGGCCGCAACGCTGGTGCGGCAGCTGATAAATTCCACAGTACACGATCCTCGTTAAGATCTCGGCATAGTAAGTCGTCATCATTTCACATGGTTAGGAGAGATAAATACATGGTTCTGGTACAACCACGGATTTGTAGGAACCCTTGGGCCTGGTGAGTGCTACATAAAATTCTCCGGTATGAGACAACCAAACGGGTGCTGGATGTTGATTCCCGGCCCAGAGTTAGATGTCCATATCATTCATCCATTGCCGACCGACCCAATGCCTAAATCAGAGGCGCCTAGCTAGTTCTTGTAGGTGTGCCACGTCCGGCCACGCAGACACGACCCGTCGATTCTTGGCGAGTGTCACCATACCGGATTGGCATCGAAGTCTTGGGAGAACTCAAGCTTTTGCACTTTCTGGGAAGTTAGCCAGTTTGGTGTGCGTATGCTTAGACAGTCAAACGCCCCTGGGACGAATTGCTAACCCTAGTTGCCACGCCGGAACCATCTTCTTAGGGAGAGAGACAAATCCGACGTTAGATATGTTCATCTTAGCGTCTTCGTGAGTCTGAAATGTATCACTCACCGCAGAATACGGCGAATGTCTGTTTGCCCTGGACTGACGGAATTGGCTTCAAAAGCCGACTAGATTTTGGTACGGTTCTATCCGCGATGTAATTACCTATCCTAGGTATATCGCTAGAATGCGAATAGCGAGTACAGTGTAGCAAGGCCCTTTGTTTAGCAAGTGAGTTTGCTCTAAACAGTTGTCAAAACGTAGGCACAATAGTGCGATTCTTCTAAATCCGGGAAGCTCATGGCCGCTGGGCAGAAAACAGAATAATTCAACCCTCCATTGTTCGTTTACAAAGCTCGATGAGTGCCCTTGCTGGACGAGGTTAGGCGGTTCTCTCGAGTTTCTGAGTTGATGGCTGGCGGGAGTAGGAGCACTTCCTACAGATTCGGAATTGCCTGGAGGACAGTTGGAAATAACCTTTGTCGATGCATGAGGTTGTGTTCTGGGAGTAGGCTCCCAAGGTAGCGGTCATGCTGGGGCAGCCCTAAGTTTGTTATTAGTGGCAGTTTGCGTCTGAAACTACATTAGCATGAGGAAGCTTCCTAACCCCGTTTTGCTCTGGAGGGATCTTCTAAAGCCAGGTATCGCCCGCTACGATGCTCGGAGCGGTGGTTCACAGGCTACCTTGCTCAAAGGCTTAAGGCTAATCATAGCAACAAGTGCGAAAGGACTCTTTCAGATTTCGGAAAGGGTGACACAAGGGCAGGGCGGTCCTACCCTTCTGATTCCCTACCGTTTTGTAGCAAGGGTCAAGGCTAGGTCTTATACGTCCCGAACCTTTAAACCACTATCCCACCCCTGAGGGGGGAAGTTGCGCGTTAAAGTATAGAATAACAGTACACTTATAGGTTCTCTTCCGGCGAGCCGTCATACAGCACCGAGCGCCGTTGAACGCGGATTAACGCGTATTGCGTGCAGAAAATAAACGCTCTGCCAGCATATTGGAGTGTCGCACTTGAAATATTGAACAACACCGCATTCAATAGCCTGATTGAGGAAGGACCGAATAGTAGGGCTTCACTACCTCCCTGACGGCCCTAGGACTTATACTCAAAAAGACCTTCCACACGACCACTTACCGCGCGAAGAGGGCTATATACGCATGCAATAGCAGATCTTGCCGTTCGCTGAGTGTCACCCGAAGGGTCAGAAAGGCAGATAGGGCGGAGAGACCAGGTCGACACCCAAGCAGCTCTCGTCTAGTGGTAGCAGCTATGTCGTGAGACGCAACATCAGGAGTCGTGTCTATCGTATGTACATCATTATTGTCAGTAATGACGGCTATCTGTGATAGGACTCGTCCTCAATACCCAGAGTTACGCTAAGAAGACGGCAGTCTATCAGTTAGAACGTCAGTATTGGCCTTTGAAGTCTATGCCATGCTACCAATCGTACGCTTAAACGCGAATCGGGAAGGCCAATCTAGGCGGTTTTGACCCCGGACTCTTAAGAGCTGTAGCCTAGTCCAATGATGGCTAGACATAAGTCAACGAATTTACTCTATACGAGGGGCGGGAACCGGCCAATTTTTAGAGAGCACGAGAGCCTTGTCAGCGGCCAGCACTACTATCCTCGAGTCCCTCTATCCTAGACGTAGTAACAATATACCCTAGAGAGAATGTCCGTCTAGGCTTCCGTCTAGCCCTTCGTTCGCGTGAACCGCCCGCTAAGTCCTTCCGTCAGTTCCTCAAGAGTGGTATTGGGCAGGCCCAGTCTTATAACGCATATACTTGTGGCACTCTATTACTTTACCAGCGATGATCACTGCGTTAATTAATCGGGAATTTACCAATGCACTCTCGAATCATGCTCACAGCTGAGCAACGGTGCTGCTCACACCAATTACATATGAGTCGTGTTTAGCGTTGGAGCGGAGATGATTTCCATCTGTTCGCGCGCATCACGAGTAACCAATATACGGTTATCCAGCGTATCTGTTCTGACCGGGTTGGTAGCGAACCCTTTTGCAAGCCGGCTTAAGTGATGTGAAGTGGGAGTGATAACTTAAGCCGCTCACTTCGGGGGGGACTCTTTATATTGGTGCTGGAATACAGAACGGCGTTCGTTAGTCGCCCTAATCGGGCGCACATGTAGTGGACGGTTTAAACGCCTACTCGATTAACACCACAGTAGGTACTCTATCAGCAGCGTGGTGCAATATGCTAGAAGTTTCACAAACTTTCCGCATGAGGCTCAGCGGCAGCGTCCACTCCCAATGGCCACGTGCCGGTAGCGATGTTTGGTCGGAATTAAGTCTCCTTCGGGATACGAACCGGATTTAAAGAGCCTCGGAGACGACTAAACGAATCGTCACGCATCTTGCCCAAGGTGCTGAGCCTTGTCGCCTTCTACATTAATGCAATGCGTTCGAAGCTCTGACCGCAAACAGGAATAAGTTCAGGACATGAAAAGTGCAAGGAGTTCGCATAATTGGAACGACCCACTTATATAGGTGCTTTTGAGAGATGTGTGTACGACCTCTTCGATGTCCTAGGTTACAATGCTCCGGTAAGTCAAGGCACATAGAAAGAACAACATAGCCAACTGAGAGTGCCTCATGTAGATGAAATACAACATCGCTTTAAGCTCTCAACCGATGTAGAGATTTTGGGCGGCGTTGACAGCGTGCGCTCCGTATTTGCATGGAAGAGACCAATTTGGTTCCGAATTCGTCTAACTCAACTAACATCATACTATATGCCGGATTCTCGCGGTTGGACCCCCCTGCCAATTCGGGTTAAAACCACTCCCCCCATGTAGGGAGCGGAACTTGTTACAATATCACAAAATATCAGTCCTTTCACGATCGCTCATATAGACGGAGAAGGGGACTGAGCTGTTAGATAGTGACGTCGAGCCCTGGCGTAACGGTGGCCCGCATTACCCAATTTTACCACTTTGTATGAGGAGCTCAACCTAAGTCAACACGCGACCATGCATACGAGGTCGCCTCAGTAATGGAGAAGGCTGCTGTTTGCATGGAGAATAGCGCTGGCTACAGCATCACACGATGTGACACTTGCTAATGTGAAGGAGGTGTTTGGGATGAGCCTACGGGGATGTTGTATCCCTGCCCTGTAGGCACGTTGGGACTTAGCGCGATATCTAGATAACTAAGGCGCCAGCCGCGGCTGTTTGCCGCGAAGTCGTGTGATGCTGTACAACGAAGGGCGAGCGTGTTAACATGAACACGTTACTAGACTAGATCCAAGCGTTATCGTTCGTTTGCAGTCTCCATGTTGTGCCGACAAGGACAAGCGACGTATCAAATCGACTGAAATGAATCAGCTACCTCAGACACATCGAGCTCTCGGTAACATGGGGCCTTGTGGTTGCACCGTAAAAGGGGGATCAGCCCATCCATCCTCTGTAAACCTACAATCGCGGCTAAGTATCACTACGCTTAATACGAACCATTAGACATTCGATCGAGAGACCTGGTTTGACTTCCCTTTTGCTTTAGTGGCCATCGCAACCGACCTCCCCTCCCTTACGCCTTATACACCTTCAGTGCAAATTCATGCTTCAGCGAACAACTGGACTGTCTGTTGGTACGTCCACGGGGGCTTATTCATTAGAAAGCCCCCTAACTGTCACCGTTATATGGTTCACACATGAGCTGATCACCTAGAGAGTCGTCATGCACATTCAGCCTAACAAGGAACAGTTATGGAGGATTATCTTCATTTGCAGCACCAATCGACGTTGTACTGGTCTATCTGTCGGTTAGTCCGCCGACCGGCGAGGCAAGCCCCCTATTTCACGGATAATGCTGGCCCGACGTCGATGAGTGTAAGTCTATAAGGCCGGCCGCGGTAGTTAACGAGACCAACATAGAACTATCATACTAGCTGGCAATGATCAATAGGGTCTAGTGCCACTGTCCTTCGAGCCCTCCCTAATTTAGCGCGACCGGTTTCCTATTGGCCTGTGGGGTTGCGGGCGCGTCCGCTTTTTAAAAGAATGGTCCTTAACACCTACCCGGAAGAATGTCATTGCGTATAGCACACTCTCCCCATTAGCCTAGACACGTCGTCGCCCGTCGGACTAGGCTGAATTTAATCCGGGGATATCGAACTTTCAGCGCTGTGCCTACGGGGACTCACGATGCTGTGAACCGCCCCAAGTCTCTGGGGCTCCCAAAATCCAGGTTGGATTACGGGACTCAGCGCCGGTACACGTTACGCATTACGGGGTGGAGTCCTAAGATAGGTGAATGAAAGGGCTTCGCTAAACCAGTAAGCATTTAACAGGACATCGGCGTCACGTCTCGCGTGATAAACCGGAGTGAGTTAACACGGCGCACAAGATCCTATTCCATGATAAACACCTTATGCCAATCCAGCGTCATCCCTCGCTGCCAATAAAATTTCACGACCTGCCTACTGACTAACCGTCATGAGAGATGAATTCCGACACCCGTCATCGACGTGTTGCAAGCACAGCCCCAGATTTAGGATAGGTACAGCTAACGTATGGGATGCTACAACGTGTGTTACATCAGAGTCCAGCGCAATAAAGTTATTAAGGCTGTTTTTTCGAGTACCTAGAACCCCGTCTATCCCGATGGCCTCTAGCTCCAGCGTGATTAAAAAGAGTATTTATTTCAAGCCGAAAAGGCGCCCTGGAGTAGTCCGGATACCAGTAACGAATTCAGGGGCGCACCCTGGTAGTGGTAACGTTGTCCCCTAACCACCAACTTTAATTAGGTAAGAGCCAGTAATTATTTACTACCCGCACCGGTCGCGACTGCCGCGACGCACAGCAAGCACTTAGGCGGTCTCTCAGGCTAGCGCGGTTCACGCCTCGTCTCTGAGTCGGTTGCCTTGTACGTGAACCGACTGATGCTTGACCATGAGGGTCATCGTCAGGGAAGTGAGGGCCGAAGTGGCCGCGCCGGAGTGTGCCTCGATGTTACCTTACACCGAGAAACTATGACATGTTACTGACCGGAGCATAGCATTTGTTCGGAGCGTCATGACCCGTCCCAGCCGATCTGCACCATTCAGTGACCATCCACAAGTCTCTAGGGTTTAGCCAAAGGTGACAGGTCAAGCACTTGCGCATCGCCTAGTCGATTATGCAACGTCTCTGAACAGTAGCACTTATCTCCCGCCGTGTACTCACGCAGTTTGAACTTACTATACATACGCCTACTATTGCGTTGCTAACACAGCGTCCTAATACCTCACTTGGCAGAGGGTACCGCGACGCCTCCTAGTATGGGGGGAGTCAGGTCAGAGTGTATAGAGATGCGATTTTTATTCCCGCATAGGGGTTCAGATGAATCGACCTCTCATTTGTAAAAGGAGGCGCAGAATTCGCTGATACGATCGCTAAGGCACGATAAGCAGGGAATGAAGGTTGGAGCAAGATAATATCCCCGGACGCGGGTCCTGTCGCAACGAGCGGCCGTGAGACCTCGGTGCGCACCGGCTTCGATCAGGCCGAAAAAATCGACTGCGTGACGATATTTTTGCTACTGTGGGGGATTTATGTCCCGGTAGTGCGTTCTAGCAGAGGATAAACTTTACAAGGGGCGAATTGGTGTCAGAGCGCCCTCCGTGCTATTCCGCGGGCCACACCGGCCGTTAATGGCACTTCGGGTTAGAGGATGGGTTATTCATCTTCCAGGCATTAAATCGACCGACCGCGGTTATGCTGCCTACTTAGCCATTTCCTAAAACAGGATGTAAAAAGGCCGCGAGGGTTCGAACCTATGGTTGAGATACAGAGTCATAGAGTCAGATGCGCAGGGAGCGCACGGATCCACATGGCAGTTAACTAATTATTAATATCGAGTTACTCCCCCCTTAGGCCTCGTATGGGGTCTTGCAGTCGTCCTCCGAGGTTATTCTGTCTCGTTCCAACGCTATTCGTTACCACTTTGCACCTCTTTGCTAAGCAGGATTGAGAACATCTCACTCACTACGAGCCTTGACTTTCAGCACGCGCGTACGAGGCACTGGGCTTGCCTCGTCCTTTGCCCCGAAACGGGAGCTAGTGTAGGTGCCTTCCCGCCCTGACTGATGTCACGTCTATCGGTTTATTAAGGTCGGGGACCATTACGAGATTACCCCGCGACCTTCGTCCAAATGGGATCACGGCAACGTTCCACGAGGGGCGTTGCCTGAGCCACTATCGGGTATCAGTCCCTTCCGAATACCGATCTAGGGAGCACCGCCAAGCCATTACCTCGATTAACAGCAAAGCCTACTCATCGCATACACGGTTCTTGGGGTTTGACGGGTCAGTAGCAGACTTCCGGCGGGATGATATTTTATCCGATTGAGCTTGCTTTAAGCCGCCCAGGCCACCCTCGCGGCCGTGGCTCTTCTCTTAAATGGCCCGCACATGTTAGCGGTTCCTTCCTTCCCCGAGCCCTATACTGAACGAGAGTGGGTGGACAGACTCGCCCTCTGATGCTGTGTTCCAACTGGTTCCAAGTCCGGCGCCTGTGGATCTACCGACGCGACCACAACATTATACCAATGTCTAGGCTTAGCTCGAAAACAGTAAGCCTTAGAACTAGGAGTCGTAGCTTCTTCTAAATGAAGGCAGCGTCATAGCCATCGCAACGTTAGCGCTTCTCAATGCTGTCATGTTCACTCGCCGTACATAAAATACAACACAAGTGATTTTAGGTTTAACAAGGATTTTTACTCGCCACGTACTGCTTAAAAATAAAACCCACGAGTAAAGACTTCTGATCGGTGCCGGTAGTGCTCAAACAAAAACCTCTAGCTAACGGGAGGAGGTAGAACGGAATCCCTACCAATCTTATCTCTACTTAAAGAACAAAGCGCGCGGTACATGGGCAGACGAGAATGAGACCTCGTTGCGTGATCGATGGTTATTAGACCCTTCCAGTTTAGCGCGCATGCGATAAATAGTGTACGGCGCGCACTTTCAGAGGAAATACACTCTCTCCATACGATGTACATCGATGCTATCTCTTTAAGCAGAGTCGCCAGGCCTATATGGGCGCTTTAGACGCTGAAGAACCTATTACTATGCTTACCAAAGCGCGCCTATCTAGGAAAACTTTGCGCATGAACGCGAGGCGTTCGCATAGGTAGCCTAGAATGCCCAAAGTACGGGGTCGTCCATATGGCACCGCCGTGTGGAGAGAATCCCGGCAGCAACCTGGAACTGTTGGGCTCACCTCATCGGCGCTCGGGTAGAGACTTTTTCTTTTTTAAGCCGTACTCTACGATCTAGCGATCGCAACTTTTCGACAGGTTGAGGAGTCTGCAACTCGGGCCGTTCGTGGGATCTTCGCATTGCGAAAGTACTGGGATACTAGAGGTTTTATCGGGCCTCGCTTGAGGTCTGTCTGGACCATCGCCCAGTCGATAGAGCGGGGGTGATTTAAATAAGAAATATGTTATGCCCGATTTGGAACCAACCAGTCCCGGTAGCGGTACAAAAGCCCCTTTCCTGCTAGTTCTATGCTTAAAGCGTACTCCTGTTACAATCCGTAGGCAACCTGAAGAGCCTGGTTTTCCTTTATTTCGGTTTGCCATTTCCAATGTGATACTGTGCGGCGACCTTAATGCTTTTTGGTAAAAAACCATACCGTAGATCCAGCGCACGCGTTCAGACCGGGTCCCGGTTTGGCGGTCACTCGTACTCTGCACTGTTCAGCTAGAGGGGTCTCCTATCCGAGGTACCGGTCGTCTAACGGGTGGTTGATCACTACCAGGGACGCGTCTGGCGTCTACTCTACCAACAGTTAAGGAGGGCCAACAAGTTCATGGGCATCGTATAACTTGAAGTGCCATGGACAAATAATAATTGCTCCACGTCCCAAACTCTCAACTGGTACGCCACCTCCGCAACCGAGCTCGTTCAAGTGTCCTTTAGCTGGCGCCGAGTGGGAACCTAGAGTCTACCCAACGCAGGATTCTCGAGTACATAATGTCTGTAGCCAGCGACTATGACACTTATGGTGAGAGAGCCCCTAAGAAAGTGTTGCGGCTCCGCCCCGGTGCGCTTGTTCGGTGGGCGTATATAGAACCATGGGGATATAATGAATGGTAACATATCTGCCCGTTGACAAGCCGCTATTATGACATTCAGGGTTGTGATACTATTATGGCCCTTCACGGTCACTTGGGACGGCCCTAAACAGGATTAGTAAAGTCGGGGTCTAAGTGTAAGCGATAGCAACTGCGGTTGTGAATCGCGTAGACCGCTTGATGATGTAAAATAACAGTTTTCATGTCTTTCGCAATTACCGCGTGTAGTCTGAGGACGGCCCCTTCTCGATATGAAATAGTTCGTCCGCTGTTGACAGGTGTCCTCAATGAGGACCGGAACCGCTTTACAGACTCTGAGGAGCGTAGCGCCCTACGTCCTTCCTGATCCAGCCGCACCCATAGCTAGTAAACAAGTGACGTGCGAGACACAAAGTCAAGGCCTGGGCAAGCTGCGAATGACATTGAAGCGTACTCGATCCAGATCTGCGCCATTGAGTTAAAAGGAGCTATACGCCTGTCTCCAGCCGATTGCAGAAACAGATCCCTAATAGGAGAACTGGGGCTCCATTGTCCCACCGACACCCTCCTTCCTATCCCACTGCGCCCCATTGCTGGTAACCCAAACCTCTCACGACGATTCAGTAGCATGTAGTAAGGTTAAAATCGGTGGGGCGAGTAGTGTTTATGATCAGAAGACTCTAATAGTTCAAGATTGCAAACCCTGATGACAAGATCCATTGATTATCGCCAGTGGGATGGCGGCAAAATCGGTACCATACCTCGAGCTTATTTGCCTCACTCCTCGGGGAACCATATAGACTTGCACTTTGGCAAAAACTGGTCGGGATTCAACCGACCTTTTATGCACTGGACCCTCTGCTGAGGGCCTCTTGTCAATAAAGCTTGCGTTATAAGTTCGCGCTTGATGTCCAGGATTATTATTCCAGACGTGGAACGGTCGAAATGATAGCCTTATCTGTTAACTACCTGAATTAGGGTTGCGCATTACATAAAGGACGACAAGGTGGCACTGGGAGGCTGCATTCTTATAACGGGCATATGCGCGGAACACCACATACCTAGAGTTGGATGGCCTACCTCCGGGTCCGGGTCGAGGCCCCCGTGGAACAATAACACTGTCCACTTGGTTTGTAAAGAACCTCCACTCGTCATGACACGGCCTAGCGGTGTTATCGGCGACGTCAAATATGGGTTCTTTACAAGTGAATCAGGCTTACCAGGCGGACCAGACACCCACGAGTGAGACCTGGATCCCGGGGGGATGGCATACATCCCATACGCTCACTCAGCATGCACGTTCCTAGCAACATGCTGGAACCTTAATTCTACGTTCACTTGTCACGTAGCCATTAGCTGGACAGAGTGTCATTCGTTGTGATGGCCCTTGAGCTATACTTCTAACGCCAATCCATGTTTGCAAACATAGCTCCAGTGCGCTATTCGACGGAGGTTTTAGCCTCTGCACCATGTTATGGCTCTTATAGGTGTTGGGTCGACGATAAGTGGGTGACTGGAGTAAAGAAGACGCTAAAAAGCTCAAGATCACGCGCGATATCTTTAACGGAGTACGCAGCAATCGGCTAAGACCAGTGTCTACTAGCTCGTGATCGGCACCGGCCGTATCTGGTGTAGTAGTCAGCCCCGCATCACCCGTGCCTGTATGCGAGCTCTTGACTCTATCAGTCATTAGAGCACACGTTTAGACCTGAGACCAAGCGTAGGTCACTATCGAGATTACCCCTAGTTGATTAATGCTCTTGACGTGTATGATTACACCGACCGGCGAATAACTCTGCACGCGCGTGACGGTTTCCCGCTAGAAGAAGCCATATCATGTGTACACACAGCTGTGAGCCGCACAAAGACCTCCCCTCGGTCGATAGCGTTATGGTCGTTCACGATTCCAATAAGTGCCAGATGTCGGAACAACTATGTTTCATAAAGACGCGTGACATGATATGGTTTGCTATGAAGCCACTACGAAAATGCCAGTGCTTCTCTTTATATTTTGCAGATGTGGGCAAGTGCATCCATTATAGTCTCTTTACGGTACCTGGATTCTCCAGCCTACTGACTACTTTCTTATATCCGTTGGGGGGGGACGCTCAACAGAGCGCGGACTCAGGATATTTCAGATAACGACACCTTAGGTGAGCTAGTCTGGCCGGCAGTCGTTCCGGGATACCCGCAAAATTTATGCCGGTGATGACTCTAGGTTTAGCTCGATCCACGCAATATCGACAATACAAGGTTTGCCTCCTCTTTCGTCTATCACGCAACTTAGAGTTGCTAAAATTGTCGTAGTCCGTGCGTTAAAGCTCCCTACATTTCTAAGCTGTAACGACACCACACGTATCCTGCAACAAGAGTCATGGTCTCTATTTCTCATATCCGAATGAATATCGTCCTGTTTGAGACACGGGTGGGAATCTCGGCAAGATGGCCGAAGATGATGCGTAGCACTGTCACGTTCAAAAGCTCACAACTCTGCCCACTGCCCAGCCCTAACAGAATCTGGAGACAATAGCGCTGTCCCATGTGGCGGAGAGTTGCTTAATAGAAACGCTATACCGTGGGATCACATACGTCACGTACTCCGGTGACACTATTTATTATTCCTTTACCTCCAATGACGCCCGTCCTTGCATCGCATTTTGTAGTTCGTTACTGCCGACCATAAAAACGTGCTGAGCCCTGACGTCACGTAAACGTCCTATCGGTGTGAGGTCCGTCGTGCTACTCTGAAATTTGGAAACTACCAGTTTGTTGGCGGGAATATCCAACCTGTGCGGCATACACGCTACGCGATGGGGTTGGTACATGCGAAAAACTACCCAAGCACCGGGCGCGGCGAGACACCGTATGAGTATGTTAGTGATGATTTACGGAGCCGTTTTTTGAACTCACACTGACGATGAATCCTTGTCAAACAGGGTTCTCGTTCGTGCAACGATTAAGCATTCTGAACGTGGTACGTGCACATAGCTGGAGAGTTGCGCGAATCTCTTTCGTACCGTATTCTACCTGATCGCTAGCTTTCCGGGGTAACGACATCGGCAATGATGAGTAGCAGCCAGTATACCATACATGACAGGAACTGCCATACTCCGCCTTAACACGCGAGATTTGAACCGCAAGGATGTGCGTAAGCCTGTTCACCATCGCCGATCTTGAAACGATACACGGGTAGGGTGTACGTGGGCAGATGCGATGCACCTTCCGCTGGTTAAAGGTGCCTCACTTGATTCGACAAGACCACCCAACCGAGCCACGTGGTTCCGACGACTCAATGATTTCCGTATGGGTCCAATCGAGCACCCCGGGTATCCACTCCTTCCCCAGAGAAATTTGAGCACTGTTGGGGGTGAGTGTTCCGTGTAATTGTGAATCCGAGTATGTGTTTTGCAGTGGGTCTGTAGCATGGAAAGTTACCCTAACCGGCTCTGGCATTATCAACGGTGGATGTGGGTGGTTAAACAGCTTCCCTTCGGAGACTTAATGGACTAAGAACGAATGACGTGACGCGAGAACGAGAACTCACCATCTGGCGCCCACGGAGCCATATTTTTGATTGGTAAATCGCCGCATAGTGCCCGATACGATGCGTATTGAGCGTAAACGGCGCAGCCTCTATCATGAGGTGATTGCTAAGTCTACGGATCATCCTACCCCAGTGCTGACGAAGGAATTAAAGACCTATTTCCGAACGGACCGTGGGGAAGGAGGGTATTGTTGGCGCGGCCTTCAATTATCCAGCGTATACCCCGATGGCTACTGCTACATCTAAAGTGACTAGCCAGAAAAACCTACCCTCGCCCCACGAGGCTCGTTGATCATCTCAATCATAGATTGATTGCACGGCTCTTGTGTGCACATTGAGACAATTTCTAAACCGACAAGTTTAATGGCTCCTGCGTCACGCTGGACCTTCATGCAATGGTCCATATATATCTGTCCTCCCATAGCCCGCGACCGGGTCTCGACTCAACTGTGTTTTCGCTATCCCCAGGCTAGCACTTCTATCTCAAGCCTTGTTACCCTAGTCATAGTGTTACTGCTAGCGTATAGGGTATTTAGTCATCAGTAGACGGCCGCTTTCGTATGGCAGCAACCGTCCCATCCGGCTCAATTAAGTCTACATCCGGACTTGGGTCTAGATATTCCTATACGAAAATATAGTCTCGCACCGCCTCACTCGTTAAGTTCAGGGCGGCGTCACACTTGTTCGCGGCTCCTCATGGGATCTTTACCCGATCGGTTGATGCCAATTAAATGTCTACACCGGACTGGCGTGTCCCGAGACGACTTTATACACGTGTGACGAGTCTATACGAATAGGAAGGTCTAGTGGGAGGACTGGAAAAACTCCTGCCTACCGGGTCGAATTATTTACGCGTGTTACAATATGTAATTTAGTGCTGGTCGATGCTGTCTCCGGGATTTTTTATCTAAAAGCATCCTTTTGGGTGTACTCTATCGCAGTCGCAGACAGCAGTGGTTTTCGACGTCAGTCGTACAGGGGAGCGTGAAAGCCACACCTTTCTGTAGCTGTTTGAAAGGTCAGCCCGGTTTACTCAAGGTGACTCCTTCGAATCACACGTCGCTGGAGTCGCCTTAGCAGGGTGCTATACGAGTGATAGAGCACTGAACCCACTATAGTCTTAGTGATTTCATGTTTTACTTACGGACCGAAAACTTCGTGGGGTTTTGTCAACGATACGTTGAATGCACGCATGCCTCATAAACTGATGCACTGCCACGTCTGAAAGAGCGAGAACCTGCAACAAGCGGAAGGTTACGCCCAAGCCAGTGGTGATTCCCCCAGCTTGGAGGGACTCCCCTTAGCGTTGGATGTGCTTTGCCCAGCGGCCTCGGTGTACGGGTTCTCCACCCCACTTGGTTTGGACTGAGAGGTAGCACGTTCTCCTGCGTATCCTACCCAGGGCACCAATCGTGAACCTCGCCTATTATATACGGATAGCAGGGTATCCATTCTTACCATGAGCTCAACCACTCCGCTGAATTCGATGGGCTTTTGGGCCCGCACATCACCGTTTCTATCAAGATGCTGTCAACGCGAATGCTAACGCTATTTACTCGGCGCACACAGATCGATGAAAACCCAACGTGGCGCGGGACGGACTCCAGGAATCGTTACCGTTGAGGATTAGGACCCCATACAACACCTCGGCAGACTACATCAAATGATAAAATTCGCATCTGAATTATAAGGATAGCGCCACATAATGACAACACAGTACAGGTGTCTTTTATAGTTTAGTAGATCGCTCGAGACTTTGCGACAAGAATGGACGTTACCTTAGGGGCGGGTTGAGGATTGAGTAATGCTCCCGCTTAAAGCTGATTCGCTCCTAGAGATCTATAAGCGAAGTTCAACCACCTAATTACCATTGCATAGACCGGGAGAACCTGTGACACCTGTTTCCCATGGGATTAGACGAAGGATTGTTCTGACTTATGCCGAGTGAGCCAGTATTGATTAGTAAAAAATGCGACGTGGTAACCAGGCCTTCGATGGGCCGTCTCTCAGGCAGTAACAACCATATACAACTACAAGTTAAACCCGAAACCGTGGCTACCATGGCTCCATCAGTCGGGTTCCCGCATGGGAACAGTTCCACGTGAGCGGCCTTAGGCCTTGTCGGCAGGACAACCGTCAATGAGATATTCGAAAGTGGGGTTAAAACTGGCCGCCCTTGATCGGTCCTACTAACCACAGTCTAGATCTGAGAACCATTCCACAGTGGAATCGGTCTACGGTTTTCATGATCCCTTCTCGGCCATCCATTGAGAACGATTCTACATAATCTGTTAAGCGCCGCCAATCACTGATTAGCTCGTCAGAAAACCTAAGATACCGTATATAATCACGGAATAGGCGAGGCCGATGACAGATCTAATGTCATAAGGAGTCTTATCCACCGTACCCAAGTCTAAACAACTTAGAATTTGGGGGCAGGTTAGTAGAGCATTGCACCACAGACTCCATGAAATAACGCTCCGCTAGCGGATATAGACTGAAGAAAGTATAGTCAGCTGCCTCCTAAAGGCAGGCGTAGTAGGAGCCAACCTAACGTCGTGGATACAGCATTACTCGGTAGCGTACGGGTAAACACCCACGAACCCGATGAGGAACTCAGAATTTTAGTCCGCGAGAAGTTCCATAATCATATTTCCTTCTGTGCTAGTCAATCTGATGGTGGTCATTATTCTCCATATGTTAGACAGTAGAGTGCGCTTCACGCAGAAGTTCCTTCCGCGCTACTACTTTACTCGAACACTGGCCTTGGAAGCCCGCCGTCGGTGTGTATGACTCAGCGAAGACTCTCCAAGCAGGGGAAATTGCGTCGGCAAACTGAGACTCAGCGTCTCGCGAATTGTATGTAACAGCGATCCCGGCAAAGTTTATACGGTCATATTAACAACAGATGGGAGTAGAGCATGTAGCATTCGGACTGGCACCTCATCGCTTTCGCTGTCTGCGGATCACCGGTCTCTCTTGAACGTAGAGCCTGAGGTGGATCTGAGGCACACACGGCACTTGATATCCGGAATAACCTATGTATAGAGCCTCGGTTGTTCCGTTCGTGGTTCCAATAGCGCCTGAGGGGATTAAACGCCTACCGGAGACAGACACGCGAGTTGTTTTGTGCACGTAAAAATCACTTGATGTTATCGTGTTCGGCCCCTAGTCGCTATTGTCTTCTTTAACTGTCTCACTTCAAACAGCGCCGTATCCATTCTATGCAATTACATACTATTTGACCGACTACGAATCAGACCCACTGAATTGCAGACCTGCGAAACGCATTCCTAGTTCGATCGTAGAGTGGAGAGCTAGCCGTTGTTTACCAGCTTTTATTCTTTCACTTGGGATATAAGGGTCGCGTTGTGTACCCTCCTCGGCTATATAGTTTGCTCCAAGCTAAACGTAAAAGGCCGCGGAACGGAATAGAAACGGGGGAATATCATGTATTTTCATATGTATCTGAGTGTCCGATTTGTATCTTCCACGTCCGGGATGTCTTTGTCATCCCTGCTAGGTCTGGTCACTCCTAGACGGAGTCCAGCGGAGCCTAAGTCTCCCGATTAGTCCACTTCAGATGACATACGAGAGCCTGAATTCGATGCTCTGGTGTCCATGGGACGAAACCCGTAGAATCGCCCGAGTCTGGTCCTATAAGGCACCCGTAATCACCAATCTGTACACGCTTCCTTCAATACGTGGTCGTTCTACCTACTTCCCAGCGGTGCCAGCGGGACCCAAGCCGCTTGGATGCGTCTTCGGGACCCTACTGCGATTTACCTGTGTTGCACTCGCGATATTAGGGAGACAGGTTACCAGCTGACACATGACTAGCTGACCCGGAGCACTCAATTCTGCCCATCGGGGATCTGATGCAAAGTTCCGTCGCATTGGACGGCTTCCCGACTCGTAGCGAAGGAATGGTTACCGTACGCCTTCCAACACACGGCCGCGACAGTAACACAATCTACTCTTGGTACACGGCCCTAGAGTAATTGTGTGCCCCCCATACTCTCTACATGTGATAACAGCGACCCACTAGGTTGCCAAACAGAGTCGGAAGTCCATCGAGTCCAGGGCGCTGTAGGGCCTACAGACTCTCCGATGTCCTGTGTTCTTCGTAATTGCAAATATTTTCGGCCCTTCTGCTTCAGATTCAGTCTGTTCCATCTTACTGGAAATGTTGAGAAACTCGAAAACCGCCGCTAACTCCCTGATATTTGTGGCCCTTACATCAACCGTCCTCATGATAGCCCAAGTTATTGTTGTGCTAAAGGGAGCTGAACGCAGACGTGCAGGAAGTAATTGTGTTAAGCTGTTGACCCTTTAAAGCCTACAGGTTCTTTCAGGTGTTCCGTACTCGCGGCGAGAGTATGATCCAGTAAGCGGCGGACGCTGCGAACCACACCGTCAAAATCCTATGCTCCCTGCGAATTACAACTCAAGGAACAGCCAGGACTTTCGAAGGGTAGTTATTGATGCACATTCTACTGCTACGAACGCAGTCATTCGAACTAAACCATTGGTAATGTAATTGTGATCATTTGCTCTAGCTGCAGAACTCCACCACGTGTTCATCCACATCGGTCTCGTGGAATGGTCCAGGGACCGTCCCAATAGGGGGAATTGCGACCCAACTAATCGATGGATTTGAACATGGGAGCAATTCCCGAATGTTAAACTTGCAACGCGCAGTACTACGAACGTATGGTAGCAATAACGACGCGTACCTTCAGCATCATGTGGGTCGCCATAAATTAGGGCCTAATTGCACCTAATCTGCTGGCTTCTCTAGATGTATCCACAGGCCATTAACTGAGAAGATTGCATAGCGTCATATGATTAGTTTGAAAATAATAATCAATGACGAGCACCCGCATCAATATAGCTACGGAGCTTGGAGAGTCCAATACACCTACATGCTGTGCTTATGTTATGAATCAAAAATTAACTTTGACTAAGTAACGTTAGCCACCAGCCGATGGCGCTGGTCACAACGACCCTGGGTTCCGTTTATTCTCTAAGACAACAAGGGTCACTCTACCAGCGGGGTTAAATATACCGGCCGACTGTCTCGAGATGGTAACTCAATTTGGATCAGCATTAAGTCTAGAGCATTCTGCGAGCGATCTATGCGCACTGACTTACTCTTGGACGATTGAGACATATTTTATGCGGTAGTCATGACTTTAATCGTTTCTACAGAAAGACCGTTTGAAATGGCAGGTAGGAAACAACCCTGCTGGATCCTCCCTAAGTCATCAGTCCGGACGGACAGATCTATAACCTCCAATAAATTGAAGAAAAATGCAAAAGGATGCCAATACCTATGTACATTTTCACGTTTCCCGTGTGGTTCGTGCCAACCCCTGGACGGTGGATGTCCCCGGTGGGTTTTGGACCGGGCGAAATTATTGGGCCACACCCGGACCCACCGAGAGCCTCACTAAGACGTGCATGATAGTTAAGTTCGTAAGTGGGAGCCATTATTGCCGACTGGGGGCGGGTATTTCGTCCCTACACCACTCGCGGCACACTATGGTTGGTTTTTGCGGCTTCACTCAACTACAATCTGGTCTGTAGAGAGTACCGTATTATCTTCCTTGCGCCCTGGGTGCTTAGCGAAGTATGGGGATTAAGGGGCGTGAACAATGCTTCTAAGAGCCCGGCGCTTATGAAACACGGTGTTAACAGCAGCCACTGTGGATACGCATGCGTAGCGAACCCGCGCGAGGGAACACATCTGAGCGTATTGTTTCCCCCGCTAGCAAGCATGACGTCACCTTAGTGAGCAAGAACGCTCGGACTCAACAGTCTAAGCGGAATAATATCGATAGCGAAGAAAGCGCGAGAGGACTAAGCAGAGGAGACGCAAAAGGTGAGCCGCGAGTGATTTAGCCCCTGAGATGGCAGGTATAGCTTCTTCACAGCACGGAATTGAACAAAGTCCGGCGCCCCTGGAAATGCTTAACCCCTTTCGAAACGTCCCAGGTTGGCCGTAAGGTTGGTAACCTAACACCCTACTAGCGGGTCTTGCGTCATGCAAGCGGTGGTTCCATACCACTAACGATACGGATAGGGAGGTTCAGGCGTGGGGCGACACAGTAAGATCTGATGAATCCATGTACCTGTTGCCTCCCCGTCGTACGCGTTGATACTTCGCATCATACTTAGCAGAAAGCATCCATTCGCGACCTCTTCGTACAATGGCAAAGGAGGGCTAGTGCACGGGGTCTCTAATGAATCAACAGTACGAGGTTCATGGCCACAAATGTAACGACGATATGACTCGTTCTATGTCTAGGTCCCACTGCGAGTCTCAGAAAGAATTGTACTTGAATAAAGCCCCCCCCTTAGCAAGTGGTACGTAGCCCACACGATTACGCAGAGTGGGGTAAGCCTCCCCCAGCGACTTGGGGAACGCGCTCACCGGATAGCTACTGCCACTGTAGAGCACTAGCGCATAGTGTATCCATCAGTGATGTACGTAGCCAAGCGGGGAGTCCTTGGTCTTATGACTAGCGCCATGGGGCTATCACTGAGAACGGACATGCAAAACGGTCCGGCCATTCGCACATCCGAGCTGCAACGATCGCCCAAGGATTGGAAATTGTTAATAAAGAGTCCGTGGACAATTTTAGTAACGCGACGCGCATCTCTCCCCGCAAGGCTCTATTTTTAGCTTGACGGCGCGTCTCACGTTGCCGGGCTCAGCTCGAGCCTCACGTGCCGCGCGGGGTACCTCGGTTTGAGGAATGTGTCTTGAACGGTTCGTACCGGCTTAGCGTCGGGTGCTACCCAGGGTTCCAGCAACATTCTTACCCAATGAGGGCGCTATCATCTAACGTATCACGTACCAAGCCAGTAACGGGGTATGCTCAACAAGAACTACGCCTTGCACGTTAGAACGTTAAGTTAGAGCACCTGCCCATCTGGATTGTATCACGGTCGATAAAATCGTAATTGTAGCCTGGATGCAGGAAATCATTACGACAAACGATCGGGTGTGGACCTGCGCCGCAACCGTGGGATGCCTGAACGCAGGCAGAAATCTACAGAGCGTTTGCAGAGGGCCACGGGTATCCACGTAAGTTCGCGCAATAGCAGCATCATCTCGTTCGGGGTTGCTTGCTCTCAGGACTGTCGAGTGGTCCTATACAAGCCGGAGTCCTAAGGGGATTTGGTGCCCCAAGTATAGTTTTGCCGAAGGGGGGGCACATGCCGTGACTACGATTGGGTCTATTGGGCCCGCGACCCGGTGCGCACACGTTGATCTCCACTCCCTCCAAGAAAGACAGAGGGCAAAAAGACAAGCCACGAGCTCTTTCGAAATACAATCTAACATAAGCTATGCTGGATAGTATCTTGGAACCTAGATCCGAGAATGGACGCGTGGATAACGAGCACGTTACCTTTGGGCGGCAGCACTTTTAACACCGTTTAAAAGTAACTCTATAGTTGTCAGCCTTTAAAGATTGCGTTCATTACGGTACGACACCGTCCTACAGCCGGGCCCCCGCGGCAGCGCTTCCATCGTGGAGGCTGTCCCCCATCCTCCGAGACTGCGTTTACCGGTCTGGGGAGACTCCCTAAAGAAACACCGACAGGTGGGGAGGCGGGAATCAAGTTAACGCATTCACGTAATTCACTCCTGTCACTTACATAAAGTTCTGGGTTCGCGCCTTAATATCCATGAGGCATACGATGCGATGGGGACCACGCCTGAGCTAGGAACACAAGTTGATAAGGAGTGAAAATAGTATAGGTCTGGCCCGCCTCGTCTGTTGAGGGCCTTTAAATCGTAATAGGCCTCCGCTCTGAACGTACCGTTGAGAAGTTCGGGTGATTTAGTCCGTACTTATCTGGTGTGGCCCGTGTATAGTAAGAACACGGTTCATCAGTCCGCAAGGTAGTATATGACTACGCGTCGATGACCTAAAGATCACGTTATGGCATCGTCCTGAGCAGCTTATGAAAATTGCTGCGCGTTTCAGGAGAATTGTGTTATAGTGCGGGACGGTAGTTTCGTGGAGAATTATGGGTAGCACGAGATCTATGGACGGGAGGTGACTGTCAGCAGACTTAGTGCGCAGGGCTGGTCGGTATAATCGCTGGGACCACGTACTGGCAAGACGCATGCAGCCTGGTGGACATCCACACCCGCCCTCGCTCAGATAGGACGGACGTGCGGCAATTACCCATCTGGTCATCCTGTGGGCTCGGACAGCGAAAAACAGCAGTTTAAAAAATGGGTTATTGGACATTATCACTTTGTCGTTCGACAGTTTATTGCGACCTCCCGATAGAACCCCTTGCTCGCATTTGAGATTAGGTTATCCGACGTGACAGTTTGATCTGCGGAGAATAGGCCGAGAAGCCCCTACGTACCCTATGATTCCCCCCATGTGCGGTGTAAAACCTTAACCACTACTTATGGATTTCATTCCAAATAAGACGCCTATTATATATACCCGAGTGTGTAAGTCCGGCCCTCGCGGTACCAAATTTCGGCTGCATACCTAGCAAGGTATGTCATCTAAACCTAAGGATCGGTAGTGACGTGTAACTAACACGTGGTTCTTAAGAAGTATTTAGTCCTACGTACTCAGGCATCGATACCCTCGATGTATCGGGTGCAGTGGGCGTCGGGCGGCTAAGAATAGTCCCACTCCTTATGTGAATGAAGACCTAGTGCATAGGCTACACGACCTACGTAGCACCTCGTACAACCTTGCTCCAGGCACGTCTAAATGTCGGATAAGCTGGGTTCGCTCCATGCCTGCGACTCCTGGGCGTCCACATATTTTACAAATCCGGACACAAAGCACTTCCAAATTCTGCGTGTGGGACCTAACACCGGAAGGCAACACAGGGGACATTTAGCCACTCTAAAGACCCGCATACTCCAGGGCATTACACGTAACGCGTTCTCTTCACTACGGAGTCCGCGAGCGAACAATGACTAAGGGCGAGGGCCGTAGATCTCCTTCTCGTAAATATAACTCAAGGTTGCCAGCGCTTATCGGTGCCACCGATTAAAAGTCGTCGGAACCTGTAGCCGAAGAGCGTAAGGACGTTACGTGAGGATACATGGTTTGCGCCCGTCCAATACATAATCGACCATCAAATCGAAAGCGCGTATGCAGTACTCGTACTGCCCAAAGGACAGGCTGCATTCGCACCCCGAGCGTAGCTTACATGTTAAGACCGTGCTCATTTTCCACCCGTAGAGATGAGCACAGATTGCTTGCTACTAGTGTAGTAACATAGTAATAAGAGAACATTCATAGACGTTGGACCACGGTTGAAAGACCGCCTCTTAACTACTGAAAAACAATATTTGTCGCTTAGTAACCAAGATACATTATATCAATCCTCCGCTAATGAAGTTTGGAGGCAAGCCTCACGTACCGTGGATTATGTGTATTACTGCATTGAGGTACACCGCGGCGGGTACGAAGCGGTGTCGGGACGCAACGCGTTCGATACTGTAAGGTTTCGTTGGGGTGCTTGTTAGCCGCTAACGTTCGGGTCGCTTACTTCTGCAGGCTTGATTACTGAGTTCATTCGATCGCGTTCCCAACATTCGGCAGTCTGCATTCCCCCTTTCCAGGTCACTATTCGCCATCATCAATTGGGGAAATCATTTTTAGCGGAATACGACCTCGTACTGCATATGACAGTCTGCGTGCAACAGACTTTCCATGATGCGAGCTGGGACCCCCTGTTCCCGTCTGCTGCGGGATGCAATGCAGTGCGCGAAGGTGCCGCTGATTACGGCATATCTGCTGTCCTGACAATGATGGTGTGAGCGTAACAATCATTCAACAATATGGTTTTCGACCACGGGCCAGGGACTTTAGGCCACTACGCACCTGGGTAACACTCGGCGAACCCGCCTGTGGACATTCCCGGAGTTTAACGACACCTCATTTTCTAACAACCACAAAAAGGCATAGGCAACCGAACTAACCTTTCTGTTAGTTACTATCTGGTGTTCATAGTGTAGGGACGTGATCGGTTAAACGCTTGTAACCCCAGCTTCTGTAGCGCTTTTCTCATAACACTACGTTGGGGAGATACTTGTTGCGCAGTCGTGGGTTAAAAGCGAGCCGACGATAAATGCAATAAGGAAAGCGGACCTGTCACCCTCCACGCGGGTAAATCTCACTCGCTCGTTAGAGGCCGTAAAGCGACATACGGTGTTCCAGTACAAGCCACATGGTAGGAATTCTCCTACTACATTCACCGTCACAGTATTTCGGCCTTTGTTCCCGCCGCCTACGGTTCGTGTGGTGTTCTGAGCATTACATGGGATTGGTCACCCTAGGACTAGCAGTTGTACTGTCACGTTAGGTTGCTGTAGCGTGTCATACATTTTCAGACCCCAATTTGTACGCCCAAGTTGTATCGTCGTGCTGGACGAGACTCCAGCCTTTACCCTAAGCGTTTAGGAAAGCATGTTTCAGACCGCAGAGAACGTTGCAAGATCGATCGTCTTTTCATCGTTCTGTAGCTAGACGCCTGACAAGCTACTAACCCGAACTTTAGGAGTTTCTCTCCTAGACGGACCAGTTGTAAGTAAGGGTTTCTATCGCTAGGCTAGGGTGATGGTAGGTGATAGCCAATGGAGCGGCGCGTTAAAAGGGTTGTAGTGATATGTGCACCAATTTAGATTGTTCCGCTTATTTTCCGTTGGTCATTTAGATACGAGATAGGGGCGCCCCAGTGCCACGAGGTCCATCTTATGCTGTTGCGTAGCTAGAGACCCTACAACTTCTAAGTAAACCTGCCATCAGTGCGCTTGGAGAATTTCAACGCATTACCAAAATGATCCTATGTGGGACCTTACTTGATCCGCGCCCCTATCTAATTAAAGACTTCGCGTTCCCGATGGGCGAACCCCGTTAATCTTGCGTGCCAGTCCAAGTTAACTTCCTCTACGCCCGATGACAAATTGCAATACCGGAGTAAGTTGTTAACCTAGCCTATTTGTACCGAATTTTGGGTTGTTCGAGATAGACCATTGTCTGCAGCGTGGCACGGTAGGAACCCGACGATCATGGGTCCTCTCAACTACGGCTAGTGATCGGTTAATGATTTATGGCAACGACAATCATCCCTCGCCTGGTTCCAATCCAACCCAATGTAAGCACCCTTGTGTCCTACTGATGAAACCGGCGCAATTATGTGAACATTCACGGACCCAACACCTAACAATGGTTTAGTTGTGATATTTAGCGCAAATTAGAGGCTGGGCTGCGAAAAGATTGTGTTCCGCAATGAACCTAACTCTGACGGCATACCCGAGATCCTGATAGAGGTGAGCCCGAATCATGCTTGATTAACGTAACGTTACATTCCTACCCGTGCGAGCTTTTGCGATTGCATACATACCTCAATTGGCGCCCTGTGTCTTAGCAGCACAGGTCGTATAATCTGAAGTACAATACGCCAGTCTACGTTAGGGCTTTGCTAACACATCACCCAAGTTTGAGCATCACGCACGACGCCCTCAAGGTTGTCGTCAACCTGGAACTCCAGCAGGCTGGGCATGAGACGCATGAACACAGGTTGCGACAGTCAGATGGGGAGCTTCATGAAAATCTGATACAGTAATGATATCGTAGCCCCTCTAACTCGGAGAGCGGTGGACTAATGAGTGAGTCCAATCAGTGCATCGGTTTTTAATGCTCGGGACCACGGCTTGCGGCTGCGCGATCTATCCCTCGCGTTAACAAGGGGAATTAAGCAACAAGCCCCAAAAAAAAGCGGCGTCAGGCTACAGACTTTTTCCCTCAGCAACGCAAGGTACAGTGAGTCGAATGTGGCGTCCGTAATCATAGCAGCTGTCTAGCGTGCTTCGTGTCTTGCAGCAAGGGCGGTGCTACACGCATGTTTCACTCCAGCAATCAGTGACATGATGCCGCTCTTCGGTTGTTCTATGCGCGCGCTGGTCGACACCTTAAGCCCAGTTCGTGCGGAATCCCAATTCACCGTTGGCAGCACTAGATAATACCGCAATACTTCGTCAGAGCACAACCAGATCACTTACAACGACCGCAAGTAGCATCCCTATCAGTGCGTATGTGTCGAGGCGCAAGTACTATTGTCGGATGAGGAGGTGTCCCTCAGGACACAGTATCGCTCCTCATTCGACGACCAGTCGTCTAGTTCTATGATAGGCGAAGTGAGTACTCGGATCACTGACGCCCACTTGGAGTGACGACGCCGGCTACTAGCGATGGCAGTTCAGAATGGTGCCTTCGGCCAAGGCGACACTCGGTCCTAATCAGGCACACGCGGTCTCAAAGGCCACTACTCATTATGAGCTCGCTGGATGTCGTGGCAGTGGTCTTACCCTGCGGCTAGCGACCAGAATTTCTACTAGCCTTAGGCGTACAAGCCGTTGGGCAGGTCCGAGTAACCTCTACACTCTATCATGGACCACCCCATCCATGTTTTAAACACAGAGGTCTTAAGAATAGCGATGGTACGGTTGAGAACGTGGGAGTTTTTGCTCTACAGCAAGCACGTTGCAGTGAAGGAGACTTAATCCTAAATCATATCTTTCGGACGAATATGGACCCAACGCTAACGGTCGGCACCTCTTGGGACACCCGCATGTGAATTGGCCCGTCTTGATTGTGTCCGTAGATGCCAACGGTTCAATCAGCCCGGGCCCATCGCACATCGACGACGAGCTTCTACCTCTTCAGCCTTGCAACGTTCTAGAGTCTTGCTGTTCGTAAATTGAGATCTACTGTGCAGACTTTATCGACCCACGATACGCTAATCCGAGCGCGACTCGGGTCTCGGAAAATTATCCGAGGGAGCTCGTTCAATGCGGCGGAGGCTCTGAAGTGAGTTTAAATAGTCACACGCATTCGGGTCCCATACACCTGTTTCGAATGTCCAACGCGAACTCTGGGCAACAGGTCGCGAGACTTTGAAATGAGGGGGCTGGTGACAGGGCTTTGTAATAGGGGTACTTGAGAATATGTGATATCCCATATGTATTTGACCGGACAAGAATCTCGATCGTAGACTGATAGATCACGATATTGGCAATGGTTCTGGTCATGTTACCGGTGACACTAGTAATAACTGCAGCAGCGTGACGATGTAGGGGAAACAACTTACTCTTGTTTACGACGTATTAGCGCTATACCTCTGTGGGTTGAGTTGTTGTCACGGTCTGCTATAAACATCCTGCTCCGGCACGGTCAAAGACGTCCAATATGCACACGCATCCATCGCCTATCGGACTCAGCTCGCATCGGGAGAAACCTCCAGTCATGGTGAGGCACACCAACAGTGTGGGGTCGGGAACCGTCAAGCCACCTTCAATTTGATCGATCGTCATTACAAGGTCTAAATGCCCAGCGCCGCTCTCCGGCCATGGAAGTATCTCTGCAGCTACGTGCAGAGTCGGTAAGCAATTGACGGCTATAGCCCTATACGTATGTGGACTCAAGGGACATGCTATACCGACTGGCGCTATCGAGGCGAACGACAATTCTATGGGTCATCACCTCATATTTAGATTCAGCCCCTGGTGGAGCGCTTTGATCCAATGTCGGGAGCGGATAATGAGGAGTTCGCTCCTCAAACCTTAGTAGATAACAGCTAGTGCTGTACCAACCTTGGCTGTGCACCAGACGAGCTGGAAGGACCGAGCTGCTAGGGGTCGCAGTATCGGATTGCTCTTTCAGCCTTCTAAGGTAGCGACAGAAACTTAAACTCCTCTCGGTAGCCTTGCTTCGATCTCTCTAACTAGGGTGTACGAGTGGATAAATTACATTAGTCCGGTACAAAAGTCCTCCATTCCGGCGCTAACCCTTAAAAAGCTATGTCCGCTTGATGTAGAAGCGCACTTACGCAGAAAGGGGCGCACGGTAACGATCCGATCTACTTATTCAAAACCGGTTAACGTCGGAATGGGCTCGAAGACGCTAATAGATACACGCGCATTGGCATGGTACCTTCCCAATACTATATCTTTCAAAGAAGGGCGGCGAGCCTATTTACCCACTTCGATTAGGGGATACACACAGGTGATTGAGTTTTCCTGGAACCGTCATCTAATACCGAAGCAGTCATTGCATTTAACTCACTAAATCGCGCCAATTTGCAGCTTATGTTGTTAGGAGGGGCCACGTAGATACTTGCCTAATCCTGAGTATATGAGGGACGATCTGACATGTATCCTCAAGTCGCGCATTCATCCTTAGATTCTAGGAGATGGATTACTAGTGTGTGTCCATAGTTTAACGCAACACATAATTGGTTCGTGTGAATCGTGATGGTTCCTTGGTCCCGACCTCTATGCTAGACCTATACGATGAGCTTCAAAGCTCCACCATCGATGCAACGTGGTCGTACTCAGTATTATGAAACCTTCGCGTTGAACCGCCTGGAAAGAAGCCTATACGTCCAATATCGGAGCTTGTGATCAGCACGCAGGGTATCAGTTAAAGAGCCCAAGACTTAGTCTATGAGCAGAAGACCGAGTTAGGGTATACACCACTGTCAGAATCGCCCTCACTAGGGCTGATATCGTACGTTACACGAGGTCGCTCTTGTCGAGTGCTCGAACGAGTCTATCCCCTATAGGGCGGAAATGTCACGCGTCTCCAGTCGGAGTATCCCGCCACTCGGATCGAACATGACGAGGCTAAAAGGTGTGGCTCAATCGCGCGTAATTCCTGCAAGCCCTCTCTGAGGTGATTACTCGCTGGTTCGAATGAGCCTGCAGGCAGTACCTACAATTCCTGACCACATTCGGAGGTACCTGTTGCGAGGGATGCCCCCATACCTGCGAGGGTAGTAGCATGAAGTATAAAGGCGGCAATCTTCTGTGACAACCCTTCTTCCCTTGGTTAACCAAGACAAGCTGGGATTTATCACCCCTCCCGGGGCACTTGCCCTGTTTTAGAATCACTTGCATCAGTCGCAGTAGTCCGCGTAGATGATGACATGACCCCTCCCACCCATGCAGAGCGTGTGGAGTATATCTCGCGTCGAGTGGCGCCCCTCCAGTCGCATATTTGATAGGTGTTCGTCATAACGCTGGTTTAAATGTACATGCTAGTTAAGTGAAACGATGTCAACATGCGGGCTCGGTTTTGCGCTCCAGGTATATCCTGATCTTGAACTTTTCATGACCGTGTCTGGCGGCAGGGCTGTCGTTTTGCAGGAGGCTTAGGGACCCAGCGACTCCATCTCGAGAATCACGGCTAATCAGTACGCGAAAAAGTTAATCTTCTATCAGTCAGCGGGCGTATAACTTGACCAACAGAGGACGGCAGGTATTGTACTGTGGAGAAACAAATCGTAAGATGGCCGGCGCCAAGTGGATTGTAATATACCGGTGGTTATCGAAGAAGTAAATAGGCCTACCTTCTGGGGAGCAATGGGGTTCTCAGACGCTAACTCTTCGTTCACCTGATATTAACAACACGATTGACTTCAGAGAGGGACCTATCCGGACCCGAAATTACACATAGGGGGGTCCCCGATAAGCCAAGGCGAGGATAGAGGTCTCTGAATCCATGGACTTCCATCAAACCCCGTGTGGGGTTCCGTTCACCAGTCAGGGAGTCATCATGAGCGACTCACTTACTAGTCACGTCCGTGTCAATATGACTGAAGTCGATAAGACGAAGGCTTAATTTACGGAACCCCCGTTTAGTAATCAAGAAACGCATTGGCGCGGGTCTACGTAAGCTCTTCACACCGCCGTCACGAACGTTCACCGGCTTGCATGTGATCGCCGGGTTCCCTTGGAGGGAGTACCTTGGCCCCCCGTATGGTCTTCCAATAGGCACCAAGTATTAGTTGACTGTTGCGACTTAAAATCCAACCCATTCGGACCAATAAGCAATATCGTGCACCCAGGGACTGGAGGGCCTCAGCCCCTTCTGAAACTTAAACCTCGTCTTCTTATGGGTGAAATGTAAGTTTCTACGTCTGGATATCAACGGTTCGGGCCACCTATAGAACGTCTCGTGTGATAGAGATTCGACCAATGAGTCTGGGAAGTTGAGAACACCACCAAGTTTAGAAAAATTCTCCAACTCAGCTACCGGCGACCCAATCCGTTGGGGTAACGCAAAGGGTATTTAGCCGCTCAGAGGCATAGATTAAGATGAAAACGCGACGCCTGCGGCTGTCTTGTGACTACTCCGACCATGCCAGGCTGAGAGGACCCTACGGTGGGTAGTTGGTAGAGCGCCGATATGCTAATGAGTGGAACTGCGGAATGTGTCATATGAGGGTAGCGAATTGGGCTATCACAAAGTCGTGAGCCTGTAAAACGGACGACTCACTAGACCAAGTAAGCACGGCCCTGGCGTGGCGGCGGTACGCGTACAAACCTCCACTGCTTGGGGAATAAGGTGCGAAACACCGTGATCCATTGAGGCGTGGAGGCATAGGCCTGGAGTGCGTACCAATTACGAGCTAAGACCGCTGTCCAGCCCTGGTGATTACGTAGTATAAGCTCGGTACAAGAGCCTGTAATTAGCTTCGGGGGCGGACATCGTTCATATTGCCAGTCACGGCAGAGGCCGCGCTAGCTAGGCCCAGCCCCGATGGAAACACCGTATCGTGCCTAAGGCGTATGGCTATCGCGGCATTGTTAACTTATCAGCAGACCGAATCGGCGATAGTGGACACAACGGTACACGCTAAGCTCTGAGTGCCAGACTCTACCGCGGCGAATCCTTGTCTAAAGGCCCTGTCCTGGGGCTCCCCCACAGAGCAGTAATGGTCGTTCTAGCGGCCGCGTGCATTCAATCGCGCTGGTCAATGCGTTCCATACGTGCCTTAAGCGGGGCAGTGTGATAAGACATTTTGGGGGGTGCATTTCATGTGAGATAATCGTTTCAGAAACCTCTTACGATACCAGCTTACAATTCTCCGACTCGGTACCTAACTTTGCTTATCATCACTAACATAAATCCTCCCAACCAATGTACGGTTTCGAAGGCAGATACCTCTCCCCTGTTAGACTCTAGTTTGCGAGTGCTGCTAGAGGAATCACACCATCGTAACATGGGGAGGCACGCGCTTGGCGTAAGTACCCGCCACGATTACTCTGTTTCATGCGCCAACGCCCGTATAGTCCGTGCTTTTAACGTCCTCAGAAATCACCGACTGATCAGACTGGCGACAATCTGGAGGGAGGTTGGCGAAATGTTGCTCTTCGTTAAAACCTAGTCGTTGGCGCGTATCGCCTCCATAGAACTTCTTACTCAACCTAGTCTGATCGGGACTGGTCGAAAGCAGCCTGCTTAGTAGCATTGGTGTTTATGAGAGCGACGTAGCTTGAGATCTGTAGCCGGATCGATCGACTGATATCACACTTAAAATATGACAGATTTTAACGGTCGATCTCCATATTCCTAGTATCCCAGCACCTTGATACCTCCTGTCCAGCCGACTGCTTGGACCCTAGCACGCGCATATTAAGGGCGCGTTGTAGTTACTCAAAGTAAAGTGGGAGACCCGAGTGATAGGTTACCGCAGGGGGGCACACCTCTGGCACGTAAGGGTGACTGACTCCCCCAGATAACACTGAATTTGTCAGCAGTACATCATAATCTGAGAACATTAGCGAAGACGATGAAACAAGCTGTCTCAATGGATCCCACGTAGGACGAGAGGAAGTGACGGTTATAATACCGACCTCTATGTGTCTAATTAAATCCCTACGGGCCGTAGCGAGCAATGCTCGGAATCTTTAGTAGCGGATCGGTCTTCTACATGGCGCCCAGGTTTGATATTTAACGAGCTAGAGTTTGCTCTAAAGCTCATCTGCTTGGGAAAGTGACCTGGGGTACGACGAAGACACGGGCCTGGTTGCATTTTTAGGCGCGATAGGTAGCATTATCCAGCACGCCGGAGGCACCTGGCATGGGCGTGAAATACAATCCGAAGAGCAGGCATGAAAAAAAAATGAGCGGTCGTGAACCCGAGGGTGCGTCCCTCCGAACGATTGTTCGTTGCCAAGGTAAGGGAGGCCACAGTGACCGACACAACATAGAGGACATCTCAATATGCTTCTGGGTATCACCTGGGTGTGTACAGTGCTCGAACTGTTACAGAGTCCCCGATCTGCGACGTCTGTTCTCGCCTATTCCCCTCTGAAAGGCCCCGACTTGAAAAAACCTACAATCCTAGACACGTTGTGGCCCAGCAACGCGTCTGCTATACAGCAAGTCATTCGTCGAATGGGGCACACAGTATAAGAAGGCCGTGATTCCCAAGGCACATGGCGGGTCTCTCAAAGTCTACGACGTGCGCAACGGGGAAAGGCTGACCGTTTCCGGTAGGCGATCCATCACGTCTGGTTCTGTTATTGTGTTGACACGTTATGAAATATCTGCTGTAGAACGATGGAGGTCTCTACGTAGCTCTGCACGATTCCCTCGGGCCTACACGTTCATGCAATTCTAAGGCGACATCACATGAAAGGGTTGGGTAACAGCCATCTCTGAAGCATTCCCCCAGCTCGCACGGCTCCTTTACCCGCTACTACGATGCGCTAGAACCCACCAACTATGGAGTCAAGTAGTAAGACCATAAAATTTTGGAGCTGAGCGAAAGCAGCTGCGATGTTAGACCAACATTGTCAACAAACTTAATCCGGCAGGCTAGCATCGCAGATTGCCGATACTATGCTAGAGCGATGAATGGGCCTCTTCGAGATCTGCAAAACCATGAACCCTAATCTGGAAAGTTTGATGTTTGGGTGTCGGTAGCCACTCCGGCAACGTAATGTACGCTTGGTTTGATCTAAACATACCTTGTTAGAGTGTCAAGAGGAGGATATTGTCATAGCAGCTACATTAGCCAGCGCAAAGGATAGCTCCGTGGCTGGTCGGAGGCTAGAATCTAGGCAGAACACGTGCGGCTTCTTCACTCTGACGCTCACGCATTGCTTGGCGGTATCTGTCTCATAGTCCGAACTCACAGTAGATAAAGATCCGCGTGATAAGATATGCTAAGTCCGTACTTCAAGGTAGCACCCTCTGTTCATATGGCGATCCTATCATTGCGGGTTCTATACATATGTTGATCCAACCACGGCCGCCGGGCGCGTCGTAGGGATCTAATGGCCAACACATCAATCAAATCAAAGTCCCTCGCGAGGAGCTGTCGGAGAGAACAAGGTTGTCCCGTCCATTAGGTGTGTATGTTGGTACCAGCACCTAATCTGGTCTGGTCAGCAACTGGCTGTTCCAGTATAATAATCTCGAGATAGACTGCCCTGAAAGTAGACATGATAACAATATGTAGGGGGAAATCCCATCGTCAGACTGTGTTGCGGACGATTAGCTTCGCAGAGGTTGGAGCGGCTGTCTTTAAATTATGGATTACGCTTCCGTCGAACGTTGACTAGAGCGTAATCTCTTGGAGGTACCACGAACGTAGTTCCTCACAGTATGTGGCATGGACTACCGGACAGGTCACTTGTATTTATCCTCTTGGGTGAACAATACATACTCCAAGCGTACTCCCTTTGGAGGTAACGGGTTTGGGTTTACATATTACCATGCGTGGTTAGTCCTATAAGCGTTCCGGGCTTTACCATCGCGGATGAACGATCGCGGATCTACCTATCAGCGACATATCTGCCCGTCCACTAAATGATTCAGTATGTGTTAACAGCGTATTAGCATCATCGAGTCATTGAGAGTGGACGTCTCGAAGAGCAATCTGACCCTTTCACTGGGCCATCCCAGTACATATCTATATGCAGACAAAAAGCTCCATACAATATTACCTCTTTCAGTGTGGCAGGTAGACCAACTTGTCGATATTGTCTCATCGTTCCGTGAATGTGCGAGAATTCTTGGTGGCCCTGGAACAGGCGTATAGAAACAATTAAGGCTTTGCTGCGATCGCAGTTCTGGGACAGAGTCTCCTAGACGCTAGATCAGCTAAAACAATGATTGTAGGTAATGTGCGTTGCCGTCGGGCCACCAGCCATTTCATTCGGTTACACCGACTCAGAATTATCTTCTATCGGGTGACTAAACTGATAATGGGGTCAAGCAGTGGTGGTTCCCGCTTTCTTGCAGTGCTTTTGTGAGCAGAATACTCTCGAGCCTCCAGTACGCCTGAGTATGGCGCGCCCACCAATTGGCGCCGTTAATGCGTACACAAGCAGAACCAGTCACATAAGCTTATGCCCTTAAGAAGATCACCGGGTTTGCGCTCCTGATTCAGGTAACCGGACGTCCGTGTACAACGAACCATACTAATGAGTTCTAGCATCGCTAGACTATTTACCAACGCGTCTTGAACCCTTCGACAATTACAAATGCAAAGTATTAGTTGGGTCAGTGACGTAGCTAAATCTCAAGGGCTGCAGTAAGGGGCCAAAAATTCCGCCGCATTAGCTGTTCCATCCAGAACCGGACAGTCTCGATATAAACTTACGGCTGCGAACTGGCCCTTATGAATTACATCCACGTGCTAGTTAACATAGGACGAGCACTTGTCCCGGACTAATTGCCGATCGACCGTCATTCTCCGTACGATGGTACTGAACCGTGTGATGGGTATGTCATACGTTTCACCCCAAGCGACCCTGCGCTTTCATTCCAGTTGAAACGCGTAGAATGGGAGCAAGCTTTGCTGAGGTGCGATATTCGGGAGACCTGGTCAGCAGGATTGATGGAATGGGTTTTATAGTGTGGATTCCCTGCTGAAATCTCTCTTCCTGGTTGAGGGCCTTGCTTCCCTTCCACAATGATTGTAAGATTTCCTAAGGCCCCAGCTGCTGGAACTGTGAGGTCTTAAACCTCTTTCCTTTATAAATTACCCTAGTCTCAGGTATCTTCCTTATCGTGGTATGGTAGATGCTTCCGTCAGAACGGATTATACAGTTGATGTTAAGCCAGCTCCCTCCTTATAATAATCTCTCTCCCCTCTACTCTGCCTGCTCATCTATGTATGTATGTATCTGTCATCTATCCTCTCTATTGCTTTTCTTTTAGAACTCTGACAACATAGACATTAAATAACAATGTTGTATACCTGAATAATTATATAACTACTGCTTGGGGGTGTGTCGTTGTGTTGTGTGGTGAGGGGGTGTAGCAAATGCTAGGTTGATCTAGCCTAACACCTTCCAGATGACCCTAGGTTACTGGCCTTTCCCCAAAGAGTCCTGGTCTACCAGTCATCTCCCACAATTTGGCTCATCTTCTTGGCTCAGGACAATAAATGACCCAGCCAGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGCGGCGTAATCATGGTCATAGACCTGTTTCTGTGTGTAAATTGTTATGCGCTCACATTGCTCCACACAACGAGCTGCGGAAGCATACAGTAGAGCCTGGCCCTAAATTGCCATGGTGGCGTATGAGGAGCTATCACACTCACATTTATGCGTTTGCAGCTCACTGCCGCTTTTCTACACGGGAAACTTCGCTGACAAGCTGCATTTAATGATCGGTCATCGCGCGGGGAGAGCGGTTTTGCGTATTGTGCCGCAGGTGGTTATTTCTCTCAACAGTGAACGGGCACAGCTGATTGTCCCTCACACGCGCTGGGCTGAGAGAGTTGCAGCAAGCCGTACACGCGGGGTTGCCAGCAGGGCGAAATTCCTTGTTGTGATGTGGTCCGAATCGGTTGCAAATGCCCTATAAATCAATAAGCATGTCCGAGGATAGGGTTTTGAGTGTGTGTCAGTTGGCAGAGGTCACTAATAAAGACGTTGACTGCACGTCAGGCAACTCGGAGACGGAGCGAGAAACTATCAGGCGTTACGAGATTAGCACTACGTCAGCTTAAGACATCACCAATCCAGTTTTTTGGGTCAGGTGCGTGAGACTTATCGGAACGTAAAGGAGCCCGTTTTAGCTGAGCGTCATGAACCTGACTAGGAAAAAGAATAAACAAAGCGGGTATCGCGGAATGTACGTGCTGAGCGAAACCAACGCGCTTACGGTCAAGCCGTGCTATGTGTTTGGAGGTAAGTTTCCCTGATAAAGCGGAAAGCAGGGGCTATGTGTTTACGGGGGTCGCATGGAGTACAAGGGCAGGACAAGTTGCGCAGGACATGGTTTTTTTTAAATTGCGGGAGATGGTTGGCTGTCCCCGATGAGATTAGAACCTTGGACGGACTTTTGTTTTAGTTCGGTTCGGTCAGTTGGACTTTGGATTGGTTTTGTTGGGTATTTAAGAAGGGTGTTTGTGGGATGTTTTTTTTGGGTCGAGCATCACTGGACTATGTGTGTCCTGGTATCGTGGCGGGGCCTCGAACTTGAGAGAGGACATTCCGAGATGCAACAACCTAATATGCCGCAAACCTTGTACAGAAGTTGCAACCGCGTTGTGGCTAGGGAACGGATATTCTCCTGGGTACTGACAACCCAGGTCTATCTGGGTTCTATCGACGGTACAGTCAAGCCTCGAGCTTTACTGTCTCCACTTAAGTCTCGCGGGCATTAGGAATGAGTCTGTGGGGTATCAAGGCGAAGTAGCTAGTCCCGTTGTACATTTCGCGCGTTACCTAGGGAGCAGTGAGCTACGAGGGTGTAGTCTCTACACAGCACGGTATATAGGAACGCACGCATAGGGATCATTACCCAGACCTCCTTCCCTATAATTGTTCTATATACATCGGAGTAAATTGTACCTCTCTGACAACATAGGGGGGTTGAAGTTTATGCCGACGACCAAGTCAAACGCAGTACTGTTACACTTTTGCCGGGAATTGTGTAGACCATGCTCAAGGTGGTGGTCGAGTTACTTCTACTATCTACTGCTTCTCATTACACATCTCTTTGGGCTACAGGCCCAGTTATCAGTATTAGAGGCTGCCTGGTAGAGAAAGTGAGATCTGCCGGACGGTCTCAGGTCGCTACAAGTGTGGGTTAGGCATAGGTAAGCCTAAGGGGTAGGTACTCGTTTTATTCGATTGAGCTACAAGGTATAACGTTGCCTCTCACCATTTCGGCTCACGGGACTCTTACCTCGCCTCACCGCTAGACACCCTGCAGACCGTTAGGGGTACTGACAACCGATCAGGCGACTCCTAAAGGACCTCAGCCTCCCAGCACATGAGGTCGCTCGCAACATGCTGTTCACGCAGTCCATACAGGAACAGCAACGAGACAAGAGCGAGAGCAACACTAGACTTGGAGACATACCACCCATCTGTTTACTGACTTCGATTCAGGTAGAAAGACCTGTGGAACTGGGCGACGCGTGCGTTTATCCGTCTTCCAATCTCCACAGAATCTGCTCCGTCAGAGTATGACTAACGCACTGATGTTTTTTGTTCAGGTAACGGATTACGGGGCGAGATCCAGGGGTGCACATTCAACGGGACCCCAAGGAAAAGTTCGGGGTACTTTGGGGCGCGGTCCAACTCTCGGACTTATTGGGCGACGTAAAGCACACCTCTTGCTCATACAGTGCACAGACCGCTGTAGCATTGTTCAAACACAGCCTCCATTCCGCGACAGTCCTGTGTACAGGTGCCTCGGGCCCAAAATTCCCACTTATACCAAAACTCTCCCGGACTTTTTTCGTCCTTGCAGGGGAAAGGACCATGACTCCACGTTTATAGGGGATCGTTGGGGCCGGACAATCGTGTTTCAACATAATAATGACGTAGGAGGTACATTTCTCGGGGCGGTAGGTCAGAAAGAATATAGACCCTAAATTTACGCAAAACGTGCACACGATTGTAGGATGGAGTCGTATTAGGAACTCAGGGCGGGTGGAAACGAGTGTAGTTTTAGGCTTACCATGAACCGTCGCGCGGAAAATGATGACAGAATGGACGGTGCTTTTTTGCTGGGGCCAACAAAACTCGCTTATGTTCGCCATTGGATGTAAAGGTACCCGCTATACTACGCAGCGACCCCTTCACGACGCATTGTTGATTCCAAATGCTTCCGTTAGGGGAGACGTCATGGAGGTGTTGTGAGCGGTCGCTAGGAATCTTCCTCCAGAGCCCAGCGCCACTAGTTAGCAACCCAGAGTTTCATATGAGCTCCAGTAACACGAAGGTACATAAGGAACGCAAGCAAGCCTTCGGGACTACATAGAACTTGGGGTGCTCTAAGCGGGGATCTTAATAGACAAGAGGCCATCGTATGGGTCAAATTTCATGTTTCGTCAGATGCCCTATCCGTGGACACCTATCAAAGCATCATATCCTAAGACTATCTCTCGCTTTGGTATGATTCAATATGCAGCCCTGTCCCGTAAAATGACGGGCCAGAGGATACCTGATCACTACCTATTTCAGCTACCACTGTTCGAAACCTTCTCTGGCCGCGTGAATTATATAATCCCCCAACCCTTCAGTCGGTGCAGTCTACGTAAACTTCCATCTAATCGACGTAGCGTAGGGGGCTACGGGAGTCGCACAAGCCGAAGCATTTCTGCTCTGTTTCGTTACAACTGAATCCTCATCACGGCAGCGCTACCGGTGCCACCTAGTCATCCCCGCGAGTGCTTAACCGTCGAGATGGCTCGAACCGTGTTTCGAAGTGCGCTATTGAACCAGTTAAAAGCAGGGCGACTGGTCCTTGTAGATTGTCGGACTTCGATAACTATCACACAATTTGGCATAAGTATAGTCAAGAAGGCTCAGATAGGCACACGAAAATAGGTTGACCGCTTGAGACACGTTCAGGTTGCCCGGCAACGAAGCGCGCTTGCTCCATAACCTATTGCAGAGCGTAACGACCCTCTTTCACCGTAGCGCCCCCATGTCGGGGCAAGCAGCAATACACGGTCACTTAATCCTCCCACCGATAAATCCTATGTTCTGACTCTACGTACCTCCTAGAGAAGGTGAGGAGACTCGGCTGGAACATAAGTATAACGTTTACCAAACAATGTCATAACACAGAAAGGAGGATGCCCGGTGGGGTCGAAGATAACTGTGGATTCTTGAGCGATATCTGCTAACGGCCAGGCTGTCATGGAAGTCACGCGCACGAAGCTATAAGTTATGAACAGATACCCATGCCGGGGCGGCAGCGGTACCTAGTCCTAAATACCGACACGTCCCTGAGGCCCCGCTAGTCAAGGCTTAAAATATACGCTGATTTGTCTACCAATCGGATCTTCGATTAACTGTCACCGGCATATAAGTCTACCCTGGACCCAGCAATGACGAAAAACTTTTCCGAATGATCATTGTGAGTTTACAGAGATTAGGATACACAAAAAAATTTACGTAAACGTCCAGTTACCCCCTGTGTGACCCTTGGCCACAAACCGCTAAGGCAGCATGGCGCGTTGAGTCCAGGGTTTGTGACACCAGACAGGCTGAATACCCTGTGGCAGGGTTGTTAGCTGTTAGCTATTCGGATCTCGATTTCAGAGGGTCCGTTGAACCGGGCAGTACAAGACACCCCACACCACTGCGCGTGTTGGGTGGTACGTCCGCCAGTCTGCAAATTCCCTACGTTATGCAAATTTCCTTCCCGGCGTTCTTGATACACCTGTACTACTCCTAAAGGCTGAAACTGCTCCGTCTTCGGGACACCCACACAACAGCTACCGGAAAATCGTGAGGATGCACTCAAGGGTCTTGCATTGTTGATCTATACAGCTCTCGCAGGTGTGCTACTGTTTTCCACAATGGCAAGGGGTCGTGTAGGTCTTATCGTAGGAGTACCCCGTGATCTGGTATACCTGCTATCTATTCCACCAAATAGATAGCCGGGGTCTTAATAGTTTTATTCCGGATCATCAAGTGACAGTCCATGGGTAAACGGTAAGTTCGTACGCTGGGCGGTGATCCCCGCTTATAAACGAGCAAACCGCCAAGCAACTATCCCCCAAACGTCACGCAACATTGCGGGCTTCCAGCTAGTAGTTGTCAATGTGCATGTGACTACTTAACTCCACAAAGGGACGCGTTGCAAGCTGCCTGAACTCGTCACGTCTCATGCCTAGCTCCCGGTTGAAACACGAAGACGCGTGAACCTCATCTTTGCCTTACTATTCGCCTCCTAGCTTCTTGATGTGGCCCTGCGACATGGACCCTGGGTATGTTAGTGAAATTACAGAGTGTCGGTACACCTCATGCCTGCACCTAAAAACGAACTTACGTGTATAGAGATTATGTCATCCGTCACCT diff --git a/test_data/volvox/output_prefix3.simseq.genome.fa.fai b/test_data/volvox/output_prefix3.simseq.genome.fa.fai new file mode 100644 index 0000000000..8824ba0ae3 --- /dev/null +++ b/test_data/volvox/output_prefix3.simseq.genome.fa.fai @@ -0,0 +1 @@ +ctgA 49186 6 49186 49187 diff --git a/test_data/volvox/trix/volvox-rev-del.ix b/test_data/volvox/trix/volvox-rev-del.ix new file mode 100644 index 0000000000..0bcecf1bb5 --- /dev/null +++ b/test_data/volvox/trix/volvox-rev-del.ix @@ -0,0 +1,73 @@ +1 ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],2 +1000 ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +2 ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1 +3 ["ctgA%3A11300..19000"|"volvox-rev-del-annotations"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1 +a ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +agt221.3 ["ctgA%3A17500..18000"|"volvox-rev-del-annotations"|"agt221.3"|"Match4"],1 +agt221.5 ["ctgA%3A11050..11500"|"volvox-rev-del-annotations"|"agt221.5"],1 ["ctgA%3A11050..17300"|"volvox-rev-del-annotations"|"agt221.5"|"Match3"],2 ["ctgA%3A15000..15500"|"volvox-rev-del-annotations"|"agt221.5"],3 ["ctgA%3A17000..17300"|"volvox-rev-del-annotations"|"agt221.5"],4 +agt767.3 ["ctgA%3A18000..19000"|"volvox-rev-del-annotations"|"agt767.3"|"Match6"],1 +agt767.5 ["ctgA%3A11150..11500"|"volvox-rev-del-annotations"|"agt767.5"],1 ["ctgA%3A11150..17200"|"volvox-rev-del-annotations"|"agt767.5"|"Match5"],2 ["ctgA%3A15000..15500"|"volvox-rev-del-annotations"|"agt767.5"],3 ["ctgA%3A17000..17200"|"volvox-rev-del-annotations"|"agt767.5"],4 +agt830.3 ["ctgA%3A15410..15500"|"volvox-rev-del-annotations"|"agt830.3"],1 ["ctgA%3A15410..17503"|"volvox-rev-del-annotations"|"agt830.3"|"Match2"],2 ["ctgA%3A17000..17503"|"volvox-rev-del-annotations"|"agt830.3"],3 +agt830.5 ["ctgA%3A11050..11500"|"volvox-rev-del-annotations"|"agt830.5"],1 ["ctgA%3A11050..13202"|"volvox-rev-del-annotations"|"agt830.5"|"Match1"],2 ["ctgA%3A13000..13202"|"volvox-rev-del-annotations"|"agt830.5"],3 +an ["ctgA%3A11659..11984"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A-38341..-38016"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],2 +another ["ctgA%3A13014..16130"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A-36986..-33870"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],2 +appear 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["ctgB%3A-38341..-38016"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],4 +f01 ["ctgA%3A4705..7713"|"volvox-rev-del-annotations"|"f01"],1 +f05 ["ctgA%3A14715..15968"|"volvox-rev-del-annotations"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgB%3A-35285..-34032"|"volvox-rev-del-annotations"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],2 +f06 ["ctgA%3A13014..16130"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A-36986..-33870"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],2 +f07 ["ctgA%3A11659..11984"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A-38341..-38016"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],2 +f11 ["ctgA%3A6990..8410"|"volvox-rev-del-annotations"|"f11"],1 +f12 ["ctgA%3A9758..10000"|"volvox-rev-del-annotations"|"f12"],1 +fake ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +fakesnp ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +fakesnp1 ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +fingerprinted ["ctgA%3A11000..30000"|"volvox-rev-del-annotations"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 +form ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A11300..19000"|"volvox-rev-del-annotations"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3 +gene:hga ["ctgA%3A11100..12000"|"volvox-rev-del-annotations"|"Gene%3Ahga"],1 +gene:hgb ["ctgA%3A11600..13000"|"volvox-rev-del-annotations"|"Gene%3Ahgb"],1 +get ["ctgA%3A14715..15968"|"volvox-rev-del-annotations"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 +i ["ctgA%3A14715..15968"|"volvox-rev-del-annotations"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 +is ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A11659..11984"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A13014..16130"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A-36986..-33870"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],4 ["ctgB%3A-38341..-38016"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],5 +kinase ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A6012..8851"|"volvox-rev-del-annotations"|"m09"|"kinase"],2 +length ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +m01 ["ctgA%3A8253..8366"|"volvox-rev-del-annotations"|"m01"|"WD40"],1 +m09 ["ctgA%3A6012..8851"|"volvox-rev-del-annotations"|"m09"|"kinase"],1 +match1 ["ctgA%3A11050..13202"|"volvox-rev-del-annotations"|"agt830.5"|"Match1"],1 +match2 ["ctgA%3A15410..17503"|"volvox-rev-del-annotations"|"agt830.3"|"Match2"],1 +match3 ["ctgA%3A11050..17300"|"volvox-rev-del-annotations"|"agt221.5"|"Match3"],1 +match4 ["ctgA%3A17500..18000"|"volvox-rev-del-annotations"|"agt221.3"|"Match4"],1 +match5 ["ctgA%3A11150..17200"|"volvox-rev-del-annotations"|"agt767.5"|"Match5"],1 +match6 ["ctgA%3A18000..19000"|"volvox-rev-del-annotations"|"agt767.3"|"Match6"],1 +message. ["ctgA%3A14715..15968"|"volvox-rev-del-annotations"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 +ok! ["ctgA%3A14715..15968"|"volvox-rev-del-annotations"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgA%3A14715..15968"|"volvox-rev-del-annotations"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],2 +protein ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN"|"EDEN"|"protein%20kinase"],1 +protein:hga ["ctgA%3A11200..11900"|"volvox-rev-del-annotations"|"Protein%3AHGA"],1 +protein:hgb ["ctgA%3A11800..12900"|"volvox-rev-del-annotations"|"Protein%3AHGB"],1 +reads ["ctgA%3A11000..30000"|"volvox-rev-del-annotations"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 +remark:hga ["ctgA%3A11000..12000"|"volvox-rev-del-annotations"|"Remark%3Ahga"],1 +seg03 ["ctgA%3A16885..17241"|"volvox-rev-del-annotations"|"seg03"],1 ["ctgA%3A17410..17737"|"volvox-rev-del-annotations"|"seg03"],2 ["ctgA%3A18055..18080"|"volvox-rev-del-annotations"|"seg03"],3 ["ctgA%3A18306..18999"|"volvox-rev-del-annotations"|"seg03"],4 +seg04 ["ctgA%3A15233..15302"|"volvox-rev-del-annotations"|"seg04"],1 ["ctgA%3A15800..16101"|"volvox-rev-del-annotations"|"seg04"],2 ["ctgA%3A16442..16854"|"volvox-rev-del-annotations"|"seg04"],3 ["ctgA%3A17106..17211"|"volvox-rev-del-annotations"|"seg04"],4 ["ctgA%3A17695..18177"|"volvox-rev-del-annotations"|"seg04"],5 ["ctgA%3A18545..18783"|"volvox-rev-del-annotations"|"seg04"],6 ["ctgA%3A18869..18935"|"volvox-rev-del-annotations"|"seg04"],7 ["ctgA%3A19404..19825"|"volvox-rev-del-annotations"|"seg04"],8 +seg07 ["ctgA%3A4191..4514"|"volvox-rev-del-annotations"|"seg07"],1 ["ctgA%3A4552..5043"|"volvox-rev-del-annotations"|"seg07"],2 ["ctgA%3A5373..5600"|"volvox-rev-del-annotations"|"seg07"],3 ["ctgA%3A5897..6315"|"volvox-rev-del-annotations"|"seg07"],4 ["ctgA%3A6491..6890"|"volvox-rev-del-annotations"|"seg07"],5 ["ctgA%3A7126..7297"|"volvox-rev-del-annotations"|"seg07"],6 ["ctgA%3A7735..7983"|"volvox-rev-del-annotations"|"seg07"],7 ["ctgA%3A8447..8709"|"volvox-rev-del-annotations"|"seg07"],8 ["ctgA%3A8931..9186"|"volvox-rev-del-annotations"|"seg07"],9 ["ctgA%3A9472..9699"|"volvox-rev-del-annotations"|"seg07"],10 ["ctgA%3A9957..10000"|"volvox-rev-del-annotations"|"seg07"],11 ["ctgA%3A9957..10000"|"volvox-rev-del-annotations"|"seg07"],12 +seg13 ["ctgA%3A9406..9476"|"volvox-rev-del-annotations"|"seg13"],1 ["ctgA%3A9762..10000"|"volvox-rev-del-annotations"|"seg13"],2 +seg14 ["ctgA%3A1137..1318"|"volvox-rev-del-annotations"|"seg14"],1 ["ctgA%3A1754..1948"|"volvox-rev-del-annotations"|"seg14"],2 ["ctgA%3A2057..2474"|"volvox-rev-del-annotations"|"seg14"],3 ["ctgA%3A2890..3270"|"volvox-rev-del-annotations"|"seg14"],4 ["ctgA%3A3395..3811"|"volvox-rev-del-annotations"|"seg14"],5 ["ctgA%3A4065..4556"|"volvox-rev-del-annotations"|"seg14"],6 ["ctgA%3A4763..5030"|"volvox-rev-del-annotations"|"seg14"],7 ["ctgA%3A5231..5488"|"volvox-rev-del-annotations"|"seg14"],8 ["ctgA%3A5790..6022"|"volvox-rev-del-annotations"|"seg14"],9 ["ctgA%3A6092..6318"|"volvox-rev-del-annotations"|"seg14"],10 ["ctgA%3A6816..6992"|"volvox-rev-del-annotations"|"seg14"],11 ["ctgA%3A7449..7829"|"volvox-rev-del-annotations"|"seg14"],12 +seg15 ["ctgA%3A1252..1365"|"volvox-rev-del-annotations"|"seg15"],1 ["ctgA%3A1492..1504"|"volvox-rev-del-annotations"|"seg15"],2 ["ctgA%3A1941..2377"|"volvox-rev-del-annotations"|"seg15"],3 ["ctgA%3A2748..2954"|"volvox-rev-del-annotations"|"seg15"],4 ["ctgA%3A3401..3897"|"volvox-rev-del-annotations"|"seg15"],5 ["ctgA%3A4043..4113"|"volvox-rev-del-annotations"|"seg15"],6 ["ctgA%3A4399..4888"|"volvox-rev-del-annotations"|"seg15"],7 ["ctgA%3A515..954"|"volvox-rev-del-annotations"|"seg15"],8 ["ctgA%3A5281..5375"|"volvox-rev-del-annotations"|"seg15"],9 ["ctgA%3A5711..6041"|"volvox-rev-del-annotations"|"seg15"],10 ["ctgA%3A6425..6564"|"volvox-rev-del-annotations"|"seg15"],11 ["ctgA%3A6738..7087"|"volvox-rev-del-annotations"|"seg15"],12 ["ctgA%3A7329..7595"|"volvox-rev-del-annotations"|"seg15"],13 ["ctgA%3A7858..7979"|"volvox-rev-del-annotations"|"seg15"],14 ["ctgA%3A8169..8453"|"volvox-rev-del-annotations"|"seg15"],15 +should ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +snp ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +splice ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A11050..19000"|"volvox-rev-del-annotations"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A11300..19000"|"volvox-rev-del-annotations"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3 +that ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 +the ["ctgA%3A14715..15968"|"volvox-rev-del-annotations"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 +this ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A11659..11984"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A13014..16130"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A-36986..-33870"|"volvox-rev-del-annotations"|"f06"|"This%20is%20another%20example"],4 ["ctgB%3A-38341..-38016"|"volvox-rev-del-annotations"|"f07"|"This%20is%20an%20example"],5 +wd40 ["ctgA%3A8253..8366"|"volvox-rev-del-annotations"|"m01"|"WD40"],1 +with ["ctgA%3A11000..11000"|"volvox-rev-del-annotations"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A11000..30000"|"volvox-rev-del-annotations"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 +ああ、この機能は、世界中を旅しています！ ["ctgB%3A-35285..-34032"|"volvox-rev-del-annotations"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],1 diff --git a/test_data/volvox/trix/volvox-rev-del.ixx b/test_data/volvox/trix/volvox-rev-del.ixx new file mode 100644 index 0000000000..592a30ecab --- /dev/null +++ b/test_data/volvox/trix/volvox-rev-del.ixx @@ -0,0 +1 @@ +1 0000000000 diff --git a/test_data/volvox/trix/volvox-rev-del_meta.json b/test_data/volvox/trix/volvox-rev-del_meta.json new file mode 100644 index 0000000000..dbe5689bd9 --- /dev/null +++ b/test_data/volvox/trix/volvox-rev-del_meta.json @@ -0,0 +1,18 @@ +{ + "dateCreated": "2022-12-11T03:48:26.257Z", + "tracks": [ + { + "trackId": "volvox-rev-del-annotations", + "attributesIndexed": ["Name", "ID", "Note"], + "excludedTypes": ["CDS", "exon"], + "adapterConf": { + "type": "Gff3Adapter", + "gffLocation": { + "uri": "volvox-rev-del.gff", + "locationType": "UriLocation" + } + } + } + ], + "assemblyNames": ["volvox-rev-del"] +} diff --git a/test_data/volvox/trix/volvox.ix b/test_data/volvox/trix/volvox.ix index 2b52f07c6d..461cde94e7 100644 --- a/test_data/volvox/trix/volvox.ix +++ b/test_data/volvox/trix/volvox.ix @@ -17,8 +17,8 @@ appear ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20 apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1 at ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 -b101.2 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 -bac ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 +b101.2 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 ["ctgB%3A1000..2000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 +bac ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 ["ctgB%3A1000..2000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 bnd_a ["A%3A2700..2701"|"volvox_sv_test_renamed"|"bnd_A"],1 ["ctgA%3A2700..2701"|"volvox_sv_test"|"bnd_A"],2 bnd_b ["A%3A34200..34201"|"volvox_sv_test_renamed"|"bnd_B"],1 ["ctgA%3A34200..34201"|"volvox_sv_test"|"bnd_B"],2 bnd_u ["A%3A23456..23457"|"volvox_sv_test_renamed"|"bnd_U"],1 ["ctgA%3A23456..23457"|"volvox_sv_test"|"bnd_U"],2 @@ -39,7 +39,7 @@ eden ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 eden.1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 eden.2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1 eden.3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1 -end ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 +end ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 ["ctgB%3A1000..2000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 example ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],3 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],4 f01 ["ctgA%3A44705..47713"|"gff3tabix_genes"|"f01"],1 f02 ["ctgA%3A24562..28338"|"gff3tabix_genes"|"f02"],1 @@ -60,7 +60,7 @@ fake ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a% fakesnp ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 fakesnp1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 finger ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1 -fingerprinted ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 +fingerprinted ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 ["ctgB%3A1000..2000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 form ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3 gene1 ["ctgA%3A1201..1500"|"single_exon_gene"|"gene1"],1 gene2 ["ctgA%3A1201..3902"|"single_exon_gene"|"gene2"],1 @@ -109,7 +109,7 @@ ok! ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20me protein ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 protein:hga ["ctgA%3A1200..1900"|"gff3tabix_genes"|"Protein%3AHGA"],1 protein:hgb ["ctgA%3A1800..2900"|"gff3tabix_genes"|"Protein%3AHGB"],1 -reads ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 +reads ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1 ["ctgB%3A1000..2000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 remark:hga ["ctgA%3A1000..2000"|"gff3tabix_genes"|"Remark%3Ahga"],1 repeat ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1 rna-apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1 @@ -190,6 +190,6 @@ the ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20me this ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5 utrs ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2 wd40 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"|"WD40"],1 -with ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],4 +with ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],4 ["ctgB%3A1000..2000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],5 zinc ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1 ああ、この機能は、世界中を旅しています！ ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],1 diff --git a/test_data/volvox/trix/volvox.ixx b/test_data/volvox/trix/volvox.ixx index d0515bd14c..592a30ecab 100644 --- a/test_data/volvox/trix/volvox.ixx +++ b/test_data/volvox/trix/volvox.ixx @@ -1 +1 @@ -1 0000000000 +1 0000000000 diff --git a/test_data/volvox/trix/volvox_meta.json b/test_data/volvox/trix/volvox_meta.json index 481ff8ec5f..5dfe578052 100644 --- a/test_data/volvox/trix/volvox_meta.json +++ b/test_data/volvox/trix/volvox_meta.json @@ -1,5 +1,5 @@ { - "dateCreated": "2022-10-07T15:35:11.613Z", + "dateCreated": "2022-12-11T03:48:26.243Z", "tracks": [ { "trackId": "volvox_sv_test", diff --git a/test_data/volvox/volvox-rev-del.fa b/test_data/volvox/volvox-rev-del.fa new file mode 100644 index 0000000000..9d94383a5f --- /dev/null +++ b/test_data/volvox/volvox-rev-del.fa @@ -0,0 +1,252 @@ +>ctgA +tgacggagtgacataatctctatacacgtaattcgtttttgaggtacttgtaatttcactaacatacccaggtacaacta +ctactgtccatgtcgcagagccacatcaagaagcctcttaaaggaggcgaatagtaagcaaagataggttcacgcgtctt +cgtgtttcaaccgggagctaggcatgacgtgacgagttcaggcgcttcaagcgtccctttgtgggtaagtagtcacatgc +acgattgacacccaacatttactagctggaagcccggcaatggttgctttggcggtttgctcgtttataagcggggatca +ccgcccagcgtacgaaacttaccgtttaccccatggacttgtcacttgatagatccggaataaaactataagaccccggc +tattttggtggaatagatagcaaggtatagccagatcacggggtactcctacataagacctacacgccccttgcccattg +tggaaaacagtagcacaccgtgcgaagagctgtatagatcaacaatgcaagacccttgtgcatcctcacgattttccgta +gctgttgtgtgggtgtcccgagacggagcagcaacgtcggatttcacggccctttaggagtagtacaggcaagaacgccg +gggaaggaattttgcataacgtagggagcagactggcggacgtaccacctcagtggtgtggggtgtcttgtactgcccgg +tatcaacggaccctctgaaatcggatccgaataacatgctaacaacccgccacagggtattcatgtctggtgtcacaaac +cctggactcaacgcccatgctgcaccttacggtttgtggccaagggtcacacaggggtaaccggacgtacgtaaattttt +ttggtgttcctaatctctgtaaactcacaatgatcattcggaaaagtttttctcattgctgggtccagggtagacttagt +atgccggtgttaatcgaagatgattggtagacaaagtcagcgtatattttaagttcccttgactagggtgggcctcaggg +gacgcgttgctacgtgtcggtatttaggactaggtaccgctgccgccccggcatgggtatctttcataaatagcttcgtg +cgcgtgatcttcatgacagcctggccgttgcagatatcaaccacagctgtatcttcgaccccaccgggcatctctccttt +ctgttatatgtatgatcattgtttggtaaactgtttacttatgttccagcggtctcctcaccttctctagaggtacgagg +atgtcatctaattaggctgacaggggttagccaatccgtttcacgtactagacagaacacgttatcggtgggaaactgtt +gccccgacatgggggcagctacggtgaaagagggtcgttacctctgatagtggattaatggagcaagcgcgcttcgttgc +cgggcaacctgaacgtaggcggtcactatttgggtgcgtgtgcctatctgagccttcttggctgtatatacttatgccaa +atttgtgatagtttatatcgaagtccgacggacagtcgcccctgctttataactggttcaatagccagccttcgaaacac +ggttcgagccatctcgactggttaaactcgcggggatgactagggatggcatccggtagcgctgcgtgatgaggattcca +gttgtaacgaaacagagcagaaatgcttcggcttgtgcgatctcccgtagccccctcacgtacgtcgattagatgggggc +taacctgggaaagttacgtagactgcaccgacgaagggtactccttgggggattatataattcacgcggcgattaacgaa 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+gccatccgcttgattcctgtaccaaatagtcccattcggcgattcaggatgaacagttggtcaccgtgacagaatgcgtg +cccacggtaccaagggcttaattgagttgctctggcacaaagaagcagtttataagccttttatgctgagatgcgtggag +gaggaagcctatgttgctgaggcgtcaaccagcttgagaaggtccaccgtttgtttatggtacccatagcgtgatctagt +agagcgcgaatcaccgatgtaccgttgtactagtcgcaatctaaggtaaaatcctttaatttgttatctaacgtctatct +tgctgactatcacccagatcaaccaacctcaaacggaccgtccggccccagacggatgttcgaactccatacatgttatc +agaatgctatgctaccatgatcgataccgtctaagtattctgcgctctttcaaagtagcctgggtacaacggagcgacca +aggagccaacagatgaacagcatctggtgacagctagtctcgtatttgtagcaatctttactcacctgtttaaattgcat +ggtgagaccacagatcgctatctaggagagaaccgccgtttccgagaagataccggttaattgacggtttggtggtcagg +ttggtcttctaataccgttgtccaacgttttggccgcactaaccctttgatttatgggcagggttccaagagaagtcagg +ctgaatcagaatttgcctagcccccgctcgagttctcaattcaggtagcattagcgccgctactactaccaatctaaacc +aaggctaaagaaccaatcataatcgtataaaagtgaGAGACGGAAGTGTTCCTAATGCCGTtgttcaactccgcaacaat +g diff --git a/test_data/volvox/volvox-rev-del.fa.fai b/test_data/volvox/volvox-rev-del.fa.fai new file mode 100644 index 0000000000..b01e0d7fa4 --- /dev/null +++ b/test_data/volvox/volvox-rev-del.fa.fai @@ -0,0 +1 @@ +ctgA 20001 6 80 81 diff --git a/test_data/volvox/volvox-rev-del.gff b/test_data/volvox/volvox-rev-del.gff new file mode 100644 index 0000000000..236f590535 --- /dev/null +++ b/test_data/volvox/volvox-rev-del.gff @@ -0,0 +1,111 @@ +ctgA example match 515 954 . + . Name=seg15 +ctgA example match 1137 1318 . + . Name=seg14 +ctgA example match 1252 1365 . + . Name=seg15 +ctgA example match 1492 1504 . + . Name=seg15 +ctgA example match 1754 1948 . + . Name=seg14 +ctgA example match 1941 2377 . + . Name=seg15 +ctgA example match 2057 2474 . + . Name=seg14 +ctgA example match 2748 2954 . + . Name=seg15 +ctgA example match 2890 3270 . + . Name=seg14 +ctgA example match 3395 3811 . + . Name=seg14 +ctgA example match 3401 3897 . + . Name=seg15 +ctgA example match 4043 4113 . + . Name=seg15 +ctgA example match 4065 4556 . + . Name=seg14 +ctgA example match 4191 4514 . + . Name=seg07 +ctgA example match 4399 4888 . + . Name=seg15 +ctgA example match 4552 5043 . + . Name=seg07 +ctgA example remark 4705 7713 . + . Name=f01 +ctgA example match 4763 5030 . + . Name=seg14 +ctgA example match 5231 5488 . + . Name=seg14 +ctgA example match 5281 5375 . + . Name=seg15 +ctgA example match 5373 5600 . + . Name=seg07 +ctgA example match 5711 6041 . + . Name=seg15 +ctgA example match 5790 6022 . + . Name=seg14 +ctgA example match 5897 6315 . + . Name=seg07 +ctgA example polypeptide_domain 6012 8851 . - . Name=m09;Note=kinase +ctgA example match 6092 6318 . + . Name=seg14 +ctgA example match 6425 6564 . + . Name=seg15 +ctgA example match 6491 6890 . + . Name=seg07 +ctgA example match 6738 7087 . + . Name=seg15 +ctgA example match 6816 6992 . + . Name=seg14 +ctgA example remark 6990 8410 . + . Name=f11 +ctgA example match 7126 7297 . + . Name=seg07 +ctgA example match 7329 7595 . + . Name=seg15 +ctgA example match 7449 7829 . + . Name=seg14 +ctgA example match 7735 7983 . + . Name=seg07 +ctgA example match 7858 7979 . + . Name=seg15 +ctgA example match 8169 8453 . + . Name=seg15 +ctgA example polypeptide_domain 8253 8366 . - . Name=m01;Note=WD40 +ctgA example match 8447 8709 . + . Name=seg07 +ctgA example match 8931 9186 . + . Name=seg07 +ctgA example match 9406 9476 . - . Name=seg13 +ctgA example match 9472 9699 . + . Name=seg07 +ctgA example remark 9758 10000 . + . Name=f12 +ctgA example match 9762 10000 . - . Name=seg13 +ctgA example match 9957 10000 . + . Name=seg07 +ctgA example match 9957 10000 . + . Name=seg07 +ctgB example contig -39999 -33921 . . . Name=ctgB +ctgB example remark -38341 -38016 . - . Name=f07;Note=This is an example +ctgB example remark -36986 -33870 . - . Name=f06;Note=This is another example +ctgB example remark -35285 -34032 . + . Name=f05;Note=ああ、この機能は、世界中を旅しています！ +ctgA example contig 10001 60001 . . . Name=ctgA;multivalue=val1,val2,val3 +ctgA example BAC 11000 30000 . . . ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads +ctgA example SNP 11000 11000 0.987 . . ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1 +ctgA example clone_start 11000 11500 . - . Parent=b101.2 +ctgA example remark 11000 12000 . . . Name=Remark:hga;Alias=hga +ctgA est EST_match 11050 13202 . - . ID=Match1;Name=agt830.5;Target=agt830.5 1 654 +ctgA est EST_match 11050 17300 . - . ID=Match3;Name=agt221.5;Target=agt221.5 1 1253 +ctgA est match_part 11050 11500 . - . Parent=Match1;Name=agt830.5;Target=agt830.5 1 451 +ctgA est match_part 11050 11500 . - . Parent=Match3;Name=agt221.5;Target=agt221.5 1 451 +ctgA example gene 11050 19000 . - . ID=EDEN;Name=EDEN;Note=protein kinase +ctgA example mRNA 11050 19000 . - . ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Note=Eden splice form 1;Index=1 +ctgA example mRNA 11050 19000 . - . ID=EDEN.2;Parent=EDEN;Name=EDEN.2;Note=Eden splice form 2;Index=1 +ctgA example five_prime_UTR 11050 11200 . - . Parent=EDEN.1 +ctgA example five_prime_UTR 11050 11200 . - . Parent=EDEN.2 +ctgA example protein_coding_primary_transcript 11100 12000 . - . Name=Gene:hga;Alias=hga +ctgA est EST_match 11150 17200 . - . ID=Match5;Name=agt767.5;Target=agt767.5 1 1153 +ctgA est match_part 11150 11500 . - . Parent=Match5;Name=agt767.5;Target=agt767.5 1 351 +ctgA example polypeptide 11200 11900 . - . Name=Protein:HGA;Alias=hga +ctgA example CDS 11201 11500 . - 0 Parent=EDEN.1 +ctgA example CDS 11201 11500 . - 0 Parent=EDEN.2 +ctgA example mRNA 11300 19000 . - . ID=EDEN.3;Parent=EDEN;Name=EDEN.3;Note=Eden splice form 3;Index=1 +ctgA example five_prime_UTR 11300 11500 . - . Parent=EDEN.3 +ctgA example protein_coding_primary_transcript 11600 13000 . + . Name=Gene:hgb;Alias=hgb +ctgA example remark 11659 11984 . - . Name=f07;Note=This is an example +ctgA example polypeptide 11800 12900 . + . Name=Protein:HGB;Alias=hgb +ctgA est match_part 13000 13202 . - . Parent=Match1;Name=agt830.5;Target=agt830.5 452 654 +ctgA example CDS 13000 13902 . - 0 Parent=EDEN.1 +ctgA example five_prime_UTR 13000 13300 . - . Parent=EDEN.3 +ctgA example remark 13014 16130 . - . Name=f06;Note=This is another example +ctgA example CDS 13301 13902 . - 0 Parent=EDEN.3 +ctgA example remark 14715 15968 . + . Name=f05;Note=Ok! Ok! I get the message. +ctgA est match_part 15000 15500 . - . Parent=Match3;Name=agt221.5;Target=agt221.5 452 952 +ctgA est match_part 15000 15500 . - . Parent=Match5;Name=agt767.5;Target=agt767.5 352 852 +ctgA example CDS 15000 15500 . - 0 Parent=EDEN.1 +ctgA example CDS 15000 15500 . - 0 Parent=EDEN.2 +ctgA example CDS 15000 15500 . - 1 Parent=EDEN.3 +ctgA example match 15233 15302 . + . Name=seg04 +ctgA est EST_match 15410 17503 . + . ID=Match2;Name=agt830.3;Target=agt830.3 1 595 +ctgA est match_part 15410 15500 . + . Parent=Match2;Name=agt830.3;Target=agt830.3 505 595 +ctgA example match 15800 16101 . + . Name=seg04 +ctgA example match 16442 16854 . + . Name=seg04 +ctgA example match 16885 17241 . + . Name=seg03 +ctgA est match_part 17000 17200 . - . Parent=Match5;Name=agt767.5;Target=agt767.5 853 1153 +ctgA est match_part 17000 17300 . - . Parent=Match3;Name=agt221.5;Target=agt221.5 953 1253 +ctgA est match_part 17000 17503 . + . Parent=Match2;Name=agt830.3;Target=agt830.3 1 504 +ctgA example CDS 17000 17600 . - 1 Parent=EDEN.3 +ctgA example CDS 17000 17608 . - 0 Parent=EDEN.1 +ctgA example CDS 17000 17608 . - 0 Parent=EDEN.2 +ctgA example match 17106 17211 . + . Name=seg04 +ctgA example match 17410 17737 . + . Name=seg03 +ctgA est EST_match 17500 18000 . + . ID=Match4;Name=agt221.3;Target=agt221.3 1 501 +ctgA example three_prime_UTR 17601 19000 . - . Parent=EDEN.3 +ctgA example three_prime_UTR 17609 19000 . - . Parent=EDEN.1 +ctgA example three_prime_UTR 17609 19000 . - . Parent=EDEN.2 +ctgA example match 17695 18177 . + . Name=seg04 +ctgA est EST_match 18000 19000 . + . ID=Match6;Name=agt767.3;Target=agt767.3 1 1001 +ctgA example match 18055 18080 . + . Name=seg03 +ctgA example match 18306 18999 . + . Name=seg03 +ctgA example match 18545 18783 . + . Name=seg04 +ctgA example match 18869 18935 . + . Name=seg04 +ctgA example match 19404 19825 . + . Name=seg04 diff --git a/test_data/volvox/volvox-rev-del.paf b/test_data/volvox/volvox-rev-del.paf new file mode 100644 index 0000000000..b0d8be9b63 --- /dev/null +++ b/test_data/volvox/volvox-rev-del.paf @@ -0,0 +1 @@ +ctgA 20001 0 20001 - ctgA 50001 1 50000 10002 10002 60 NM:i:0 ms:i:20004 AS:i:20004 nn:i:0 tp:A:P cm:i:1890 s1:i:10000 s2:i:0 de:f:0 rl:i:0 cg:Z:10002M30000D10000M diff --git a/test_data/volvox/volvox-rev.fa b/test_data/volvox/volvox-rev.fa new file mode 100644 index 0000000000..642b3203a0 --- /dev/null +++ b/test_data/volvox/volvox-rev.fa @@ -0,0 +1,730 @@ +>ctgA +GTGACGGAGTGACATAATCTCTATACACGTAATTCGTTTTTGAGGTACTTGTAATTTCACTAACATACCCAGGTACAACT +ACTACTGTCCATGTCGCAGAGCCACATCAAGAAGCCTCTTAAAGGAGGCGAATAGTAAGCAAAGATAGGTTCACGCGTCT +TCGTGTTTCAACCGGGAGCTAGGCATGACGTGACGAGTTCAGGCGCTTCAAGCGTCCCTTTGTGGGTAAGTAGTCACATG +CACGATTGACACCCAACATTTACTAGCTGGAAGCCCGGCAATGGTTGCTTTGGCGGTTTGCTCGTTTATAAGCGGGGATC +ACCGCCCAGCGTACGAAACTTACCGTTTACCCCATGGACTTGTCACTTGATAGATCCGGAATAAAACTATAAGACCCCGG +CTATTTTGGTGGAATAGATAGCAAGGTATAGCCAGATCACGGGGTACTCCTACATAAGACCTACACGCCCCTTGCCCATT +GTGGAAAACAGTAGCACACCGTGCGAAGAGCTGTATAGATCAACAATGCAAGACCCTTGTGCATCCTCACGATTTTCCGT +AGCTGTTGTGTGGGTGTCCCGAGACGGAGCAGCAACGTCGGATTTCACGGCCCTTTAGGAGTAGTACAGGCAAGAACGCC +GGGGAAGGAATTTTGCATAACGTAGGGAGCAGACTGGCGGACGTACCACCTCAGTGGTGTGGGGTGTCTTGTACTGCCCG +GTATCAACGGACCCTCTGAAATCGGATCCGAATAACATGCTAACAACCCGCCACAGGGTATTCATGTCTGGTGTCACAAA +CCCTGGACTCAACGCCCATGCTGCACCTTACGGTTTGTGGCCAAGGGTCACACAGGGGTAACCGGACGTACGTAAATTTT +TTTGGTGTTTCTAATCTCTGTAAACTCACAATGATCATTCGGAAAAGTTTTTCTCATTGCTGGGTCCAGGGTAGACTTAG +TATGCCGGTGTTAATCGAAGATGATTGGTAGACAAAGTCAGCGTATATTTTAAGTTCCCTTGACTAGGGTGGGCCTCAGG +GGACGCGTTGCTACGTGTCGGTATTTAGGACTAGGTACCGCTGCCGCCCCGGCATGGGTATCTTTCATAAATAGCTACGT +GCGCGTGATCTTCATGACAGCCTGGCCGTTGCAGATATCAACCACAGCTGTATCTTCGACCCCACCGGGCATCTCTCCTT +TCTGTTATATGTATGATCATTGTTTGGTAAACTGTTTACTTATGTTCCAGCGGTCTCCTCACCTTCTCTAGAGGTACGAG +GATGTCATCTAATTAGGCTGACAGGGGTTAGCCAATCCGTTTCACGTACTAGACAGAACACGTTATCGGTGGGAAACTGT +TGCCCCGACATGGGGGCAGCTACGGTGAAAGAGGGTCGTTACCTCTGATAGTGGATTAATGGAGCAAGCGCGCTTCGTTG +CCGGGCAACCTGAACGTAGGCGGTCACTATTTGGGTGCGTGTGCCTATCTGAGCCTTCTTGGCTGTATATACTTATGCCA +AATTTGTGATAGTTTATATCGAAGTCCGACGGACAGTCGCCCCTGCTTTATAACTGGTTCAATAGCCAGCCTTCGAAACA +CGGTTCGAGCCATCTCGACTGGTTAAACTCGCGGGGATGACTAGGGATGGCATCCGGTAGCGCTGCGTGATGAGGATTCC +AGTTGTAACGAAACAGAGCAGAAATGCTTCGGCTTGTGCGATCTCCCGTAGCCCCCTCACGTACGTCGATTAGATGGGGG +CTAACCTGGGAAAGTTACGTAGACTGCACCGACGAAGGGTACTCCTTGGGGGATTATATAATTCACGCGGCGATTAACGA +ACACTCTACGAAGATCGATTTCAGAGCAAGGTTTCGAACAGTGGTAATCTGAAATAGGTAGTGACAGGTATCCTCTGGCC +CGTCATTTTACGGACAGGGCTGCATATGAATCATACCAAAGCGAGAGCAAATAGCATTAGGATATGATGCTTGATTTAGG +TGTCCACGGATAGGGCATCTGACGAAACATGAAATTTGACCCATACGATGGCCTCTTGTCTATTAAGATCCCCGGCTTAG +ACGCACCCCAAGTTCTATGTAGTCCCGAACTTGCTTGCGTTCCTTATGTACCTTCGTGTTACTGGAGCTCATATGAACTC +TGGTTGCTAACTAGTGGCCAGCTGGCTACTCGCTGGAGGAAGATTCCTAGCGACCGCTCACAAACCTCCATGAAAGCATT +GGAAATCAACAATGTCGTAAGGGGTCGCTGCGTAGTATAGCGGTACTTACATCCAATGGCGAACATAAGCGAGTTTTGTT +GGCCCCGCAAAAAAGCACCGTCCATTCTGTCATCATTTTCCGCGCGACGGTTCATGGTAAGCCTAAAACACACTCGTTCC +ACCCGCCCTGAGTTCCTAATACGACTCCACCTACAATCGTGTGCACGTTTTGCGTAAATTTAGGGTCTATATTCTTTCTG +ACCTACGCCGGAAATGTTTACCTCTAGTCCATAATCCACCGTCACCTCCGGCTTTAAACTAGAACCCATTTATTATGTTG +AATACACGATTGTCCGGGCCCAACGATCCCCTAATAAACGTGGAGTCAGGTCCTTTCCTCCTGCAAGGACGAAAAAAGTC +CGGGAGAGTTTTGGGTATAAGCTGGATTTGGGACCCGAGGCACCTGTACACAGGACAATAGTCGCGGAATGGACGGCTGT +GTTTGAACAATGCCGGTCTTCGTGCACTGTATGAGCAGAGGTGTGCTTATCATTACGTCGCCCAATAAGTCCGAGAGTTG +GACCGCCTCCTTAAATACCCCGAACTTTTCCTTGGGGTCCCGTTGAATGTACCCCTGGAATACGCCCCGTAATCCGCGCC +CGGTTACTGAACAAAAAATCAGTGCGTTAGTCATACATCCCTCTGACGGAGCAGATTCTGTGGAGATTGGAAGACGGATA +AACGCACGCGTCGCCCAGTTACCACAGGTCTTCCTGAATCAAGAGTAAACAGATGTGGTGGTATGTCTCCAAGTCTAGTG +TTGCTCTTGCCTTGTCTCGTTGCTGTTCCTGATATGGACTCGCTGAACAGCATGCGAGCGGACCTCATGTCTGGGAGGCT +GAGAGGTCCTTTAGGAGTCGCCTGATCGGTTGTCAGTACCCTAACGGTTGGTCAGGGTGTCTAGCGGTGAGGCGAGGTAA +GAGTCGTGAGCCGAAATGGTGAAGGCAACGTTATACCTTGTAGCTCATCTCGAATAAACATCGCGAAGTACCATTACGAG +CCCTTAGGCTTACCCTATGCTCAACCCACACTTGTAGCAGACGAGCGTCCGGCAGATCTCAGACTATCATCCCGTGTGCG +GGGATCTGATCATGAATGTTGGCCTTCTCTTAAGGCAGCCTCGTAACTGATAACTGGGGCCTGTAAGCCAAGAGATGTGT +AATGAGAAGCAGTAGATAGTAGAGTAACTCGCACCACCACCTTGAGTCATGGTCTACACAATTCCCCGGCAAAAGTGTAA +CAGACTGCGTGGCATAAACTTCAACCCCCCTATGTTGTCAGAGAGGTACCAATTTACTCCGATTGTATATAGAACAATTA +GTAGGGAGCGAGGAGAGTCTGGGATAAATGACCGTCGGAGAGTCACTTCTCCCTGTTATGCATAGGGACATACTACTATG +TTTGCGTTCCTATATACCGTGCTGTGTGCAGCTACACCCTCGTAGCTCACCGTGCTCCCTAGGTAACGCGCGAAATGTAC +AACGGGACTAGCTACTTCGTTGGGTGACCCTTGATACCCCACAGACTCATTAATGCCCAGAGCGGACTTAAGTGGGAGAC +AGTAAACTCGAGGCTTGACTGTACCGTCGATAGAACCCAGTAGACCTGGGTTGTCAGTACCCAGGAGAATATCCGTTCCT +TGGGCCGACCCAGCCACAATGGCGGTTGCACTTCTGTACAAGGTTGCCTCACCATCGCTTGGAGTAAAGCATAAGGTTGT +TGCATCGGAATCGTCCTACCTCTAAGTTCGAGGCCCCGCCACGATACGCAGGACACACATAGTCCAGTGATGCTCGACCC +AAAAAAAAACATCCCACAAACACCCTTCTTAAATACCCAACAAAACCAATCCAAAGTCCGAACTGACCGAACCGAAACTA +AAACAAAAGCAGGTTCTAATCTCATCGGGACAGCCAACCATCTCCCGCAATTTAAAAAAAACCATGTCGCGCAAATCTTG +TCCTGCCCCCTTGTACTCCATGCGACCCCCGTAAACACATAGCCCCTGTTCCGCTTTATCAGGGAAACTTACCTCCAAAA +CACATACACGCTTGACCGTAACGCGCGTTGGTTTCGCTCAGCACGTACATTCCGCGATACCCGCTCTTCGTTTTCCTTCT +TCCGACACTTCGCGTTTCCCCGAAGCTAAAACGGGCTCCTTTAGTTCCGATAAGTCTCACGCACCTGACCCAAAAAACTG +ATTGGTGATGTCACGTAGTGCAATCGCCTGATGACGTTTCTCGCCCTTGACGTGCAGTCAACGTTCTTTATAGTGACCTC +TGTCCCAAAACTGAACACACTCAAACCCTATCTCGGACTATGCTTTGATTTATAGGGCATTTGCCCGATTCGGAATCCAC +ATCACAACAGGAATTTCGCCCTGCTGGGCAAACCCCGCGTGTACGCTTGCTGCAACTCTCTCAGCCCAGCCGGTGAGGGC +AATCAGCTGTGCCCGTCTCACTGTTGAGAGAAATAACCACCTGCGGCACAATACGCAAAACCGCATCTCCCCGCGCGATG +ACCGATCATTAAATGCAGCTGTCACGACAGTTTCCCCGACTGAAAAGCGGCAGTGAGCGCAAACGCAAATTAATGTGAGT +TAGCTCACTCATACGCAACCCCAGGCTCTACACTGTATGCTTCCGGCTCGTATGTTGTGTGCAATGTGAGCGCATAACCA +TTTCACACAGCAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCTGGCTGGGT +CATTTATTGTCCTGAGCACCCAAGAAGATGGCCAAATTGTGGGAGATGACTGAGTAGACCAGGGCTCTTTGGGGAAAGGC +CAGAACCTAGGGTCATCTGGAAGGTGTTAGGCTAGATCAACCCCTAGACATTTCTACACCCCCTCACCACACAACACAAC +CACACCCCCAAGCAGTAGTTATATAATTATTCAGTATACAAATTGTTTATTTAATGTCTATGTTAGTCAGAGTTCTCAAA +AGAAACAACTTATAGGAGATAGATGACAGATACATACATACATAGATGAGAGGCAGAGAGAGGGAGAGAGATTTATTATA +AGGAGCTGGCTTACACAACTGTATTAATCCGTTCTCATACCACGATAAGGAAATACCTGAGACTGGGTAATTTATAAAGG +AAAGAGGTTTAATTGACTCACAGTTCCACGCAGCTGGGAGGCCTTAGGAAATCTTACAATCATGTGGAAGGGAAGCAAGG +CCTTCTTCACATGCGGCAGAAGAGAGAATTTCAGCAGGGAATCCAGCACTATAAAACCATCAATCCTGCTGACCAGGTCT +CCCGAATATCGCACCTCAAGCAAAGCTGCTCATCCCATTCTACGCTCAACTGGAATGAAACTCAGGTCTATAGGCAGGGT +CGATGGGTAAACGTTGACATACCCATTCACACGCCTGGGTTCAGTACATCGTACGGAGAATGGGACGGCCGATCGGCAAT +TAGTCCGGGCGATCCGTCCTGTTAACTAGCACGTGGATGTAATTCATAAGGGCCAGTTCGCAGCCGTAAGTTATATATCG +AGACTGTCCGGTTCTGGATGGCATTGTTAACAGCTAATGCGGCGGAATTTTTGGCCCTTATGCCGTCCGTCTGTCATGGG +GACGACTTACTGCAGCCCTTGGAAAAGCTACGCACTGACCCAACTAATACTTTGCATTTGTAATTGTCGATAGGGTTCAA +GACGCGTTGGAGCGATGTAGAACTCATTAGTATGGTTCCTGTACACGGACGTCCGTTACCTGAATCAGGATGGCGCAAAC +CCGGTGATCTTCTTAAGGGCATAACTTATGTGGACTGGTTCTCTTGTGTCGCCACGCATTAACGGCGCCAATTGGTGGGC +GCAGCCATACTCAGGCGTACTGGAGCGCTCGAGAGCTATTCTGCTCACAAAGCACTGCAGAAAGACGGGACCACCACCAT +TTGACCCCATTATCAGTTTGAGGGTCCCGATAGAAGATAATTCTGAGTCGGTGTAACCGAACTGAAAGGTGTGGCCCGAC +GGCAACGCACATTACCTACAATCATTGTTTTAAGCTGATCTAGGTCTAGGAGACTCTGTCCCAGACACTGCGATCGCAGC +AAAGCCTATAATTGTTTCTATACGCTCACCGCGATAATGCAAATGCTAACGGTCTCGACAGTCGGGCCCTTCTAATTATT +CCGTACGAGTGAGTACAATATCGATCAAGTTGGTCTCTGCACACGGTGTGAAGAGGTATTATATCTGTATGGAGCTTTTC +GTCTGCATATAATTGGGTGTACTGGATGGCCCAGTGGAAAGGGTCAGGAATCTTGCTCTTCGAGAACGGTCCACTCTCAA +TGACTGATGATGCAATACGCTGATTAACACATACTGAATCACTTTTGGACGGCCAGTATGTCGCTGACATAGGTAGATCC +GCGATCGCATCCGCGATGGTAAAGTACCCGGAACGCTTATAGGGTTACAAATCGGTCCACACCATGGTAATATGTACCCA +AACCCGTTACCCAAAGGGAGTACGCTTGGAGTATGTATTGTATAACGACTCGACACACTATATCACGTTCAATGGATAAA +TACAAGTGACCTGTCCGGTGTCCATGCCACATACTGTGAGGAACCTACGTTCGTGTGTACCTCCAAGAGATTCTCTAGTC +AGACGTTCGACGGAAGCGAGGAGTCCATAATTTAAGACAGCCGCTCACACCTCTCTTTGCAAGCTAATCGTCCGCAACAC +AGTCGACGATGGGATTTCCCCGCTTACATATTTATCATTGTCTACTTTCAGGGCAGTCTATCTGAGATTATATACTGGAA +CAAGCCAGTTGCTTGACCAGACCAGATTAGGTGCTGCGTACCAACATACACAAACCTATGGACGGGACCTCCGCGTCCTC +GCGAGTGATTTGATTGATGTGTTGGCCATTAGATCCTACGACGGCCCGGCGGCCGATGGTTGGATCAACATATGTATAGA +ACCCGCAATGATAGGATCGCCAAGAACAGAGGGTGCTACTTAAGTACGTAGGCATATCTTATCACGCGGATCTTTATCTA +CTGTGATTCGGACTTATGAGAACCAGATGACCGCCAAAGTCCAATGCGTGAGCGTCAGAGTGCAAGAAGCCGCACGTGTT +CTGCCTAGATTCTAGCGCGTCCGACCAGCCACGGATCTATCCTTTGGCGCTGGTTGTAGCGCTATGACAATATCCTCCTC +TGACCAACTCTAACGAAGGTATGTTTAGAGCTCAAACCAAGCACGTACATTACGTTGCCGTCGCGACACAGGAGTGGCTA +TCACAGCGGCATCAAACTTTCCAGATTAGGGTTCATGGTTGATATTCGCAGGTACGGACGCGTCTCGAAGAGGCCCATTC +ATCGCTCGTTAGCATTAGTATCGGCAATCTGCGATGCTTAATGAGCCTAGCCGGATTAGAATAGTTTGACCCAATGTTGG +TCTAACCATCGCAGCAACTCGCTTTCGCTACAGCTCCAAAATTTTATGGTCTTTACTTTCACAATAGTTGGTGGGTCTCT +AGCCAGTGCATGACGTAGTAGCCGGTAAAGGAGCCGTGCGAGCTGGGGGAATGCTTCAGAGATGGCTGTTACCCAACCCT +GTTCATGTGATGTCGCCTTGCCATGAACGTGAGCCCGAGGGAATCGTGCAGAGCTACGTAGAGACCTCCATCGTTCTACA +GTCAGATATTTCAAACGTGTACACAATAACCACAGAACCAGACGCCTTTTATGATGGATCGCCTACCGGACAACGGTCCA +GCCTTTCCCCGTTTGCGTCACGTCGTAGATCATTGAGAGACCCGCCATGTGCCCTTGGAATCACGGCCTTCTTATACGTG +TTGCCCCATTCGACGAATGACTTGCTGTATAGCAGACGCGTTGTGCTGGGCCACAACGTGTCTAGGATTGTAGGTTTTTT +CAGAGTCGGGGCCTTTAGGAGGGAATAGGGACGAACGACGTCGCAGATGGCGCGACTTGTAACAGTAGCACTGCTACACA +CCCAGGTGATACCCAGAAGGCATATTGAGATTGTCCTCTATGTTGTGTCGGTCACGCTTCCCTAACCATGCTTGGCGTGG +GTCCCTTACCTTGGCAACGAACAACGTTCGGAGGGACGCACCCTCGGGTCACGACCGCTCATTTTTTTTTCATGCTGCTC +TTCGGATTGTATTTCACGCCCATGCCAGGTGCCTCCCGTGCTGGATAATGCTACGCTATCGCGCTCGATGAATGAAGGTG +AGACGGTATGCAACCAGGCCCGTGTCTTCGTCGTACCCCAGGTCACTTTCCCAAGCAAGAGCGTTTCTTTAGAGCAACTC +TAGCTCGAAATATCAAACCTGGTGCGCCATGTATAAGACCCGATCCGCTACTAAAGATCCCGAGCTTGCTCGCTACGGCC +CGTAGGGATTTAATAGACACATAGAGGTCGCGTATTATAACCATCACATTCCTCTCGTCCTACGTCCATTGAGACAGCTT +GTTCTCGTCTTCGCTAAATGTTCTCAGATTATGATGTACTGCTAGACAAATTCAGTGTTTCTGGGGGAGTCATGTCACCC +TTACGTGCCAGCGGTAACCTCACTCGGGTCGTCCCACTGGTTACTTTGAGCTACAACGCGCCCTCTAATATCGCGTGCTA +GGGTCCAAGCAGTCGGCTGGACAGGAGGTATCAAGTGCTGGGATAGATATATGGAGATCGACCGTAGTAAAATCTGATCA +TATTTAAGTGTGATATCAGTCGATCGATCCAGATCTCAAGCTACGTCGTCTCCATTTCGACCAGTCCCGGGATCAGACTA +GGTGAGTAAGAAGTTCTATGGAGGCGATACGCGCCAACGATAGGTTTTAACGATCTATAAAAGCAACATTTCGCCAAGCT +CCCTCCGATGTCGCCATACTGATCAGTCGGTGATTTCTGAGGACGTTAAAAGCACACTATACGGGCGTTGGCGCTATGAA +ACAGAGTAATCGTGGCGGGTACTTACCGCCAAGCGCGTGCCTCCCCATGTTACGATGCTGATACCTTGGTTTAATGCTGG +TGTGATCTCTAGGTAGCACTGCAAAACCTAGAGTCTAACAGGGGAGAGGTATCTCCTTCGAAACCGTACATTTGGGAGGA +TTATGTATTGATAAGCAAAGTTAGGTTACCGGCCGCGGACTGAATTGTGTGAAAAGACCGCCGCGCGTGTGGTATCTAAA +CGCACCTCGCGAGGTTTCTGAAGATATCTCCATGAAACCCCCAAAATTGTCTTATCACACTGCCCCGCTTAAGGCACGAT +GGAACGCATTGACCAGCGCGGATTGAATGCACGCGGCCGCAGAAGACCATTACTGCTCTGTGGGGGAGCCCCAGCAGGGC +CTAGGATTCGCCGCGGTAGAGTCTGGCACTCAGAGCTTAGCGTGTTCATGTTGTGTCCACTATCGCCGATTCGGCTGCTT +GATAAGTTAACAATGCCGCGATAGCCATCGATCCTTAGGCACGATAGAAAACTAGCACGTGTTTCATCGGGGCTGGCCTA +GCTAGCGCGGCCTCTGCCGTGACTGGCAATATGAACGAATGTCCGCCACCCGGAAGCTAATTACAGGCTTGTACCGAGCT +TACTACGTAATCACCAGGGCTGGACAGGCGGTCTTAGCTCGTAATTGGTACGGGAACACTCCGGCCCTATGCCTCCACGC +CTCAATGGATCACGGTGTTCGCACCTTATTCCCCAAGCAGTGGAGGTTTGTACGCGTACCGCCGCCACGCCAGGGCCGTG +CTTACTTGCTAGTGAGTCGTCCGTTTTCACAGGCTCACGTACTTGTGATAGCCCAATATCGCTACCTCATATGACACATT +CCGCAGTTCCACTCGAGAATTAGCTATCGGCGCTCTACCCAACTACCCACCGTAGGGTCTCCAGCTGACGGCATGGTCGG +AGTAGTCACAAGACAGCCGCAGGCGTCGCGTTTCTCTAATCTTTGGCCTCTGAGCGGCTAATACCCTTGCGTTACCCCAA +CGGATGGGTCGCGGTAGCTGAGTTGGAGAATTTTTCTAACTTGGTGTGATTCTACTTCCCAGACTCATTGCGAATCTCTA +TCACACGAGACGCTTCATGGTGGCCCGAACCGTTTATTCCAGACGTAGAAACTTACATTTCACCCATAAGAAGACGGTTT +AAGTTTCGAAAGAAGGGGCTGAGGCCCTCCAGTCCCTGGGTGCACGATATATGCTTATGGGTTGGATTTTAAGTCGCAAC +AGTCAACTAATACTTGGTCGCTATTTAGGAACGACCATACGGGCAGGGCACAAGGTACTCCCTCCAAGGGAACCCGGCGA +TCACCATGCAACGCCGGGAACTGGTTCGTAGACGGCGGTGTGAAGAGCTTACGTTAGACCCGCGCCAATGCGTTTCTTGA +TTACTAAACGGGGGTTCCGTAAATTAAGCCTTCGTCTTATCGACTTCAGTCATATTGAGGACGTGACTCAGTAAGTGAGT +CGTGATACTCCCTGACTTGAACGGAACCACCACAGGGGTTTGATGGAAGTCCATGGATTCAGACTCTATCCTGCCTTGGC +TTATCGGGGAACCCCCCTATGTGAATTTCGGGTCCGTAGGTCCCTCTCTAAGTCCAATCGTGTTGTAGGTGAACGAAGAG +TTAGCGTCTGAGAACCCCATTGCTCCCCAGAAGGTAGGCCTTACTTTACTTCTTCGATAACCACCCCGGTATATTACAAT +CCTTGCCTCATGGCCGGCCATCTTACGATTGTTTCTCCACAGTACAAATACCTGCGATCCTCTGTTGGTCAAGGAGTTAT +AGCCCGCTGACTGATAGAAGATTAACTTTTTCGCGTTGATTAGCCGATGATTCTCGAGATGCGCTGGGCATCCCCTCCTG +CAAAACGACAGCCCTGCGCCAGACACGGTCATTGAAAAGTTCATCAGATGCAGGATATACCTGGAGCGCAAAACCGAGCC +CGCATGTTGACATCTTTCACTTACTAGCATTTACATTTGTTATGACGCCCTACAAATATGCGAACTCGCTCACTGACGCG +AGATACTACTCCATCACGCGTTGCCATGTAAGGTGGGAGGGGTCCCCACATCTACGCGGACTACTGCGACTGATGCAAGT +CCGCGATATAAAACAGGGCAGTGTCCCCGGGAGGGGTGATAAATCCAGCTTGTCTGGTTAACCAAGGTGAAGAAGGGTGT +TTGTCAGAAGATTGCCGCCTTTATACTTCAGCTACTTACCCTCAGCAGTGTATGGGGGCATCCCTCGCAACAGGTCCTCC +GAGCAGGAATTGTAGGTACTGCCTGCAGGCTCATTCGAACCAGCGAGCAGAACTCAGAGAGCTTGCAGGAATTACGCGCG +TGATTACACCTTTTAGCCGTCATTTCGATCCGAGGCGGGATACTCCGACTGGGACGCGTGATCTAGGGGATAGATCGTTC +GAGCACTCGACAAGAGCGACCTCGTGTAACGTACGATATCAGCCACTAGTCTGGAGGCGATTCTGACATGGTGTATACCC +TAATCGGTCTTCTGCTCGATAGACTAAGTCTTGGGCTCTTTAACTGATACCCTGCGTGCTGATCACACGATATTGCGTAT +GCTTCTTTCCAGGCGGTTCGAACTGCGAAAAAAGGTTTCATAAGTACTTGTACGACCACGTTGCATCGATGGTGGAGCTT +TGAACGCTATCGTATAGGTCTAGAGTAGTAGGTCGGGACCAAGGATACGCATCACGACACGAACATTATGTGTTGCGTTA +AACTATGGACACACACTTAGTAATCCATCTCCTAGAATCTAAGGATGAGCGCGAACTTTGAGGATACATGTAGGATCGTC +CCTCATATAACTCAGGATAGGCAAGATCTAGCGTGGCCCCTCCTAAACAACATAAGCGCAAGATTGGCGCGATTCCTAGT +GGTTAAATGCAATGGACTGTAATGTGGACTGCTTCGGCTATTAGATGACGGTTCCAGAAAACTCAATCACCTGTGTTATC +CCCTAATCGAAGTGGGTAAATAGGCTCGCCGCCCTTCTTTAAAGATATAGTATTGGTGAAGTACCATGCCAATGCGCGTG +TATCTATTAGCGTCGTTCGAGCCCATTCCGACTACACCGTTTTGACAGTCTGTAAGTAGATCGGACCGTGCGCCCCTTTC +TCGTAAGCGGACATAGCTTTAAAGCAGCTTAAGGCGCCCGGAAGGAGGACTTTTGTACCAGGACTAATGTAATCGAGTTA +TCCACTCGTACCCCTAGTGTTAGAGTACCGAGAGGTTCAAGTTTCTGTCGCACCTTTAGAAGGCTGAAAGAGCAATCGAT +ACTGCGACCTCCTAGCAGCTCGGTCCTTCAGCTCGTCGGTGCACAGCCAAGGTTGGTACATGGCCTAGCTCGTTATCAGG +TTTGAGAGCGAACTTCTCAACCTTAACTAGTTGGTCAAAGCGACGCCACCAGGGGCTGAATCTAAATATGAGGTGATGAC +CCATAGCAATTGTCGTTCGCCTCGATACCAGTCGGTATTGCATGTCGCCTTGAGTCCCACGTACGTATATAGGGCTATAG +CGTCAATTGCTTACCGCCTGCACGTAGCTCTTCCATCTGGCCGGAGACGCGGCGCTGGGCATTTATGAACCTTGTAATGA +CGATCGATCAAATGAATGAGGACGACTATTCTAGATGAGTTTGGGCCGAAAAATGGTGGCTTGGTAACCACGAACCGACC +CCACACTGTTGGTGTGCCTCACCATGACTGGAGTTTCTGCCCGAGTGCGATAATAGGACGTCTTTGACCGCTGCCGGAGC +AGGATGTTTATGGCAGACGAGACCCGTAAACAGAGTAAGTCCCCTACATCGTCACGCTGCTGCAGTTATTACTAGTGTCA +TCCGGTACGTTAGACATGATCACTTTCAGAACCATTGCCAAACTCTAATCGTGATCTATACAGCAGTCTACGAGTCAGAT +TCTTGTCCGGTCAATTTAAATAACTGACCCAGACCATAGGAATACATAGGTATCACATTGTGCCGCCCTTAAAGTACCCC +TATTACAAAGGCCCTGTCACAGCCCCCTCATCTTTCAAAGTCTCGCGATGTTGCCCAGAGTTCGCGTTGGACATTCGAAA +CAAGGTGTAGGGACCCGAATGCGTGTGACTATCTCAGCCTTAAACTTCACTCAGAGCCTCCGCCGCATTGAACGAGCTCC +CTCGGATAATTTTCCGAGACCGAGTCGCGCTCGGATTAGCGTATCGTGGGTCGATAAAGTCTGCACAGTAGATTCTTCAA +TTTACGAACAGCAAGACTCTAGAAACCGTTGCAAGGCTGGAGACGTAGAAATGCTTCTCGTCGTCGGGGCTGATTGAACC +GTTGGCATCTACGACACAATCAAGACGGGCCCAATTCACATACATGTGGGTAGCGGGTGTCCCAAGAGAATGTGCCGACG +AACAGGCACATTAGCGTTGGGTCTTCATATTCGTCCGAAAGATGCTCGGCACCAGTATCACTTATGATTTAGGATTAAAG +CTCTCCTCACTGCAACGTGCTTGCTGTAGAGCAAAAAACTCCCACGTTCTCAACCGTACCATCGCTATTCTTAAGACCTC +TGTGTTTAAAACATGGATGGGTGTGGTCCATGATAGAGTGTAGAGGTTACTCGCGACCTGCCCAACGCTTGTACGCCTAA +GGCTAGTAGAAATTCTGGTCGCTAGCCGCATAAGACCACTGCCACGCCAGCGAGCTCATGAATGAGTAGTGGCTTTGAGA +CGCGTGTGCCTGATTAGGACCGAGTGTCCCTTGGAAGGCACCATTCTGAACTGCCATCGCTAGTAGCCGGCGTCGTCACT +CCAAGTCTTGGGCGTAGTGATCCGCAGTACTCGCTTCGCCTATCATAGAACTAGACGACTTGCGTCGTCGAATGAGGAGC +GATACTGTGTGTCCTGAGGGCACACCTCCTCATCCGACCATAGTACTTGCGCCTCGACACATACGCACGATAGGGATGCT +TAGCTTGCGGTCGTTGTAAGTGATCTGGTTGTGCTCTGACGAAGTATGCGGTATATGATCTAGTGCTGCAACGGTGAATT +GCATGGATTGAACTGGGCTTAAGGTGCGACCAGCGCGCTGCATAGAACAACCGAAGAGCGGGCATCATGTCACTGTGGAG +TGAAACATGCGTGTAGCACCGCCCTTGCGCAAGACAGCTGCTGGTTATGACCACATTCGACTACACGTGTACCTTGCGTT +GCTGAGGGAAAAAGTCTGTACCTGACGCCTGCGTGAGGATTTTTTTGGGCTTGTTGCTTATGCCTACCCGTTGTGTAACG +CGAGGGAAATAGATCGCGCAGCCGCAAGCCGTGGTCCCGGCATTAAAAACCGATCACTGATTGGACTCACTCATTAGTCC +AACCGCTCTCCGAGTTAATACGATATCACGAGGCCACCTTATGTAGAGGTTTTCAGAAGCTCCCCATCCTGACTGTCGCA +ACCTGTGTCAAGTGCGTCTCTTAAGATTGTTCGTGAAGGATGCCATACTGCCCAGCCTGCTAGGAGTTCCAGGTTGACGA +CAACCTAATGAGGGCTGTGCGTGATGCTTCAACTGTGGGTGATGTGTTAGCAAAGCCCTAACGTAGACTGGCGTATTGTA +CTTCGATTATCGACACGTCGCTGCTAAGACACAGGCCCATATCGGTATTACCAGCCCCATTGAGTATGCCTTGAGTAACG +CATCGCAATCGCAAAAGCCCACGGGTAGTGATAGACGTTACGTTAATCAAGCATGATTCGGGCTCACCTAACTATCATCT +CGGGTATGCCGTGAGGTTCCCTAGCATTGCGGAAACACAATCTTTTCGCAGCCCATGCCTCTTATTTGCGCTAAATATCA +CTAACTAAACCAATAGTTAGTGTTGAAGTTCACATAATTGCGCCCATATGGGTGCTACATTGGGGGATTGTTTGCCATAA +ATCATTAACCGACACTAGGTATAGTTGAGAGGAACCCATGATCGTCGGGTAGAAATGGTCTTCTCACAACCCAAAATTCG +GTACAAATTAGGCTAGGTTAACAACTTACTCCGGCTAAATTTGTCATCGGGCGTAGAGGAAGTTAACTTGGACTGCAGCA +AGATTAAGGTCGCCCATCGGGAAGCGGTCTTTAATTAGATAGGGGTCGCGGCATCAAGTAAGGTACCGCCACGGTACATG +AAATTCTCCAAGCGCACTCGATGGAGGTTTTACTTAGAAAGTTGTAGGGCTCTAGCTACGCAACAGCATAAGATGGACCT +CGTGGCACTGGGGCGCCCCTATCTCGTATCTAAATGACCAAGGAAAATAACGGAACAATCTATGGTGCACATATCACCGA +GATTACAACCCTTTTAACGCGCCGCTCCATTGGTATCACCTACCATCACCCTAGCCTAGCGATGAGAAACCCTTACTTAC +AACTGGTCCCTGCGTCTAGGAGAGAAAACATCCTAACAGTTCGGCAGTTAGATTAGCTGCAGGTCTAGCTACAGAACGTG +CGCGAGAAAGATCGATCTTGCAACGTTCTCTCATATGCGTCTGCGGTAAAACATCGCTTTCCTAAACGCTTAGGGTAAAG +GCTGAGTCTCGTCCCAGCACGACGATACAACTTGGGCGTACAAATTCGGGGTGCTGAAAAGTATGGACGCACTCCAACAG +TTGCCTACGCAACCTTAACGTGACTTACAACTGCTAGTCCTTACGCGCAGGGGTGATAGTCCATCCCATGTATGCTCAGA +ACACCACGAATACCGTAGGGCGCGCCGAAATACGGACGGTGAATGTAGTAGGAGAAGAATTCTCTAAACCAGTTGGGCTT +GTACTGGACACCGTTATGTCGCTTTACGGCCTCTAAACGAGCGAGTAGATTTACCCGCGGGAGGTGACAGGTCCGCTTTC +CTTATTGCAGTTTATCGTCGGCTCGCTTTTAACCCACGACTGCGCAACAAGTATCTCCCAACGTAGTGTTATCGTTCAGA +AAAGCGCTACAGAATGGGGTCCGTACAAGCGTTTAACCGAGCACCTGCCCTACACTATGAACATACCAGAAGTAACTAAA +CAAAAGGTTAGTTCGGTTGCCTATGCCTTTTTGTGGTTGTTGAAAATGAGGTGTCGTTATAACTCGGGAATGTCCACCCA +GTGTTAGGCGGGTCGCCGAGTGTTAACCCAGGTGCGTAGTGGCCTAAAGCCCTGGCCCGTGTCGAAAAATTGGAATGATT +GTTACGCTCTACACCATCGATTGTCAGGACAGCAGATATGTCCGTAATCAGCCCAGCCTTCGCGCACTGGGCCAATTGCA +TCCCGCAGGACGGGAAGCCCAGCTCGCATCATGGAAAGTCTGTTGCACGCAGACTTCATATGCATGTACGAGGTGTATTC +CTGAAAATGATTTCCCACATTGATGATGGCGCAATAGTCCGAAGTTGGGAACCGATCGAATGAACTCAGTAATCAAGCCT +GCAGAAGTAAGCGACCCGAACGTTAGCGGCAACAAGCAACCCCAACGAAACCTACCGTATCGAACGCGTGTGCGTGCCCG +ACACCGCTTCGTACCCAGCCGCGGTGTAAATGCAGTAAACACAAATCCACGGTACGCTACTGAAGGCTTGCCTACCAACT +TCATTAGCGGAGGATTGATTAATGTATCTTGGTTACTAAGGACAAATATTGTTTTTCAGTAGTTAAGAGGCGGTCTTTCA +ACCGTGGTCCAACGTCTATGAATGTTCTCTTATTACTATGTTACCTAGAGCAAGCAATCTGTGCTCATCTTACGGGTGGA +AACCATGAGCACGGTCTTAACATGGTAAGCTACGCTCGGGGTGACGTAATGCGCTCTGTCCTTTGGGCAGTACGAGGTAC +TGCATACGCGCTTTCGATTTGATGGTCGATTATGTATGGACGGGCGCAAACCATGTATCCTACACTGTAACGTCCTTACG +CTCTTCGGATCGGTGGCACCGATAAGCGCTGGCAACCTTGATTATATTTACGAGAAGGAGATCTACGGCCCTCGCCCTTA +GTCGTTCGCTCGCGGACTCCGTAGTGAAGAGAACGCGTTACGTGTATGCCCTGGAGTATGCGGGTCTTTAGAGTGGCTAA +ATGTCCCCTGTGTTGCCTTCCTTAAGGTCCGCGAGAGTAACGCGACTTTGGAAGTGCTTTGTTGTCTCGGATTTGTAAAA +TATGTGGACCGCCAGGCTAGTCGCCAGGCATGGAGTCCGAACCCAGTACGACATTTAGACGTGCCCTGGAGCAAGGTTGT +ACGGAGGTGCTACGTAGGTCGTGGCCTATGCACTGGTCTTCCCGGTTTGATAAATTCACATAAGGAGTGGCTGGACTATC +TTAGCCGCCCGGACGCCCCACTGCACCCAACATCGGGGAGTATCGATGCCTGAGTACGTAGGACTAAATACTTCTTAAGA +CGTAGCTCAGGACAGACATTGTCCCACGTGTTAGTTACACGTCACTACCCGATCCTTAGGTTTAGATGACATACACTTCT +AGGTATGCAGCCCGAAATTTGGTACCGCGAGGGCCGGCTTACACACTCGAGGTATATATAATGCGTCAGTTAATTTGGAT +GAAATCCATAAGTAGTGGTTAATTTTACACCGCACATGGCGGGAATCATAGGGTACGTAGGGGCTTCTCGGCCTATTCTC +CGCAGATCAAACTTCACGTCGACTCCGTGTTACGATAATAAATCTCAAATCAGAGCAAGGGGTTACTAGCATGCTGGGAG +GTGCAATAAACTGTCGAACGGACAAAGTGATAATGCACAAAACCCACTTTTTTTTAAACTGCTGTTTTTCCGTGTCCAGG +AGCCAGATAGGGTATTGCCGCACGTCCGTCCTATCTGAGCGAGGGCGGTGTGGATGTCACCAGGCTGCATGCGTCTTGCC +AGTACGTGGTCCCAGCGATTATACCACCAGCGCCTGCGCACAGTCTGCTGACAGTCACCTCCCGTCCATAGATCTGTACT +ACCCATAATTCCCTACGAAACTACCGTCCCCGCACTAATAACACAGATTCTTCCACCTGAAACGCGCAGCAATTTTCATA +AGCTGCTGCAGGACGATGCCAAACGTATCTTTAGGTCCATCGACGCGTAGTCATATACTACCTTGCGGACTGAGAACCGT +GTTCTTACTATCCAACAGATAAGTACCGACTCGTTCAGAGCGGAGGCCTATTACATTTAAAGGCCCTATCAACAGACTAG +CGGGCCAGACCTATACTAATTTTCACTCCTTATCAACTTGATGGTGTTTCTCTAGTCTACAGGCGTGGTCCCCATCGCAT +CGTATGCCTCATGGATGGCACTTAAGGCGCGAACCAGAACTTCTCTTATGTAAGTGAACAGGAGTGAATTACGTGAATGC +GTTAACTTGATTCCCGTCCACCTCACCTGTGGTGTTTCTTTAGGGAGTCTCCCCAGACCGGTAAACGCAGTTCTACGGAG +GATGGGGGACAGCCCTCCACGATGGAAGCGCTGCCGCGGGGGGACCTAAGCTACGGTGTGTTGACGGTAGTAGACGGTGC +GTACCGTATTGGGAACGCAATCTTTAAAGGCTGACAACTATAGAGTTACTTTTACGGTGTTAAAAGTGCTGCCGCCTCAA +AGGTAACGGTGCTCGTTATCCACGGTCCATTCTCGGATCTAGGTGTGGACCAGAACTTATCCCAGCATAGATGTAGATTG +ATTTCGAAGAGCTCGTGGCTTCGTCTTTTTGCCCTCTGTCTGAGATCAAACGTGTGCGCACGGGGTCGGGTTGCCCAATA +GCCCAATCGTAGTCACGGCACTGTGCCCCCCCTTCGGCAAAACTATACTTGGGGCACCAAATCCCTTAGGACTCCGTAAA +TATTACAAAGCCTCGAGGGGTTGCTGGTATTCGGACGTATCGACAGTCTGAGAGCAGCAACCCCGAACGAGATGATGCTG +CTATTGCGGGAACTTACGTGGATACCGCGTGGCCCTCCTGCAAACGCTCTGTAGATATTCTGCTGCGGCATCCCACGGTT +GCGGCGCAGGTCCACACGATCGTTTGTCCGCCATATTCCTCATCCAGGTGACAATAATCGATTTTATCGCCGCAATCCAG +ATGGGCAGGTGCTCTAACTTAACGTTCTAACGTCACGGCGGTAGTTCTATGTTGAGGCAAGCACATATATCGCCCCCGTA +ATACTGAGTTTTACTGGGTCAGAGATACGTTAGATTGGTAGCGCCCTCAGTATTGGATTGCGGTAAGAATGTTGCTGGGA +ACCCTGAGGAGCACCCGACGCTAAGCCGGTACGAACCGTTCAAGACACATTCCTCAAACCTGAGGTAACCCCGCGCGGCA +CGTGAGCTCGAGCTGAGCCCGGCAACGTGAGACGCGCCGTCAAGCTAAAAATGAGCCTTGTTAGGCGGGGAGAGATGCGC +GTCGCGTTACTAAATTGTCCACTGGACTCTTATTAACAATTTCCAATCCTTGGGCGATCGTTGCAGCCTCATGCAGACCG +GTCATTAGTGACCGGCGGACTGTGCGAATGGCCGGACCGTTTGTGCATCCGTTCTCAGTTGATAGCCCCATGGCGCTAGT +CATAAGACAAGGACTCCCCGCTTGGCTACGTACATCACTATGGATACACTATGCGCAAGTGGCTCTACAGTGGCAGTAGC +TATCCGGTGAGCGCGCGTTCCCCAAGTCGTGGGGGAGGTCTTACCCCACTCTGCGTAAATCGTGTGGGCTACGTACCACT +TGCTAAGGGGGGGGCTATGAGATTTATACAATTCGCTTCTAAGGAGATCCGCAGTGGGACCTAGACATAACGAGTCATAT +CGCGTCGTTACATTTGTGGCCATGAACCTCGACTGTTGATTCATTAGAGTGCGGAAGACTCTACCCCGTGCACGAAGCCC +TCCTTTTTGCCATTGTACGAGAGGTCGCGATGATGCTTTCTGCTAAGTATGATGCGAAGTATCAACTGCGTACGACGGGG +AGGCAACGTACATGGATTCATCAGATCTTACTGTGTCGCCCCACGCCTAACCTCCCTACCGTATTATGTCTGTGCAGGCT +ACACGCCCCGCTTGCATGACGCAAGACCGCTAGTCTTAGGGTGTTGAGTTACCAACCTTACGGCCAACCTGGTGACGTTT +CGAAATTCCAGGGGCGCCGGACTTTCTGTTCAATTCGTTGTGAACGGAAGCTATACCTGCCATCTGGGGCTAAATCACTC +CGGCTCACCTCTTCGTCTCTCTGCTTAGTCCTCTCGGCTTCCTCGCTATCGATATATTTCCCGCTTAGATCTGTTGCAGT +CCGAGCGTTATTTCTTGGGCTGCTCACTAAGGTTTGACGTCATGCTTGCTAGGCCGGCTGATAGGAGGAACAATCGCTCC +CAATGTGTTCCTACTGACTCGCGCGGTTCGCTACGCATGCGTATTCCACAGTGGGGACTCTGCCTAGACACTCTGTGACA +CCGTCCGTTAGCGCCGGGCTCTTAGAAGCATTGTTCACGCCCCTAAATCCCCATACTTCCGCTAACGCACCCAGGGCGCA +AGGGAAGATAATACGGGGTTACTCTCTACAGACCAGATTGTAGTTGAGTGAAGCCGCAAATAACAACCATAGTGTCGGTG +TAGGAGACAAATACCCGCCCCCATCGGTTGCAATTAAGGCTCCCATTAAACTTATAACTATCATGCACGTCTTAGGCTCT +CGGTGGGTTTCCGGGTTGGCCAATAATTTCGCCCGGTCCAAAAACCCACCGGGGACATCCACCGTCCAGGGGTTGGCACG +AACCACACGGGAAACGTAAAATGTACTATAGGTATTGGCATCCTTTTGCATTTTTCTCAATTTATTGGAGGTTAAGTAGA +ATCTGTCCGTCCGGATGTGACTTAGGGAGGATCCAGCAGGGTTGTTTCCTCTGCCATTTCAAACGGTCTTTTCTGTAGAA +ACGATTAAAGTCATGACTACCGCATAAAATATTCAATCCGCGGAACAAGGAGGCATGTAAGCCGCGAGTGACATTCCAAG +AGTAAGTCAGTGCGCATAGATCGCTCCGCGAGAATCGCTCTAGACTTAATGCTGATCCAAATTGAGTTATCTCAACCCAC +TCTCGAGACAGTCGGCCGGTATATTTAACCCCGCTGGTAGAGTGACCCTTCTTAGAGAACTAAACGGTAACCCAGGGTCG +TTGTGACAGCGCCATCGGCTGGTGGCTAACGTTAGTCAAGTATGAATTTTCATAACCTAAGCACAGCATGTGCTAGGTGT +ATTGGCACTCTCCAAAGACTCTCGTAGCTTATTGATGCGGGTGCTCGATTTTCATGTATATTATTTTCAAACTAATCATA +TGACGCTATTCTTTGCACTGTTAATTGGCCCTGTGGATCTACAATCTAGAGAAGCCAGCAGATTAGGTGCAATCGTTCGC +CCTAATTTAGACCCATGAGCTGAAGTAGCGCGTCGTTATTGCTACCATCGTCGTAGTACTGCGCGTTGCAAGTTTCTATT +CGGGAATTGCTCCCATTTTCAATCACTCGATTAGTTGGGTCTCGCAATTCCCCCTATTGGGACGGTCCTGGACCATTCCA +CAGAGACCGATGTGGATGAACACGTGGTGGAGTTCTTGCAGCTTTAAATAGATTCCCACGTGTCACAATTACATTACCAA +TGGTTTAGTTCGAATGCTGCGTTCGTCAGTAGAATGTGCATCAATAACTAAGAAAGCCTAGGCTGTTCTCTGTGAGTTGT +AATTCGCAGGGAGCATAGGATTTTGTAGGGACCTCATCATGTGGTCGCAGGTCCGCCGCTTACTGGATCATACTCTCGCC +AGCGAGTCGGAACACCTGACAAGAACTAGAGCTTTAAAGGGTCAACAGCTTCTTCCTGCACGTCTGGTTCACTCCTTTAG +CATTGGGCTTCACCTGAGGACGGTTGATGTAAGGCCACAAATATCAGGGAGTTAGCGTTTTCGAGTTCCTCAACATTTCC +AGAAGATGGAACAGACTGAATCTGACAACAGCAGAAGGGTCCCGAAATTATTGCAATTACGAAGAACACAGGACATCGGA +GAGTCTGTAGGCCCTACAGCGCCCTGGACTCGATAGGACTTCCGACTCTGTTTGGCAACCTAGTGGGTCGCTGTTATCAC +ATGTAGAGAGTATGGGGGGGCACACAATTAACTCTAGGGCCGTGTACCAAGAGTACTAGGAAGAGATTTGTGTTACTGTT +GCTGAAGACTATTTTGACCGCCGTGTGTTGGGAGGCGTACGGTAACCATTCCTTCGCTACGCAGGGAAGCCGTCCAATGC +GACGACGAATTTGATCAGATCCCCGATGGGCAGAATTGAGTGCTCCGGGTCAGCTAGTCATGTGTCAGCTGATTGTAACC +TGTCTCCCTAATATCGCGAGTGCAACACAGGTAGAGTGGCTAGCGTTGTCTTACCAGCTTTTATTCTTTCATTGGGATAT +AAGTGCGTCGCGTTGTAGTACCCTCCTCGGCTATATAGTTTGCTCCAAGCTAAACGTAAAAGGCCGCGGAACGGAATAGA +AACGGGGAATAGTATTTTCTAGAGGTATGTATCTGAGTGTCCGATTTGTAGTCTATCCACGTCCGGGATGTCTTTGCATC +CCTGCTTCTGGTCACTCCTGACGGAGTCCAGCGTCTCCCCGATTAGTCCCTTCAGATTGACATACTGATTGCGATGCTCG +GGTCCATAGTGTGGACGACCCCGTAGAATCGCCCGAGTCTGGTCCTATAAGAGCACCGTAATCACCAATCTGTACACGCT +TCCTTCAATACGTCTCTACCTACTTCCCAGCGGTGCCAGCGGGACCCAAGCCGCTTGGATGCGTTCGGGACCCTCTGTCG +ATTTAATCGAACAGGACTGGAGGTCGCACTGTATGTTATCGCAGGTCGCATTCATGGGTAACTGATTCGTAGATCGGGTC +AAAAGTATAATCGTAATTGCATAGAATGGATACGGCGCTGGTTTGAAGTGAGACAGCGACTGGGGCCGAACACGATAACA +TCAAGTGATTTTTACGTGCACAAGAACAACTCGCGTGTTTCCGGAGGCGTTTAATCCCCTCAGGCGCTATGGACCACGAA +CTAGTACTGGCAACCGAGGCTCTATACATAGGTTTTCCGGATACAAGTGCCGTGTGTGCCCTCAGATCCCTCAGGCTCTA +ACACGTTCAAGAGAGACCGGTGATCCCGCAGACAGCGAAAGCGATGAGGTGCCAGTCCGAATAAAAGCTGCTGCTCTACT +CCCATCTGTTGTTAATATGGACCTATAAACTTTGCCGGGATACGCTAGTTACATACAATTGCGAGGCTGAGTCTCAGTCA +AAGGCTAGTCATACACCCGACGGCGCGCTTCCAAGTGTTCGAGTAAATGTAGTAGCGCCGTATGGACATATGTGAGCATC +CTGGAACTTTGCGTGAAGCGCAAGCTCTACTGGATGCATATGGAGAATAATGACCACCATCAGATGAAGCCGGAGCACGA +AGTAGAAATATGATTTATGGAACTTCTCGCCGCTAAAATTCTGAGATCGGGTTCGTGTGTTTACCACGCTACCGAGTAAT +GCGTATCCACGACGTTAGGTTGGCTCCTACTACTGCCTCCTTTAGGAGGCAGCTGACTATACTTTCTTCAGTCTATATCC +GGTCCTAGCGGATGCGTTATTCATTGGAGTCTGTGGTGCAATGCTCCCAAATGTCTGTACAAAGTTGTTAACGACATCCC +GCTTGACTAGGTCTTGGGTACGGTGGATTAAGAGCTCCTGTATGAACTTGATCTGTTCATCGGCAACCTGCGCCTTCCTA +CTTTAGCAGGTTGATTCTTATATACGGTAATCTTAGGTTTTCTGGAGCTAATCAGTGATTGGCGGTCGCTTAACAGATTA +ATGTAGAATCGTTCTCAATGGATGGCCGGAGAAGGGATCATGAAACCGTTATAGACCGATTGCACTGTTGCTAGCACACA +TTGCACTCGGAATGGTTCTAGCATCTGAGACGCTACTAAGTAGGACCGATCAAGCGGCGGCCAGTTTTAACCCCACTTTC +GAATATCATTATTGGCGTCCATCTTGCTTTAACCGCTGTTGCGAATCGTGACGGTTGTCCTGCCAAATGGTGGTCCGACA +TCCAAGGCCGCTCACCGTGGAATGTTCCATCGGGAACCCGACTAGATGAGCATGGTAGCCACGGTTTCGGGTTTAACTTG +TAGTTTGTATATGGTTGTTACTGGCCCATTCGGAGACGCCCATCGAAGGCCTGGTTACTTCACGTCGCATTTTTAATCAA +TACTAGGTCACTCGGCAATAAGTCAACAATCCTTCGCTAATCCCATGGGAACAGGTGTCACAGGTTCTCCCGGTCTTATG +CAATGGTAATTAGGGGTTGAACTTCGCTTATAGATCTCTAGGAGCGAATCAGCTTTTGTAAGCGGGAACCCGCCCCTAAG +GTTAACAGTCCATTCTTGCTCGCAAAGTCTCGAGCGTCTACTAACTATCTAAAACGTGTGTGTCATTATGTGGGCGCTAT +CACTTATAATTCAGATAATTTTATCATTTGATGTACAGCTACTATTAATACCATATAGCTCTAATGTCGTCAAGACTTAG +CCGAAGGTGATAACGCGTAACGATTCCTGGAGTCCGTCCCGCGCCACAGTTGGGTTTTCCGATCTGTGTGCGCCGAGTAA +ATAGCGTTAGATTCCGTTGACAGATCTGTGATAGAAACGGTGATGTGCGCCAAAGCCCATCGAATTCAGCGGAGTGGTTT +ACGAGCTCATGGTAAGAATGGATACCCTGCTATCCGTATATATAGGCGTAGGTTCACGATTTGGTGCCTCGGGTAGGTTG +CCGTACCTCTTCATAGTTCCAAACCATAGTGGGGTGGAGAACCCGTACACCGAGGCCGCTGGGGCAAAGACATCCAAGGC +TAAGGGGAGTCCCTCCAAGCTTATGGGGGATCACCACTGGCTTGGGCGTAACCTTCCGCTATGTTGCAGACTGTCGCTCT +TTCAGACTTGTGGCAGTGCATCAGTTTAGGATGAGGCATGTGCATTCAACGTATACGTGTTGACAAAACCCCACGTTTTC +GCGTAAGTAAAACATGAAATCACTAAGACTATAGTGGGTTCATCGTTGCACTAATGTACCGCTACCTCGAAAGTAAGGTG +CTCTATCACTCGTATATGCCACCCTGTGGCGACTCCAGCGACGTGTGATTCTGAAGGGAGTCACCTTGAGTAATATCCGG +GCTAGCTACCTTTCAAACAGCTACAGAATAGGTGTGGCTTCAACGCTCCCCTGGGATTAATAAACAACAAACGAGTCTGT +GGGCCTACGGACTGCGTCAAAACCCACTGCTGTCTGCGACGTGCGATCAGAGTACACCCAAAAGGATGTTTTTAGATAAA +AAATCCCTTGGAGACGCATCGACCAGCAATCCCTTTTTCTAAATTACATATTGTAACACGCGTAAATAATTCGACCCGGT +AGGCAGGAGTGTTTTCCATCCTCCCACTGGGATAGGTGAGACAGACCATTCGTACGATCTGATCTACTCGTCACACGTGT +ATAAAGTCGTCTCGGACACGCCAGTCCGGTGTAGACATTTATTGCATCAACCATCGGGTAAAGATCCCATGAGGAAAAGC +CGCGAACAAGTGTGACGCCCCCTGAACTACGCAGTGAGGCGGCGAGACTATTTTCGATAGGAATATCTAGACCCAAGATC +CGGATGTGACTTAATTGGGTAGCCGGTGGACGGTCTCGGGCCATACGAAAAAGCGGCCGTCTACTATGACTAAAATTACC +CTATAGTAACACTATGACTGGACGTAACAAAGAATAGAAGTGCTAGCCTGGGATAGCGAAAACACAGTTGAGTCAGACCC +GGTCGGCGGGCTATGGGAGGACAATATATATGGACCTTCATGCCTGCATGAAGGTCCAGCTGGACGCAGGAGGAGCTCGG +CCATTAAACTTGTCGGTTTAGAAATTGTCTCAATGTGCACACCAAGAGCCGTGCAATTCAATGAACATTACTCTATGATT +GAGATGATCAAGGCCTCGTGGGCGAGGGTTAGGTTTTTCTGGCTAGTCACTTTAGACATGTAGCGGTAGCCATCGGGGTA +TACGCTGGATAATTGAAGGCGCGCAACAAGTACGGAAATAGGTCTTTAATTCCTCGTCAGCCACTGGGGATGACCGTAGA +CTTAGCAATCACCTATGATTAGAGGCTGCGCCGTTTACGCTCAAGTACGCATCGTATCGGGCACTATGCGAGCGATTTAC +CAATCAAAAATATGGCTCCTGGGCCAGATGGTGAGTTCTCGTTCTCGGCGTCTGATTCATTCGTTTTAGTCCATTAAGTC +TCCGAAGGGAAGCTGTTTAACCACCCAATCCACCGTTGATAATGCCAGAGCCGGGTTAGGGTACATCTTTCCATGCTACA +GACCCACTGCAAAACACATACTCGATCCCCAACAGTGCTCAAATTTCATGAGTGGAAGGTGCTCGATTGGACCATACTGG +AAATCATTGAGTCGTCGGAACCACGTGGCTCGGGTTGGGTGGTCTTGTCGACGCAGCTCATCAAGTGAAGCGGGGCACCT +TTACAAGCCAGCGGAAGGGTAAGCATCATCTGCCCACGTTACACCCCTACCCGTGTACAAGATCGGGATGGTGACTAGGA +CTCAGCACAATCACTGTGCGGTTCAAATCTCGCGTGTTGAAGCGGGAGTTTTATATGGAGTACCTGTCCAGTATGGATAC +TGGCTGCTACTCATCATTGCCGATGTCGTTACCCCGGAAAGCTAGCGATCAGGTAGAATACGGTACGAAAGAGATTCGCG +CAACTCTCCAAGCTATGTGCACGTACCACGTTCAGAATGCTGTAATCGGTTGTCACGAACGAGTAACCCTGTTTGAAGGA +TTCAATCGGTCTGTTGAGTTCAAAAAACGTGCTCCGTAAATCATCACTAAACTCATAGTGTCTCGCGCGCCCGGTGCTTG +GGTAGTTTTTCGCATGTACCAACCATACGCGTGAGCGTGTATGCCGACAGGTTGGATATTCACCGCCAACAAACTGGTAG +TTTCCAAATTTCAGAGTCGTACGATGAGCGGACCTCACCGATAGGACGTTTACGTGGGCTCAGCACGTTTTATGGTTCCG +TGGCAGTAACGTCGTCTGATGTCTTACTACAAAATGCGATGCAAGGACGGGCGTATTGGAGGTAAAGGAATAATAAATAG +TGTCACACGGAGTAGTGACGTATGTGATCCCACGGTGATAGCGTTCTATTGAAGCAACTCTCCTCCACATGGGACAGCGC +CGGTATGATGTCTCCAGATTCTGTTAGGGCTGGCAGTGGGCAGAAGTTTGAGCTTTTGAACGTGACAGTGCTACACATCT +CGGCCATCTTGCCGAGATTGCCACCCGTGTACAGGACGATATTCATTCGGATATGAGAAATAGAGTGACTCTTGTTGCAA +GATAGTGTGGTGTCGTACAGCTTAGAAATGTAGGGAGCTTTAACGCACGGACTACGAAATTTTAGCAACTCTAAGCTTGC +GTGATAGACGAAAGAGGAGGCAAACCTTGTATTGTCGTATTCGTGGATCGAGCTAAACCTAGAATCACCGGACAAAGGCA +TAAATTTTGCGGGTATCCCGGAACGAACTGCCGGCCCCTTAGCAGCCCAAACTCAATCGCTTTACAACAACGAATGCTGG +GCATATGCCCCGTTCCGGTCGTTATCTGATTCCTGAGTCCGCGCTCTGTTGAGCGTCCCCCCCCAACGGATAGTAAGAAA +GTAGTGGCAGTGCTGGCGGAGAATCCAGGTACGTAAAAGGACTATAATGGATGCACTTCTTCCACATCTGCAAAATATAA +AGAGAAGCACTGGCATTTTCGTAGTGGCTTCATAGCAAACCATATCATGTCACGCGTCTTTATGGAAACATGTTGTTCCG +ACATCTGGCACTTATTGGAATCACGACCAAACGCTATCGACCCGAGGGGAGAAACAACTGTCCACCTGTACGTAAACCAA +AGGTAAGTCTTGTCGGTCACAGCAGTGTGTACAGTATATGGCTTCTTCTAGCGAGGAAACCGTCACGCGCGTGAGAGTTT +ATTCGCGGTCGGTGTAATCATACACGTCAAGAGCATTAATCAACTAGGGTTAAGGTTGACTCGATAGTGACCTACGCTTG +GCTCAGGTCTAAACGTGTGCTCTTAGACTGATAGAGTCAAGGCTCGCATAGGCACGGGTGATGCGGGGCTGACTACTACA +CCAGATAACGGGCGGCCGGTGCCGATCACGAGTAGTAGACACTGGTCTTAGCCGATTGCTGGTATCCGTTAAAGATATCC +GTCGTGATCTTGAGCTTTTTAGGTCTCGTTCAACCACGGCATACTCTCTTTACGTCTAGTCACCCACTGTCGACCCAACA +CCTATAAGAGCCATAACATGGTGCAGAGGCTAAACCGTCGAATAGGCCACTGGAGCTATGTTTGCAAACATGGATCTGGC +GTTAGAAGTATAGCTCAAGGGCCACAATACACTCTGTCCAGCTTGCAAGATTCCAGCAGTGTGCTAGGAACGTGCATGCT +GAGTGAGCGTATGGGATGTATGCCATCCCCCCGGATCCAGGTCTCACTCGTGGAGTGTTTCCTCCTGGTCCGCCTGGTAA +GCCTGATTCACTTGTAAAGACCCATGATTATCGTCGCCGATAACACCGCTAGGCCGTGTCATGACGAGTGGAGGTTCTTT +ACAAACCAAGTGGGACAGTGTTATTGTTCCAGGAAACGGGGGCCTTCGACCCCGACCTCCGCGGAGGTAGGCCATCCAAC +GCTGGTGTTCCGCGCATATGCCCGGTTATAAGAATGCGCCCTCCCAGTGCTCACCTTGTCGTTCCTTTATGTAATGGCAA +CCCTAATTCAGGCGCCCTGAGTAACAGATAAGCTATCATTTCCCGTTCCACGCTGGAATAATAATCCTGGACATCAAGCG +GCAACTTATAAGCAACGCAAGCATTTTGATCAAGAGGCCCTCAGCAGAGGGTCCAGGCATAAAAGGTCGGTTGAACCCGA +CCATATTTTGCCAAGTGCAAGTCTATATGGTTCCACGAGAAGTGAGGCACCCAAGTAAGCTCGAGGTATGGTACCTTTGC +CGCCATCCCACTGGCGATAATCAATGGATCTTGCATCAAACACTACTCGCCCCAACCGATTTTAACCTTACTCCACTCTT +TAATCGCAGCGCTGAATCGTCGTGAGAGGTTTGGGTTACCAGCAATGGGGCCAGTGGGATAGGAATAGGAGGGTGTCGGT +GAGAGAATGGAGCCCCAGTTCTTCTATTAGGATCTGTCCTTTCTGCAATCGGCTGGAGACAGGCGTATAGTCCTTTTAAC +TCAATGGCGCAGATCTGGATCGAGTACGCTTCAATATTCGACAAGCAGTCCGGCCCGCGCTTGCCCAGGCCCTTGACTTT +GTGTCTCGCAGTCAACTTGTTTACTAGCTATGGGTGCGGCTGGATCAGGAAGGACGTAGGGCGCTACGCTCCTCAGGAGC +TGTAAAGCGTTCCGGTCAGGACACCTGTCAACAGCCGGACCTGAACTATTTCACTATCCGAGAAGGGGCCTTAAGTCCTC +AGACTACACGCGGTAATTGCAAAGACATGAAAACTGTTATTTTACATCATCAAGCGGTCTACGCGAATAACCGCAGTTTG +CCTATCGCTTACACTTAGACCACCGACTTTACTAATCCTGTTTGGGGCCGTCCTACAAGTGACCGTGAAGGGCCATAATA +GTATCCAACCCTGAATTCATAATAGCGGCTTGTCAACGTGGCAGATATGTTACCATTCATTATATCCCCATGGTTCTATA +TAACGACCTCCCACCGAACAAGCGCACCGGGGCAGGAGCCGCAAACACTTTCTTAGGCGGCTCTCTAAGTGTCATAGTCG +CTGGCTCCAGACATTATGATACTAGATCGTTGGGTAGACTCTCAGATGCAGGTTCACTCGGCGCCAGCTAAGAAGGACAC +TTGAACGAGCTCGGTTGCGTGCAGGTGGCACCTATGCGTACAAGGTCAGTTGAGGTTTGGGACGTGGAGCAATTATTATT +TGTCCAATGGCATTCAAGTTATACGATGCCCCATCGAACTTGTTGCCCTCCTTAACTGTTGGTAGAGTAGGACCAGCCCC +TGTAACCACCCGTTAGACGACCGGTACCTCGGGATAGGAGACCCCTCTAGCTGAACAGTGCAGAGTACGAGGTTGACCGC +CAAACCGGGACCGGTCTGAATGTCGCGTGCGCTGGATCTCGGTATGGTTTTACCAAAAAGCATTAAGGTCGCCGCACAGT +ATCACATTGGAAATGGCAAACGAAGTCGAAATAAAGGAAAACCAGGTTGCCTCTTCAGGTTGCCTACGGATTGTAACAGG +AGTACGCTTTAAGCATAGAACTAGCAGGAAAGGCTTTTTGTACCGCTACCGGGACTGGTTGGTTCCAAATCCGGGCACTA +ACATATTTCTTATTTAATCACCCCGCTATCGACTGGGCGACGAGCGATGTGCGCCAGTCCCAGACAGACCTCAAGCGAGG +CCCGATAAAACCTCTAGTATCCCATACTTTCGCAATGCGAACCGTACATGGGACCTCGTTGCGTGATCTGGTTATTAGAC +CCTCCAGTTTAGCGCGCATGCCGATAAATAGTGTACGGCGCGCACTTTCGTGAAAATACTCTCTCCATCGATGTACATCG +ATGCTATCTCTTTACCACTAAAGCAGAGTCGCCAGGCCTAATGGGCGGGCTTTAGACGCTGAAGAACCTATTACTATGCT +TACCAAAGCGCGCCTATCTAGAGAAAACTTTACGCATGAACGCGAGGCGTTCGCAGTAGGTAGCCTAGAATGCCCAAAGT +ACGGGGTCGTCCATATGGCACCGCCGTGTGGAAGAATCCGGCAGCAACCTGGAACTGGTTGGGCTCACCGCTCGGGTAGA +GACCGTCTTTTCTTTTTTAAGTCCGTACTCTACGATCTAGCGGATCGCAACTTTTCGACAGGTTGAGGAGTCTAACTCGG +CCCGTTCGGGGATTCATTCTCGTCTGCGCCATGTACCGCGCGCTTTGTTCTTTAAGTAGAGATAAGATTGGTAGGGATTC +CGTTCTCCTCCTCCCGATGCTGAGGTTTTTCGTTTCACTACCGGCACCAGTACGTGGCGGTAAACAATCCTTGTTAAACC +TAAAATGTGTTGTATTTTATGTTCACGAACTTACGGCAGCGGTAACATGACAGCCGACAGGCGATTGAGTAAGCGCTAAC +GTGGATGGCTATGACGCTGCCCTTCATTTAGAAGAAGCTACGACCCTAGTTCTAAGGCTTACTAGTTTTCGAGCTAAGCC +TAGACATTGGTATAATGTTGCTGGTCGCGTCGTAGATCCACAGGCGCCGGACTTGGAACCAGTTGAACACGCAGCCTCAG +AGGGCGAGTCTGTCCACCCATAGGGCTCGGGGAGGAGTAGGAACCGCTAACATCGTGCAGGGCACATTTAAGAGAAGAGC +CACGGGGCCCGAGGGTGCGCTGGGCAAGCTCAATCGGATAAAATATCATCTCTACTGCCGCCGGAAGTTGCTATCTGACG +CAAACCCCAAGAACCGTGTATGCGATGAGTAGGCTTTGCTTAATCGGGTAATGCTTGGCGGTGCTCCTAGCTAGACTTCT +GCGGATATCGGAAGGGGATACCCGAGTGGCTCAGGCAACGCGCCCCTCGTGGAACGTTGCCGTGATCCCATTTGGACGAA +GGTCGCGGGGTAATCTCGTAATGGTCCCCGACCTTAATAAACCGATAGACGTGACATCGTCATGAGGGCGGGAAGGCACC +TACATCTAGCAAAGGACGAGAAGCCCAGTGCCCTCGTACCGCGTGCTGAAAGTCAAGGCTCGTAGTGAGTGAGATGTTCT +CATCCTGCTTAGCAAAGAGGTGCCAAAGTAGTAACGAATAGCGTTGGAAGACAGAATCGCTCGGATACGCGTCCGCGAGT +GGACAAGACTGCACACGCCCATATACGAGGCTAAGGGGGTATTAATATTAGTTAACTGCCATGTGGATCCGTGCCGTCCC +TGCGCATCTGACTCTATGACTCTGTTCTCAACCATAGGTTCGCAACCCTCGCGGCCTTTTTAAGCCTGTTTTAGGAATGC +AGCTAAGTAGGCAGATAACCGCGGTCGAGTAAACCCACGATTGCGGCTGGGCGTTTCTGTGGAAGATGAATAACCCATCC +TTCTAACCCGAAGTCCATTAACGGCCGGTGGCCCGCGGAATAGCACGGGATCATTAGGGCGCTCTGACACCATATTCGCC +GTCCTTGTAAAGTTTATCCTCTGCTAGAAGCAGAGTTCTACCGGGACATAAATCCCCCACAGATAGCAAAAATATCATTT +GAGTCACGCAGTGGGTTCCGATATTCGGCCGATCGAGACACGGTGCGCACCAGGTCTCACGGCCGCTCGTTGCGACAGGA +CCCGCGTCCGGGTGATATTATCTTGCTCCAACCTTCACCGCCCTGCTTATCGTGCCTTAGCGATCGTAGCAGAGCTTATC +AGCGAATTCTGCGCCTCTCTTTTGAGAGGTCGATTTCACTGAACCCCTATCGGGAATAAAAATCAGTCTCATACACTCTG +ACCTGACTCCCTCCCATACTAGGAGCGTGCGCACCTCTGCCAGTGAGGTATTAGCGCTGTGTTAGAACAACGAACATTCA +ATAGTAGGCGTATGCTATAGGTAAGTTCACTGCGTGAGTCACACGGCGGGAGATAAGTGCTAACTGTTCAGAGACGTTGC +ATAATCGACTAGTGGACATGCGCAAGTGCTTGACCTGTCACCTTTGGCTAAACCTAGAGACTTGTGGATGGTCACTGAAT +GGTGCAGATCGGCATAGGGTCTGGGAGGTCAATGACGCTCCCGAACAAATGCTATCCGTGTAGGTCAGTAACATTCCATA +GTATGCTACAACGTGTTGTACATAGGTTAGTCCAAGCGCAATAAAGTTATTAGGCCTGTTTTTTCGAGTACCTAGAACCC +CGTCTATCCCGATGGCCTTCTAGCTCCAGCGTGATTAAAAAGGTATTTAAGGCCGCAAAAGGCGCCCTGGATAGTCCGAT +ACCCGAATTCAGGGGCGCACCCTGGTAGTGCGTAACGTTGTCCCTAACCACCAACTTTAATTAGGTAAGACCAGTAATTA +TTTACTTTAGCCCGCACCTCGCGACTGCCGCGACGCACAGCAAGCACTTAGGCGTTCCTCAGGCTAGCGCGTGAGATTCA +CCCTCTCTACTGAGACGGTTGCTCCTTGTTACGAATCATTCGACTGATGCTTGACCAATGAGGGTCATCGTCAGGGAGGG +GCCGAAGTGGCCGCGCCGGAGTGTGCCTCGTGTTACCTTACCCGAGAACCCATACGGCTGTGCTTGCAACAAGCGTGGGT +GTCGGAATTCATCTCTCATTGCGTAAACGTTAGTCAGTAGCGCAGGTGTGACAATTTTATTAGGCAGCGAGGGATGTGGA +TTGGCATAAGGTGTTTATCATGGGAATAGGATTTGTGCGCCGTGTAAACCCGCGAGACGTGACGCCGATGTCCTGTTAAT +GACTTACTGGTTTAGCGAATCCCTTTCATTCACCTATCTTAGGACTTTCCACCCCGTAATGCGTAGTACCGGCGGAGGTC +CGTAATTCCAACCTGGATTTTGGGAGCCCCAGAGACTGGCGGGCGGTTCACAGCATCGTGAGTCCCCGTAAGGCACCCAT +TTACCAGCCAGGCGACGGTAGGTTTCCTCGTCGTTAAAGGGCGTGAAAGTTCGATATCCCCGGCGATTAAATTCCAGCCA +AAGTCGACGGGCGACGACGTGTCTAGGCTAATGGAGAGAGTGTGCTATGCAATGGATCTCCGGGTAGGTGTTAAGGACCA +TTCTTAAAGCGGACGCGCCCGCAACCCCACAGGCCAATAGGAAACCGGTCGCGCTAAATTAGGCGAGGGCTCGAAGGACA +GTGGCACTAAAGTGACCCTATTGATCATTGCCGGCTAGTATGATAGTTCTATGTTGGTCTCGTTAACTACTCGCGGCCGG +CCTGTATAGACTTAACTCATCGACGTCGGGCCAGCACAGGGAACTGCCTAAGTTTCCTGAATAGATGGGCTTGCCTCATT +GCCGGTCGGATAATCGGACCTAACCGACAATAGACCAGTACAACGTCGATTGGTGCTGCAAATCGAAGATATCCCCTCCC +GGTTACTCATATGTCCTTGTTAGGCGAATGTGCATGACGACTCTCTAGGTGATCAGCTCATGTGTGAACCATATAACGGT +GACAGTAGGGGGCTTTCTATAATGAATAAGCCCCCGTGGACTACGTACAACAGAAGTCCAGTTGTTCGCTGAACGCATGA +ATTTGCACTGAAGTGTATAAGGCGTAAGGGAGGGGAGCAGGGTTGCGATTTGGCCCACTAAAGCAAAAGGGAAGGCTCTT +GAAACCAGGTCTCTCGATCGAATGTCTAATGTGAGCGTATTAAGCTACGCGCGATTGTAGGTTTACAGGATGGATGGGCT +ATCCCCCTTTTACGGTGCAACCACAAGCCTCCCATGTTACCGAGAGCTGAATGTGGTCTGAGGTAGCTGATTCAATTTCA +GTCGATTTGATGATCGCTTGTCCTTGTCGGCACAACATGGGACTGGAACCGAGGACTGTACTACCCGACCTAAATTGGGA +CTTTCAGACTTGGACTAGTCTAGGTCAACGTGTAGCATGTTAACACGCTCGCCCTTCGTTGTACAGCATCAGCACGACTT +CGGCAAACAGCCGCGGCTGGCGCCTTAGTTATCTAGATAGTCGCGCTAAGTCCCAACTGCCTACAGGGCAGGGATACACA +TCCCCGTAGGCTCATCCCAAAAGAGCACCCTCCTTCACATTGCAAGATGTTCGTTGTGTGCTGTAGCAGCGCTTCTCCAT +GGCACAGCAGCCTTCTCATTACTGGCGACCTGTATGATGGTCCGTGTTGACTTAGGTTGAGCTCCTCATACCAAGTGGTA +AATATCGAATGAAGCAGTGTAAATCCTTTCAACTGGGTGTCACGGTAATGCGGGCCTCGACCCGGTTGCGCTCGTCTACG +CCATGCTCGACGTCACTATCTAACAGCCTCAGTCCCTTCATCCGTCTATATGAGCGGATCGTGAAAGGACTGATATTTTG +TGAGCGTCCATCTGGGATCGTCGATATTGTAATTGCGGCAGCTCCCTACATGGGGGGAGTGGTTTTAACCCGAATTGGCA +GGGGGGTCCAACCGCGAGAATATCCTGGCGCATATAATATGATGTTAGTTGAGTTAGAGCGAATTCGGAACCAAAACGGT +TGTAGCCCGTCATCTGGCAGTCCAGTCACCAAAGTCGTCTCATGGTTATTTGGTGAGAAGGGAGCAAACCGGTGAGCGGG +CACGCTGTCAACGCCGCCCAAAATCTGTTCTACATCGGTTGAGAGCTTAAAGCGATGTGTGTATTTCAGTCTACATGAGG +TAATCTTGTATACACTCTCAGTTGGCTATGTTTTCTATGTGCCTTGACTTACCGGAGCAATTGTAACCCGTAGGTATGCT +CGAAGGACGGTCGTACACACATCTCTAAAAGCACCTATATCAAGTGGGTCGTTCCCAATTATTGCGAAACTCTTGCACTC +TGTCTGAACTTGATTCCTGTTTGCGGTCAGAGCTTCGAACGCATTGCATTAATGTAGGTGGAACTGAGAAAGGCGACAAG +GCTCAGCACCTTGGGCAAGATGCGTACGGATTCGTTTAGGTTCTCCGAGGCTCTTTAAATCCGGTTCGTATTCCGAAGGA +ACTAATTCCACCAAACATCGCTACCGGCACTGGCCATTGGGAGTGCGACGCTGCCGCTGAGCCTCATGCGGAAAGTTGTT +GTGAAACTTCTAGCATAATTCTGCTGATAGAGTACCTACTGTGGGTTTAAACCGCCTCGACAGTACTACATGTGTTGTCG +CGCCCGATTAGGGCGACTACGAATCACGCCGTTCGTATTCCATCACCAATATAAACGAGTCCCCCCCGAACGTGGCGGCT +TAAGTTATCACTCCCACTTCACATCCACTAAGCCGGCTTGCAAAAGGGTTCGCTACCAACCCGGTCAGAACTAGATAGCG +CTGGGATAACCGTATATTGGTTAGTGATGCGCGCGAACAGATGGAAATTCATCTTCCGCTCCAACGCTAAACCACGACTC +ATATGTAATTGGTGAGCAGCACCGTTGCTCAGCTGTGAGCATGATTCGAGAGTGCCATTGGTTCCCATGGTAAGTAATAG +AGTGCACAAGTATATGCGTTATAAGACTGGGCCTCAATACCACTCTCACACCAACGCGCTTGAGGAAGGGAATGCGGAAG +ACTTACGGTTCACGCGAACGACGGAGAGGGCGACGGAAGTCTAGACGGCTATTCTCTCTAGGCGTATATGTATATCTACG +TCTCAGGATAGAGGGACTCGAGGATAGTGTGCTGGCCGCTACAAGGCTCTCGTGCTCTCGTAATAAATTGGCCGGTTCCC +GCCCCTCGGTATAGAGTAATTCGTTACTTATGTCTAGCCACATTGGACGTCTTAAGAGTCCGGGGGTCAAAACCGCCAGA +TTGGCCTTCCCGATTCGCGTTTAACTACGATTGGGTATGAGCATAAGATCTTTCAAAGGCCAATACTGACTCCTTCTAAC +TGATAGACCTGCGTCTTCTCGTAACTCTGGGTTTGAGGAAACTCCCGAGTCTATCAGCATCATTACTGCATTGATGTACA +TCGATAATGTTCCAACTCGGCGCGACGACACGACTCCTTAGCTGCTACCACCTAGACGAGAGCTGCTGTCGATGGCTCTC +CGCCCAATCTCCTTTCTGGAGCAACCCTGGGTGACACTCAGCGACGGCAAGATCTGCTATTCATGCGTATATAGCCCTCT +CGCCGGTAAGGGACATCGTGATGGAAGGTCTTTTTCGAGTATAAGTCCTAGGGCCGTCAGGTGGAGGTAGTGAAGCCCTA +CTATTCGTCCTTGATATGCGGTGTTGTTCAATATTTCAAGTCGACACTCCAATATGCTGGCGAGCGTTTTTTTTTCGCAC +GACAATACGCGTTAATCGCGTTTCAACGGCGCTCGGTGCTGTATGACGGCTCGCGGAAGAGGAACCTAAAGTGTACTGTT +AAATCTTATTCTTATACTTAACGCGCAACTTCCCCCCGTCAGGGGTGGGATAGTGTTTAAAGCGTTCGGGAGTATAAGCC +TAGCCTTGACCCTTGCTAAAAAACCAGGTAGGGAATCAGAAGGGTAGGACCGCCCTGACCCTTGTTGTGTCAGCACCTTT +CGAAATCTGAAAGACGTCCTTTCGCACTGTTGCTATGATTAGCCTTAAGCCTTTGAGCACAGGTAGCTGTGAACCACCGG +CTCCGGCATCGTAGCGGGCGATACCTGGCTTTAGAAGATCCCTCCAGAAAGCTTACGTTCCTCATGCTAAATGTAGTTTC +AGACGCAAACTCACATAATACAAACTTAGGGCTGCCCCCAGCATGAACCGCTACCTTGGGAGCCTACTCCCAGAACACAA +CCTTCATGCAATCGAACAAAGGTTAATGTGAAGTTCCAACTGTCCTCCTCGAGGATTCCGATCTGTAGGGGTAAAGTGCT +CTACTCACCGCGTAAACCTTTCGACATGCCATCAACTCAGAACGCTCGTCTCAAGCAAGGGGCACTCATCGAGTAAAACG +AACCAAAATGGAGGTTGATTATTCCCGTATGTGATATTTCTGCCCAGCGCCATGAGCTTCCCGGATTTAGAAGAATCGTA +CTATTGTGCCTACGTTTTGACAACTGTTTAGAGCAACTTGCTAACAAAGGGCCTGCTACACTGTACTCGCTATTCGTCTA +GCGATAACCTAGATAGGTAATTACATCGCGGATAGGAACCGTACCAAAATGCTCTAGTCGGCTTTTAAGCCAATTCCGTC +AGTCCAGGGCAAACAGACATTCGCGTATTCTGCGGTGAAGTGATACATTTCAGACTCACGAAGACGCTAACATATCTAAC +TCGGATTTGTCTACTCTCCCGAAGATGGTTCCGGCGTGGCAACTAGGGTTAGCAATTCGTCCCAGGGGCGTTTGACTGGG +AATAAGATTCTAAGCACCGCACACCAAACTGGCTAACTTCCCAGAAAAAGACTTCGATGCCAATCCGGTAATGGTGATCA +CTCGCCGAGGGTCGTGTCTGCGTGGCCGGACGTGGCACACTACAAGAACTAGCTAAGGCGCCTCTGATTTAGGCATTGGG +TCGGTCGGGCAATGTATGAATGATATGGACATCTAACCTGGGCCGGGAAGTCACATCCAGCACCCTTTGGTTGTCCCATA +CGGAGAATTTTATTGTAGCACTCACCAAGGGCCAAGGGTTCCACAAATCCTGGTTGAGCTACCAGAACCATGTATTCTAT +CTCTCCTAACCATGTGAAATGACTTACTATGCCCGAGATCTTACACGAGGATCGTGTACTGTGGAATTTATCAGCTGGCC +GCACCAGCGTTGCGGCCATAAGGAGCTCGGCTGGGCTCATAGTTTAGCTTCGAACGACAGTGCTCGGTATGTGCGAGACA +GCGTAACTCGCGCGGGGGCAGACAGGGTATTCCTTCGTACGTGCATCGCGGGCCGGCATGACCGTAGTAAGCACGATCGA +TGCAGTACGCCAATGGACGAGGTAGCTGTGTAAACCTACCGATTTGTTCGGATCATGTTTAGACCTCTGTTTTCTGTACT +TGAGGATCCCGCTCCGGCATGGTAAACGTTGTATGCTGTGCGTTGCGTTCGTTTCGATGAGCAATGGTAGACGACGTAGC +ATTCACACAGCCTTTGTAAATTTCTCCTCGTTGATCGTCGTGGGCGCTACGGCTCACATTATGGCGTCGGAAGGCTGGAT +GTCGTCCAGGTACTATTTCTGGGCTGGCCAGGAAGGTGCTGTTATGTCGTGTAGGACGTGAATCTAGACTAGTGTCCCAC +ACCTGTCTAGGGGCCGCTAAAGTCAATTCCCCGCGAGCGTAGATTGCCACAGTTTTTCTCTGGCGACAAGCTCTGTAGAG +CCGAATCAAATGTCATCCGTTGGTCCGCCTCTAGTGTTTCGAGCTCACGATGATCCCAATAGGGTAGTCGGTTACCGACA +CTAGGCTGATCTATTTGTGAAATACCGCTTAACGGCCAACAGGCTCGTTGGAAAGTCCCAAAAGGTGCTTTGGAGTGGAG +CCGCGCTAAGTCGTAGACGCGCTGGTCTACACGTTATTCGGTACACAGGTCACACTGGACTGAACGACTTCAATGTACCG +CGTAAGTGGAGTTGTTAAGTCTCACGCTGGCCAAAGTAGAACTCTGAATGCGGGGACCGCATCCCTAGAAAGCGGTTCTG +TCACGATATGAAGGTTTCGACCGCAGTATTTATGGATTATGGGGTCCTACGTGGGCGGATTCTCCCAGGGACGTCGCTTG +CGTAAATAACCGTGCTTATACCGTGAGATTACCTGTCAACTCGCAACAAAAGAAAAAGTCTCCGCCTACACCTGCGGGAT +GCGATAGCTGCCCTGACCAAATTAGCGTTATCCATCGCTACTCTGGTAATAGTGATCATGATGAGGGATGCAGTTGCTCT +TCACTTTGTTTGTCATGGAAGTCTTGAGCGTCCCAGCCCCATATCGTCAAAATATTACGAAGCCACGTATTCCGCGTATT +GCTTCGTCTTCACGGAACGGTGGACAAGGCACGAGTGAGATTGGGATCACTTACGTTACAGCCTGTCATCATTGAGGTAA +CGAAAGCATCGTTTCGGAGGGCGATAACGAGTCGCCCTAGAGTCGGTGAACGGTCAAGAGACTAACTTAGATACGCTCTG +GGAACCAATATATGCAAGAATGCGGTCCCGGACAGGGCCGTTACCTGAGGTGGAGGGAGTTTTGAGGATTCCGTCAAAAT +AGATATTCAACTGTCCATCTCTTTCAACCCTGCACGTCAATATCGGGTAAGTATTGTAGTAAGTATCGCGACAATAATTC +TCGCTGCTAGTCCTGGCGTTTGACTACGCGAGTACTCACGACCATGTACGTAGGACAACGCTGTAACTTAATAACAGGTA +GAGGGTCACCAGTATAAAACCGGTACTGCGTTGTTGCGACCATCCTGGAGATCTGGCCCGGAACAAACTCACAGAACTCG +TTAGCGCTAGCCTTTGGCGGCGAATGGTTTAGCAACGTCATAGCCGTCCTCGTGGGAGTCTGAAGGTGCCGCCATAACTA +TTGGGTTTAGCTAAAGAAAGCATCCTGAGGTGGGAAACTGTGGGAATCACGTAAGAGCATCATGTCGCAACTTGACTGTT +GTTCATACGGAATAGTTGCACAAAGAGTACGCCGAGTGAGCCCACCACGTTAACACCCATTGAGGCTAAAGGTTAGATGC +TAATGGTTCGCGCGGTTGAATCGTATTTCGTCCGTCTTCCGACCTCGTCGCAGATACGAGCATCCGGATCCGATCGGGTA +ACATAAACTTGGATATGACTCGGTCAAGTCCTGTAACTCCGATTCGAGTTCCGCGCCTACTGAAGGCGGGAGCCGTTACC +GCCTACCTCGAGCAGTCCTTATTATAGCACATATCCCGACGGATCTACGCGCAACTTTGGGCATAAACTATGCCCTCCAG +CGCTTTCACCTTATAGCAGGAGTTTGAAACAAGCAATGGAACGCCGAGATATAGACTCCCTGTTAACGGCACCGACCCAT +AGGGTTCGGAGTCAACCTTGACTTAAGTAGATATCAAGGATACGTTTGGCTGAGGCCCGTCGCCCTGGTCACGTGGGAAT +CTTAGTGCTGCTGAGGGAGATGGAGCTAGCTGTGTGAGTACAGCCGTCCGGGCCTTGCGCGGATGATGTCTGCATTGTGC +AAACCTAGACGACCCTGTATATTAGTCATCTACCCTGTCCGCTCATTACAAATAATCAAGTATCACGTGCAGATAGGTCA +GAGGGCGCTTTAGGGCTAAGGGTCATCTACCAGGCTTGTGGGATCGATTAGTCGTGCCAGGCGCTGTAATTATGCAGCCG +CTTGGCTGGGAATATGGCTGGCGCCCTGAAGTATTGGCTACGATGTACCACGCTGCTTAATGACCATCGGATGACTGGCA +ACCAGAGATTCCGTAAGGCGAGGTGAAGTTGGATAAGCAGTTGGGGTACCCGAGCAGGGCGCGGACAGGTGGGCCTAGCC +AGAGTTCAACTCGTAGAGGCGTCCTCGGACATAGTAACTTACTGACGATTAGAGACGAGTACGCCTCATTACGGGCAGGG +GCTCGTTACTGCACGTTAGGTAGATCCCCTCCTGCCGTAGCACTTGCAGCTGCCGGGACAGGACCTCAAGCTTGCGACCC +GTAAAATATGGAGTTCTAACGCAGCTAGTTCCCGCGATGGTTTTATCGACGTTTTCAAAGTCCTCAGCTCTTCCCTAGTG +CCGAAATGTCCCTAACAAGGTAAGAGAGTCATGAGCAGCCGTTGGTCTTGGAGGTATTATGATTATGTAATGAGACTACA +CGTCGAAGCAACAGCCTGAGTGAATTCCCGTAGCTCGAGTGGTTATGCGGGCGTTTTATGCGTGTTAGCCCCATTCGCTG +CAGGGCAGCGGCCGCGCACCGTCGCTGACGGGGCTAGTGTGCCGGTGTCTAATTTCAGCTTCGTAGGTCCGGCGGCGCCT +GAAGGACATACGATTATAGCACTGCCTACCGGTGCGTCACGACATGCTCTATAGTCACTTCCGGCACCATTACGGCACCA +ACATCATTTTTACTCCCATATACAAGCAACTTTCCCTTCTTCTAGTCTGTCCGGCATGGTTGAAGTTTCATTACTGTTCC +GGTCAGGACTCCGGGTTGGAATAGCAATTTAAATGTTCAAATTTAGCTCACTCTCTTTGAGAGCGCCCCGGTGGGGAGCA +CCAAACTTTCATTCATTCATTGCATAATCCACAAGTGATCTACCTCCAATATGGACAGGGGAGCCAAACAGTACATTTCT +TTGGAACAGAGAAGCTTCGGGTCCTGATACCCTATAAACATGAGTACTGGGGTGAGAAATTTGCCGCACTTTATGAAGCG +CCGTACCGATGAATATGCAATGTACCAGACCCATTGCGACGAGTCGCCTATTACTCGGGCGCACAACAACTTGCAACCCT +TGAGCGCAGGTCGGGTCAGATTGAAAAATAAAGCACGCACCACTGAACGGACGTTCTCCGCCTGCACTAAGCACGCTGGA +GTTCCGCCAATCTGTGGAAAAAGCTTCCGCACATTCCCTCTGGTCTGGGAATAAGAAGCGCCCGCGTGGTAGTAGTAACA +AACAAGAATGCGCTCTCGGGGGTAGAACGTCAAATCGTAATCCGGCCACTTCCGATATAGAACGTGGCCTGTGATATAAC +CAAGAAATATGCGTTCGACTGCTTCCCCACTTACCAATACCGAGTCGGGTACGTATGGAGGCGGTCTTTTCTCCGCAACC +AGGCAGAATTGGGAACAAGGATGGTATAGACTTTGGTTCTTTTTGAAACGGCGAGGGCTGTTAGGAGAATCTGTTCCAAG +CGCGCGGCGTAAAAAGTATACGGATAACTAAACCTGATATCTACGTTAACATACAATTGAACGTCTTGATGATCATTGAG +GGGCGCAGACAGCCATAATGTCACACACGACCCTGGAATACACGCGTTTGTTTACTAACACTTAGAATTTCAGTGTGAAC +ATGCACTTTCAGAACCCTTCGTTGTAGTAGCGCGCGCGTCCGACGCGAATAGGCCGAACGCCACCTGGGTCATTACGACG +TCTACGCTACGACTGCGACGCATCTCTGGTGGGCATGCTCTTGGTAGTGCAGTAGACAGAACTCAATAACGCTATTTGAC +ATTCTCTACTCTATAAGACTGTTCCCTTTCTGGGGAGACTTCGGTAATCACCTACTAGCAGCTCATTCTCCTAGCCCTGC +GAGGTTAACCGACAGGCTGAAACCAAACACTGGTCGGAAGTCACTACTCACACTCCCATAACCGGTGTCTGTTTAATTCG +GGAGTTTGTCTTTGAACGGGCTCTCGGGCTACATTGCCTCTAACACGTAGGTCACACTCCAAGGGTGAATGAGACGTTGA +TAGAAGCCTGACATGAATGCTGACTACCCGCGCATTCTGCCCGGAATATCAATAGGGGGAAGAGAGCCCCCGCAGTACTA +GCTAGCGCAGCAGGGCAATATAAAGTCCGGCCATTACTATGCGGGTAAATCCTGCTAACAAGGCGTGATGATATCCAGAT +CACTGAGGACACTTGACACCAGGCCCTGTTTTTGTCACAGTATACTTTTCTACAACATTCAACACTATGCTTCAAGGCTT +AGTTCTCACTCAAGTGTCAGTAAACTGCAGTTGTGCGGCCACTGCCCTTATCATTATAATTATAGCACAAGCACCGGCCC +GCGGCAAAAGCCGAGCAGAGATCGAACCTGTAAGATTCGGTAGGAGCGACTAGTAGCGTCTCGAACAACGATACATATGA +TCTAGCAACAGGAGCGGTTAAACGACGACCTCGAGGATACAGCTATAGCTAAAACACCCAGAAATCTGCCATCAAAATTT +AACCACATCCGCAAACACTTGCTTAACAAGTGTACCGGTGTATAGTAAGTGGCAGTACCTCGAAAGTGATAGAACTCGAC +GCTCCTGAAGCGTTTGTGGCGAAGACTTAGAATTAAAGCCTTTCACCGGGATGTAGGAAGTTACGATCGACTAATCTTCC +AAGGGTTGATCAAAGGCCTATTGCGCCGATACTGGGTACGCCGAGAGTTAACGAAACCTTGGCCACTGACAACGATATGG +TGATCTAGGAAAAGCTTTTCCAAAGACTGCCTAGGTATTTCCGGCCAAACCGTCCGGGATTCACAGCAGGCGCGGCCCAT +CATTTATTAAGTTTGTCAAACCTGTTAGAATGCTGTGAGGGCCGTTCCATCATATATAACCGTAGTCTTCGGTTTTTCTT +GCACTATATTATTCGTGCCGCCGGACAGCGGCCGCTCATGGGGCGCAGATGCCGACATATAGCGCGCTCGTCATGAACCG +TCTCCGAACCAGTGTATAGTAACACAGCGCTTTTGATCCGTGCGCTACAACGTAGCGGCGCGCCACGGAGGAACGGCCAC +CTATATGCAGATATGCGGATTGGGTGCAAGCTGTTGCTTCTTCCTCTAAACAGCAAGTAGACAGCGGCGCTGGGGCGAGG +CACTCGCAGTTCATGCGTGTGGTTATACGAACCGAGCTGTGTCGAACCCACGCTAGATCCAGCTTGGTTACACCTGTCCA +AAGCATTGCTCGGCTGGAGTGCCATGATGCGCAATAGGGGTACGACAGGACGCACCGAAAGAAGCGTGTGTGCGCGTATT +GGGGGGGATAAAACCGCAGCGTTATCATCAGTGTACCGGTGTAATAGCATGAAACGTTCAATAAGTACCAATAATGAGTT +TGATCGAGCGGCGAATTCTCCGACAAGAAGAAGGAATCCGGAAGATGCAGGGAAGAATAAAATCGCACCGAACTGCACGG +ATGGACTCAGACATTGAACGCGCTCCCGTTAAAGAGTGTGACTGTCCCAGACGCCACGATCCAAAATACCGCAGTGGAAG +TCTGAGGATATATTAATATATGCGACGTAAAGACTATGGTTATCTACTGCAAGACGAGCCGTGCGCTACAAGCCTGTGTC +GATCAGCGCCCATGGGGCGCTCATATGCGCCAATGAAACAAATGAGGGTAGAAAATGAGTTTTAATTCGGGAAGTTATGA +TGGATAGGACAGTATGGTACGATCGAATCCGAATAACAACGTCATCCAAGCGTTAAGCATGGTTCGCTCAAGCCGTAGAT +GGACATGCAAGTGCATCGATAGAGAGCTTCAGCGTCGAGGTGTCCGCTTTGAGAAGTAATCTCCGTAAGCTGAATCGTCG +CGCTCAAGATGGCTATCGTGCTTAAAGTACGCGCGGGCTGCATCTATCTCGATTTTCAGCGTCTTGTCGGATGGTGGTTT +TTCCCTGGCGACACGTGCGTGCCTATTAGGTTTCTCATAGATAAGCAAGCAATCATTCTTTACGAGAGTGGCACGACACT +TGTGCGCGGATTTCGTAACCACCTATCCATTTGGTTCTATTAGGCTCTCGTTCCGGTCGTTGTTCGCATGCAGTGTTTTA +AGCATCGCTCACTATGTTGGGTTTACGTAACTTCCCTTAACCTGTACTCGCTTCCAACCACGTGCAAACCGCGTTTTCGT +GGTGGGTTATGCAAAGTGTCAACCAGCCACAGGATTTAGTCACCGGTATGCGTCATTGAGAAGGGTATATGCAACATCGT +GCACGTCAATTAGTGGGCTGTTCCGAAGAGTCAGGCCTATAAAGGAGTTCTATACAAAAATGCAGCGTTATTGGAGGTGC +ACACGAGACCTTACACTAACGAAGTTAGGCGGTAGCACATTAGACCCCAGGGCACCTGTACGAACCTTCCAGGGGAAGCT +GTGGAGACTATTACGGACTGTGTAAGCTCATTCTCCGAGTTGTGAGTGCTAACGGAGTATAAGCAACTGTTCTAACGAGA +CTACCGATCGTTGAGGCGGGGCCCGCCCCTGGTAAAATAGAGGTGATAGTACGTAATTACGACCAGGGTGTGTGCCAAGC +GCGTTACCAGCATCAGAATCTGCCGTCCAAGGCAGTAAAAATCCCAATGATGAGGGTCTGGCCTGGCGGGTCGGGCCTCC +GTCGAAAAAAACGTAAGGCGAGGCCCCAATGCAACAGGTAGCGAAATCTCCACACCTGCGGACGACGCGTAAGGTCCTCC +ACCGCGTGGGTACAAGCTGTACACTCTTACCGGAGGCAAGTAAACAATATAACACGAAGGACCAGCATTGGGCGGCCCGT +CGTACTCGTATCCGTGCGCGTACACCTCCATATTTGTCCGTTGGACTATGGTGAGGACGTATCCAAGATCTCTTTCGTGT +TGTGGCCATAGGCAGCAGGATCGGAATCCGAAGCAGAGAGATGAACCAGCCATCGCAATGTATGTCGAATGACTCTCGCA +GCTGGTCGGGCCAAATAGAAAGAGCGAGGGTTTGCATAGCACTGGCTCCATTTCGGTCTCCAGCATAGGTACCAGCCGTT +CGGGATGGGATTTTTCGGGGTACCGCTGGCAGATTATCCTTGAGTTGTAAAACCCCGAGACAATGACTAGTACCATTTCT +CTCGGGAGGTGCAAAATCGGGGCATAAGTCGGTTCTGTGCACCGAATAATAGTTATAAACCATAAGAGCCAATGTCGCGC +CCGACCACAACAAATCATATAGTATTTTGACCCAGCATAAAGGCGGCGGGCACACTCCACGCCACCAAAACAGAGTCCAT +GTGCGGTTTTGGTTACAGGTTTTGCTAAGTCCCACCGACAAACTGCAGTGGGTACTTTCTTCTGTGGAGCGTATAACCGC +AGAGCACGACCTATACGCACTAGGACTGAGTTTTGTGCTATTCGGATAGAGCCCTTGTAGCCACCTATCAAACTAGGCTG +TATCGCGAATGTCCGGGGCGTGGAACGAGAAGAGTCTCAGTATTAAGGGATAAACGTGGTCACACTCTCCACCCAAGAGC +TACGGACAAGACTCCAATATTTTGATCTGGGGCTTTCACCTTGTACTCACAGAGTATAGCTGGCGTTCTCAACGTCGGCT +GAATTAGAAGGTGATCCGCATAAGATTAGGACGTTGCACCGCAGGTATGGGCATCGCATCACAGAACAACCTTTATGGTG +TTTACATCGTCAACGTGACACGTGTGCAGTACCCTAATCTTTCACGTGCATAATTGTTTAATAGTCTCCGTTAACTACTT +AGGGCGTTAAATATACACCCGTGGTGGGTGAGACCTATTGCCCCTATAATATCGGCGATATCGTTGCTTACGCTAAGGAC +TAGAATGCTACGACGATTCTACCCGAGAACTCACAAGTAACGCTAGCGATAAGATACTCAACTATAGATGCGATATTATG +TGACACCTGTTAGCTGGACATAGGGCAGCGGTGCCAGCACAGTGCTCGTATCATCAGGAGCGGTACCACCACGTTGACGT +GGCTCTCGCGTTCTAGCCCTCCCGCACGCGGTCGCCTCTTGGTGTCGAGTTTGTAGTGATTAGCAGCACATCGGGTGCCT +CCGCATACTATAACCAGCGCGCCCAATAGACACTGGGTCTTGGTGACACGCAATGTGGGCGATCTCTCGGCGTACCGGCG +TATTTCACAAAGAGATGTTCATTATGATACGTGGTAGTAAATAGCTTGGACTGCACTGTTTAGATTTATGTAACGACAGC +GATTCCGCGAAGTTTTCCCACGACACAGGAGTCTGCAATCTATTGAGAGGAAATGTCAGACAAAGGCTACTCATGAGAAC +GATCCGGCCTTGAGGGAATTCTACGGGGAGATCAACCGTCTGTTACCTGCGCTGTAGCATATGAGGGTATTTCGCAGCCT +GATATCTGTTCCGTGCGCTAAATACTCGCATGCACGGCCGCTTTATCACCGGACTAGCTATGTGCGAGCATCTATGTTAA +CGTGAGAGAAGGTTTGTGAACTTTGATCTTTCGAAAGGTAGACTCAATTACCGGAGTGTACATACGAATGTGGGGGCCTA +TAGCTGGACGTCCATAGCCACCTAGCGAGTGGCATTTTCGCTGCGGTCTCTAGCTAGAATCTACGCTGCCCCCAAGTTCG +GACAGCAGTCACTGTCCGGTGAGCGAAGTTCTGCGCGAAATCAGCCGACTACACGTGTCCTTAGTAAAGAGCCACGCTTA +TGATGCCATAGCTTTCGGTCATGTATTCGAATTCCTTCCTGGATTTCGTACGACGACTGACAATGGCGATCGCATGTAAT +CATACCTAGAAAAGGTGGAAATCGGTAGCAAGGTTACTCCACGAATCGCCAGTGCAAGAGGCATTGCCCTCAAAACCAAG +TGGCACCTACGGTTTTCCCGGTATCTTAGATGTTAGTGCTGAAGTAATTCTAGGGTGTTGTGAAGCGGTTTCTCCATCCT +TGCATAGCAATGGGTTATCTCTATATAACATTTTATTAGCGACAGTTGGCGTGATAGGAACGCAGGAGCTGGAAAAATAA +TCAGGCCCGTTCGATCCCGCGAGCCAATAGTGTGAACGTTTCTGCGACGAGGAAACAAGCATGATTGACCTTTCCTGCCA +ACATACGTATGGTGCCCACGCGTACGTAGACCCAGCCACAAGGCTGGATGCGCCATTAAGATACCTCTGTAATAGAGGCA +GTACCCGAGGTGACATCCACCTCAAGCTTGGGCCTGGGACAAACCCATTCAGTCCCTCAAGGACTCTAACTCTGACACAC +GTTTCATGCCCAGTCCGAACTTTTTTCAATGCTGTTAATATCTTCACAATCTTCTTGGTAGTACTGATAACCCCTATTGC +CGATGGATAAACCCGCCTCCCAGTAGCAAGTGCTTTCCGGGGGTTATTGCGCTCGGCCGTAGTGCTAAGTAGGTCGTCTA +CAAGAGCCTGTGTAGCAATAAAACAAACCGAACTACCCATGAAATACATTGTCTTAGAAACTTTAAGAATACCGTCGTAA +ATAAGCTGCAGTAGTGCCATCCGCTTGATTCCTGTACCAAATAGTCCCATTCGGCGATTCAGGATGAACAGTTGGTCACC +GTGACAGAATGCGTGCCCACGGTACCAAGGGCTTAATTGAGTTGCTCTGGCACAAAGAAGCAGTTTATAAGCCTTTTACG +CTGAGATGCGTGGAGGAGGAAGCCTATGTTGCTGAGGCGTCAACCAGCTTGAGAAGGTCCACCGTTTGTTTATGGTACCC +ATAGCGTGATCTAGTAGAGCGCGAATCACCGATGTACCGTTGTACTAGTCGCAATCTAAGGTAAAATCCTTTAATTTGTT +ATCTAACGTCTATCTTGCTGACTATCACCCAGATCAACCAACCTCAAACGGACCGTCCGGCCCCAGACGGATGTTCGAAC +TCCATACATGTTATCAGAATGCTATGCTACCATGATCGATACCGTCTAAGTATTCTGCGCTCTTTCAAAGTAGCCTGGGT +ACAACGGAGCGACCAAGGAGCCAACAGATGAACAGCATCTGGTGACAGCTAGTCTCGTATTTGTAGCAATCTTTACGCAC +CTGTTTAAATTGCATGGTGAGACCACAGATCGCTATCTAGGAGAGAACCGCCGTTTCCGAGAAGATACCGGTTAATTGAC +GGTTTGGTGGTCAGGTTGGTCTTCTAATACCGTTGTCCAACGTTTTGGCCTCACTAACCCTTTGATTTATGGGCAGGGTT +CCAAGAGAAGTCAGGCTGAATCAGAATTTGCCTAGCCCCCGCTCGAGTTCTCAATTCAGGTAGCATTAGCGCCGCTACTA +CTACCAATCTAAACCAAGGCTAAAGAACCAATCATAATCGTATAAAAGTGAGAGACGGAAGTGTTCCTAATGCCGTTGTT +CAACTCCGCAACAATG +>ctgB +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGTTGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGAGATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCAACAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATACTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACGTGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGC +TACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATG +CTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGC +ATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCC +TGATGCTGATACATGCTAGCTCCGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGCCATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CACGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTATGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGC +TCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCA +TCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCT +GATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATA +CATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCT +ACGTGCATGCTCGACATG diff --git a/test_data/volvox/volvox-rev.fa.fai b/test_data/volvox/volvox-rev.fa.fai new file mode 100644 index 0000000000..a3a966a7d0 --- /dev/null +++ b/test_data/volvox/volvox-rev.fa.fai @@ -0,0 +1,2 @@ +ctgA 50016 6 80 81 +ctgB 6078 50654 80 81 diff --git a/test_data/volvox/volvox-rev.gff.gz b/test_data/volvox/volvox-rev.gff.gz new file mode 100644 index 0000000000..da7c5cef90 Binary files /dev/null and b/test_data/volvox/volvox-rev.gff.gz differ diff --git a/test_data/volvox/volvox-simple-inv-paired.bam b/test_data/volvox/volvox-simple-inv-paired.bam new file mode 100644 index 0000000000..0fcefdfc18 Binary files /dev/null and b/test_data/volvox/volvox-simple-inv-paired.bam differ diff --git a/test_data/volvox/volvox-simple-inv-paired.bam.bai b/test_data/volvox/volvox-simple-inv-paired.bam.bai new file mode 100644 index 0000000000..d8477ea87a Binary files /dev/null and b/test_data/volvox/volvox-simple-inv-paired.bam.bai differ diff --git a/test_data/volvox/volvox-simple-inv-paired.cram b/test_data/volvox/volvox-simple-inv-paired.cram new file mode 100644 index 0000000000..661801e5e8 Binary files /dev/null and b/test_data/volvox/volvox-simple-inv-paired.cram differ diff --git a/test_data/volvox/volvox-simple-inv-paired.cram.crai b/test_data/volvox/volvox-simple-inv-paired.cram.crai new file mode 100644 index 0000000000..396f8914a6 Binary files /dev/null and b/test_data/volvox/volvox-simple-inv-paired.cram.crai differ diff --git a/test_data/volvox/volvox-simple-inv.bam b/test_data/volvox/volvox-simple-inv.bam new file mode 100644 index 0000000000..f97ee0f4fc Binary files /dev/null and b/test_data/volvox/volvox-simple-inv.bam differ diff --git a/test_data/volvox/volvox-simple-inv.bam.bai b/test_data/volvox/volvox-simple-inv.bam.bai new file mode 100644 index 0000000000..b57d6b7846 Binary files /dev/null and b/test_data/volvox/volvox-simple-inv.bam.bai differ diff --git a/test_data/volvox/volvox-simple-inv.cram b/test_data/volvox/volvox-simple-inv.cram new file mode 100644 index 0000000000..5c16aab7c7 Binary files /dev/null and b/test_data/volvox/volvox-simple-inv.cram differ diff --git a/test_data/volvox/volvox-simple-inv.cram.crai b/test_data/volvox/volvox-simple-inv.cram.crai new file mode 100644 index 0000000000..11cd3ac78d Binary files /dev/null and b/test_data/volvox/volvox-simple-inv.cram.crai differ diff --git a/test_data/volvox/volvox-simple-inv.fa b/test_data/volvox/volvox-simple-inv.fa new file mode 100644 index 0000000000..3dfd41eb4a --- /dev/null +++ b/test_data/volvox/volvox-simple-inv.fa @@ -0,0 +1,627 @@ +>ctgA +cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagcct +tggtttagattggtagtagtagcggcgctaatgctacctgaattgagaactcgagcgggggctaggcaaattctgattca +gcctgacttctcttggaaccctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagacca +acctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcac 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+actggaatcctcatcacgcagcgctaccggatgccatccctagtcatccccgcgagtttaaccagtcgagatggctcgaa +ccgtgtttcgaaggctggctattgaaccagttataaagcaggggcgactgtccgtcggacttcgatataaactatcacaa +atttggcataagtatatacagccaagaaggctcagataggcacacgcacccaaatagtgaccgcctacgttcaggttgcc +cggcaacgaagcgcgcttgctccattaatccactatcagaggtaacgaccctctttcaccgtagctgcccccatgtcggg +gcaacagtttcccaccgataacgtgttctgtctagtacgtgaaacggattggctaacccctgtcagcctaattagatgac +atcctcgtacctctagagaaggtgaggagaccgctggaacataagtaaacagtttaccaaacaatgatcatacatataac +agaaaggagagatgcccggtggggtcgaagatacagctgtggttgatatctgcaacggccaggctgtcatgaagatcacg +cgcacgaagctatttatgaaagatacccatgccggggcggcagcggtacctagtcctaaataccgacacgtagcaacgcg +tcccctgaggcccaccctagtcaagggaacttaaaatatacgctgactttgtctaccaatcatcttcgattaacaccggc +atactaagtctaccctggacccagcaatgagaaaaacttttccgaatgatcattgtgagtttacagagattaggaacacc +aaaaaaatttacgtacgtccggttacccctgtgtgacccttggccacaaaccgtaaggtgcagcatgggcgttgagtcca +gggtttgtgacaccagacatgaataccctgtggcgggttgttagcatgttattcggatccgatttcagagggtccgttga +taccgggcagtacaagacaccccacaccactgaggtggtacgtccgccagtctgctccctacgttatgcaaaattccttc +cccggcgttcttgcctgtactactcctaaagggccgtgaaatccgacgttgctgctccgtctcgggacacccacacaaca +gctacggaaaatcgtgaggatgcacaagggtcttgcattgttgatctatacagctcttcgcacggtgtgctactgttttc +cacaatgggcaaggggcgtgtaggtcttatgtaggagtaccccgtgatctggctataccttgctatctattccaccaaaa +tagccggggtcttatagttttattccggatctatcaagtgacaagtccatggggtaaacggtaagtttcgtacgctgggc +ggtgatccccgcttataaacgagcaaaccgccaaagcaaccattgccgggcttccagctagtaaatgttgggtgtcaatc +gtgcatgtgactacttacccacaaagggacgcttgaagcgcctgaactcgtcacgtcatgcctagctcccggttgaaaca +cgaagacgcgtgaacctatctttgcttactattcgcctcctttaagaggcttcttgatgtggctctgcgacatggacagt +agtagttgtacctgggtatgttagtgaaattacaagtacctcaaaaacgaattacgtgtatagagattatgtcactccgt +ca diff --git a/test_data/volvox/volvox-simple-inv.fa.fai b/test_data/volvox/volvox-simple-inv.fa.fai new file mode 100644 index 0000000000..3eda8be37a --- /dev/null +++ b/test_data/volvox/volvox-simple-inv.fa.fai @@ -0,0 +1 @@ +ctgA 50002 6 80 81 diff --git a/test_data/volvox/volvox-simple-inv.paf b/test_data/volvox/volvox-simple-inv.paf new file mode 100644 index 0000000000..4c5383ded9 --- /dev/null +++ b/test_data/volvox/volvox-simple-inv.paf @@ -0,0 +1,3 @@ +ctgA 50002 29995 50002 + ctgA 50001 29993 50000 20006 20007 60 NM:i:1 ms:i:40008 AS:i:40008 nn:i:0 tp:A:P cm:i:3790 s1:i:20147 s2:i:10001 de:f:0.0000 zd:i:2 rl:i:0 cg:Z:20007M +ctgA 50002 0 19911 + ctgA 50001 0 19911 19911 19911 60 NM:i:0 ms:i:39822 AS:i:39822 nn:i:0 tp:A:P cm:i:3722 s1:i:19780 s2:i:10001 de:f:0 zd:i:1 rl:i:0 cg:Z:19911M +ctgA 50002 20000 30001 - ctgA 50001 19999 30000 10001 10001 60 NM:i:0 ms:i:20002 AS:i:20002 nn:i:0 tp:A:P cm:i:1883 s1:i:10001 s2:i:0 de:f:0 rl:i:0 cg:Z:4000M1000D1000M1000I4001M diff --git a/test_data/volvox/volvox-vs-rev.paf b/test_data/volvox/volvox-vs-rev.paf new file mode 100644 index 0000000000..710e428883 --- /dev/null +++ b/test_data/volvox/volvox-vs-rev.paf @@ -0,0 +1,7 @@ +ctgA 50016 0 50016 - ctgA 50001 0 50001 49907 50019 60 NM:i:112 ms:i:99387 AS:i:99372 nn:i:0 tp:A:P cm:i:9120 s1:i:49218 s2:i:0 de:f:0.0020 rl:i:0 cg:Z:15603M3I859M1I4611M1I190M1D5717M1I4622M1I928M9I10296M2I108M2D7064M +ctgB 6078 0 6078 + ctgB 6079 0 6029 6020 6078 60 NM:i:58 ms:i:11529 AS:i:11931 nn:i:0 tp:A:P cm:i:1153 s1:i:5825 s2:i:5551 de:f:0.0017 rl:i:0 cg:Z:2980M49I3049M +ctgB 6078 0 5778 + ctgB 6079 350 6079 5720 5778 0 NM:i:58 ms:i:10929 AS:i:11331 nn:i:0 tp:A:S cm:i:1093 s1:i:5519 de:f:0.0017 rl:i:0 cg:Z:2980M49I2749M +ctgB 6078 50 6078 + ctgB 6079 0 5629 5626 6028 0 NM:i:402 ms:i:10790 AS:i:10721 nn:i:0 tp:A:S cm:i:1118 s1:i:5551 de:f:0.0014 rl:i:0 cg:Z:893M50I292M100I460M50I985M149I1124M50I1875M +ctgB 6078 100 6078 + ctgB 6079 0 5579 5576 5978 0 NM:i:402 ms:i:10690 AS:i:10621 nn:i:0 tp:A:S cm:i:1108 s1:i:5501 de:f:0.0014 rl:i:0 cg:Z:843M50I292M100I460M50I985M149I1124M50I1875M +ctgB 6078 150 6078 + ctgB 6079 0 5529 5526 5928 0 NM:i:402 ms:i:10590 AS:i:10521 nn:i:0 tp:A:S cm:i:1098 s1:i:5451 de:f:0.0014 rl:i:0 cg:Z:793M50I292M100I460M50I985M149I1124M50I1875M +ctgB 6078 200 6078 + ctgB 6079 0 5479 5476 5878 0 NM:i:402 ms:i:10490 AS:i:10421 nn:i:0 tp:A:S cm:i:1088 s1:i:5401 de:f:0.0015 rl:i:0 cg:Z:743M50I292M100I460M50I985M149I1124M50I1875M diff --git a/test_data/volvox/volvox.sort.gff3 b/test_data/volvox/volvox.sort.gff3 index 1d3eb99e84..68256cdc32 100644 --- a/test_data/volvox/volvox.sort.gff3 +++ b/test_data/volvox/volvox.sort.gff3 @@ -241,6 +241,7 @@ ctgA example match 49762 50000 . + . Name=seg13 ctgA example match 49957 50000 . - . Name=seg07 ctgA example match 49957 50000 . - . Name=seg07 ctgB example contig 1 6079 . . . Name=ctgB +ctgB example BAC 1000 2000 . . . ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads ctgB example remark 1659 1984 . + . Name=f07;Note=This is an example ctgB example remark 3014 6130 . + . Name=f06;Note=This is another example ctgB example remark 4715 5968 . - . Name=f05;Note=ああ、この機能は、世界中を旅しています！ diff --git a/test_data/volvox/volvox.sort.gff3.gz b/test_data/volvox/volvox.sort.gff3.gz index f90e827efa..170bc39383 100644 Binary files a/test_data/volvox/volvox.sort.gff3.gz and b/test_data/volvox/volvox.sort.gff3.gz differ diff --git a/test_data/volvox/volvox.sort.gff3.gz.tbi b/test_data/volvox/volvox.sort.gff3.gz.tbi index 4b849659a4..643e0371df 100644 Binary files a/test_data/volvox/volvox.sort.gff3.gz.tbi and b/test_data/volvox/volvox.sort.gff3.gz.tbi differ diff --git a/test_data/volvox/volvox_del.paf b/test_data/volvox/volvox_del.paf index 8e1c01442b..864ae503ce 100644 --- a/test_data/volvox/volvox_del.paf +++ b/test_data/volvox/volvox_del.paf @@ -1,7 +1 @@ ctgA 45141 0 45141 + ctgA 50001 0 50001 45141 50001 60 NM:i:4860 ms:i:90254 AS:i:85398 nn:i:0 tp:A:P cm:i:8494 s1:i:44546 s2:i:0 de:f:0.0000 rl:i:0 cg:Z:28498M4860D16643M -ctgB 6079 0 6079 + ctgB 6079 0 6079 6079 6079 11 NM:i:0 ms:i:12158 AS:i:12158 nn:i:0 tp:A:P cm:i:1213 s1:i:6077 s2:i:6027 de:f:0 rl:i:0 cg:Z:6079M -ctgB 6079 50 6079 + ctgB 6079 0 6029 6029 6029 0 NM:i:0 ms:i:12058 AS:i:12058 nn:i:0 tp:A:S cm:i:1203 s1:i:6027 de:f:0 rl:i:0 cg:Z:6029M -ctgB 6079 0 6029 + ctgB 6079 50 6079 6029 6029 0 NM:i:0 ms:i:12058 AS:i:12058 nn:i:0 tp:A:S cm:i:1203 s1:i:6027 de:f:0 rl:i:0 cg:Z:6029M -ctgB 6079 100 6079 + ctgB 6079 0 5979 5979 5979 0 NM:i:0 ms:i:11958 AS:i:11958 nn:i:0 tp:A:S cm:i:1193 s1:i:5977 de:f:0 rl:i:0 cg:Z:5979M -ctgB 6079 0 5979 + ctgB 6079 100 6079 5979 5979 0 NM:i:0 ms:i:11958 AS:i:11958 nn:i:0 tp:A:S cm:i:1193 s1:i:5977 de:f:0 rl:i:0 cg:Z:5979M -ctgB 6079 0 5929 + ctgB 6079 150 6079 5929 5929 0 NM:i:0 ms:i:11858 AS:i:11858 nn:i:0 tp:A:S cm:i:1183 s1:i:5927 de:f:0 rl:i:0 cg:Z:5929M diff --git a/test_data/volvox/volvox_ins.paf b/test_data/volvox/volvox_ins.paf index effcf00f16..b0aba955a7 100644 --- a/test_data/volvox/volvox_ins.paf +++ b/test_data/volvox/volvox_ins.paf @@ -1,7 +1 @@ ctgA 54801 0 54801 + ctgA 50001 0 50001 50001 54801 60 NM:i:4800 ms:i:99974 AS:i:95178 nn:i:0 tp:A:P cm:i:9413 s1:i:49418 s2:i:0 de:f:0.0000 rl:i:0 cg:Z:31198M4800I18803M -ctgB 6079 0 6079 + ctgB 6079 0 6079 6079 6079 11 NM:i:0 ms:i:12158 AS:i:12158 nn:i:0 tp:A:P cm:i:1213 s1:i:6077 s2:i:6027 de:f:0 rl:i:0 cg:Z:6079M -ctgB 6079 50 6079 + ctgB 6079 0 6029 6029 6029 0 NM:i:0 ms:i:12058 AS:i:12058 nn:i:0 tp:A:S cm:i:1203 s1:i:6027 de:f:0 rl:i:0 cg:Z:6029M -ctgB 6079 0 6029 + ctgB 6079 50 6079 6029 6029 0 NM:i:0 ms:i:12058 AS:i:12058 nn:i:0 tp:A:S cm:i:1203 s1:i:6027 de:f:0 rl:i:0 cg:Z:6029M -ctgB 6079 100 6079 + ctgB 6079 0 5979 5979 5979 0 NM:i:0 ms:i:11958 AS:i:11958 nn:i:0 tp:A:S cm:i:1193 s1:i:5977 de:f:0 rl:i:0 cg:Z:5979M -ctgB 6079 0 5979 + ctgB 6079 100 6079 5979 5979 0 NM:i:0 ms:i:11958 AS:i:11958 nn:i:0 tp:A:S cm:i:1193 s1:i:5977 de:f:0 rl:i:0 cg:Z:5979M -ctgB 6079 0 5929 + ctgB 6079 150 6079 5929 5929 0 NM:i:0 ms:i:11858 AS:i:11858 nn:i:0 tp:A:S cm:i:1183 s1:i:5927 de:f:0 rl:i:0 cg:Z:5929M diff --git a/test_data/volvox/volvox_inv_indels.paf b/test_data/volvox/volvox_inv_indels.paf new file mode 100644 index 0000000000..2d2974c93e --- /dev/null +++ b/test_data/volvox/volvox_inv_indels.paf @@ -0,0 +1,7 @@ +ctgA 49186 26805 49184 + ctgA 50001 27258 50001 20447 24398 60 NM:i:3951 ms:i:29302 AS:i:26545 nn:i:0 tp:A:P cm:i:1101 s1:i:8814 s2:i:212 de:f:0.0807 zd:i:2 rl:i:0 cg:Z:39M3D58M1I4M1I3M2D20M3I2M1D42M15D1M1D15M6D2M4D24M1D10M1D64M1D62M1I11M2D10M4D23M1I25M4I23M1I20M2D3M1I7M10I7M1I4M1I5M1I15M10I21M1D3M3I6M1D12M1I6M1D30M1I5M1I6M9D4M1D33M1D2M1D8M1D3M1I5M5I25M2I10M1I34M1I6M5D4M4D6M1D34M1D13M1I25M2D19M1I25M1D1M2I24M1I3M1I20M1D2M1I7M1I3M2I6M4I14M2D29M1D3M2D7M1D4M1D6M2D8M4I30M1I8M4D18M1I7M1D3M1D1M1D9M1D11M3D21M5I6M1D1M1D2M1I5M4I27M1I19M1D7M1D9M5I50M1D3M7D33M1D5M1D2M1D32M34D1M1D6M3I40M1D21M2I33M1I2M1I14M1D4M2D17M1I30M1D9M1I53M1D22M1I5M1I6M2D13M4I19M2D6M2I3M1I15M3D4M1I15M1I3M1D8M7I1M1I56M3D12M1D17M1D5M1D52M7D13M1D2M1D4M1I2M3D9M1D18M1I9M6D9M1I1M2D5M1I6M2D3M3D1M2D3M2D17M2D11M5D4M4D12M1D6M1D9M2D3M1I12M1I7M1I17M1I6M1I13M1I15M2I19M2D6M2I2M1I9M2D20M12I12M1D35M3D6M1I23M3D7M1I8M2D7M1I10M1I41M2I20M1D34M1I2M1I10M1I12M2D10M1D13M13D18M1I27M2D13M2I26M3D4M1D9M2I5M3D39M1D19M1D9M1I12M2D33M1D22M1I31M1I28M1D11M2I5M1D22M1D3M27D38M1I8M1D8M1I29M5D8M1I46M1I18M1D6M1D61M1D16M6D4M3D13M1D19M5D4M1D5M2D6M6D4M7D7M1D7M1D7M1I41M5I3M1I11M1D17M1I3M1I3M1I5M1D11M2I30M5I4M1I6M1D18M1D10M1D50M1I8M1I16M1D9M26D11M1I44M1D19M1I9M2D2M1I18M1D8M15I19M1D13M1I8M1I6M1I4M3I7M1D4M1D3M1I2M1I3M3D1M1D20M1I15M1D11M1D22M2I41M2D12M1I7M2D6M8D3M7D2M2D27M1D19M1D2M1D41M1I13M1D38M1D11M4D7M1I14M1D1M3D37M1D2M1D4M1D3M4D2M1D21M1D18M1I11M2D13M1I23M25I15M1I2M1I3M7I18M1I35M1D11M1I5M1I45M4D5M1D7M1D6M1D35M1I34M2I9M1D6M1I47M1I10M1I34M1I5M1D6M1I1M1I4M8I28M3D6M1I19M1D18M1I7M5D5M1D22M1D3M2I5M12D8M1I71M2I23M1I6M1D3M2D5M2I12M1D12M1I24M1D14M1I3M1D24M1D26M22D42M1D9M1I1M1I9M1D6M1D12M1I6M3D17M12D7M1I11M2I19M1D17M1D17M2I2M2I9M2D10M1D6M2D29M1D3M1D19M1I4M3I8M1I1M2I55M1I43M3I42M1I33M22I22M1D3M1D24M1I40M1D21M1D2M1I5M1D2M1D18M1D20M2D12M1I22M1I4M4I84M1I21M1I35M1D3M4D13M1I5M1I10M4I11M1D20M1D5M1D16M1I14M1D8M1I58M1I9M1I5M26I6M1D30M2I7M1I9M1D9M1I38M5I1M2I8M2I14M2D1M2D13M1D2M1I12M1D21M1D8M1D17M2I4M4I7M1I12M1I23M1D12M1I8M8D12M1I5M1D18M1I39M1I2M1D9M1I5M2D16M1D23M3D6M2I17M3D1M1D13M1I49M1D25M1I5M1I13M1I9M1D21M1D6M1I13M1I2M2D3M2D3M1D3M3D22M1I1M1I10M4I1M4I3M2I7M2D3M2I15M1I9M1I3M4D6M7D1M1D16M1I9M1D6M9D4M3D7M1D5M1I7M1D5M1D31M1D10M1I29M1D6M5D4M1I3M5D22M1I1M1I4M4D2M1I15M2I4M1I1M1I5M2D5M2D7M1D6M1D1M1D14M4D25M1D30M1I30M6D15M3I12M1I9M1I72M1I9M1D8M1D6M1I5M1D18M5I3M1D4M3I3M7I17M1D5M1D19M2I3M1I14M3I2M1I10M1I2M1I38M4I2M1D25M1D23M2I4M1I8M1I3M19I16M1D21M1I21M2I6M23I9M1I9M11I3M5I17M1I2M8I5M1I5M1D12M1D25M1D20M1D10M3I2M4D3M1I18M3I6M2D35M1D2M3I2M1D9M1I1M1I14M1D2M10D1M2D4M1I6M5D3M6D1M6D18M1D8M1I6M1I49M1D18M1I1M1I7M2D24M1D13M1D1M26D8M2D2M1I19M1D13M1I9M1I5M1I3M10D10M5I1M1I15M1D27M1I15M1I30M2D12M1D10M3D22M5D4M1D9M1I33M1D3M1D12M9I4M1D6M5I3M8I8M1I33M5I13M1D22M1D12M1I17M6I5M3D12M1I12M1D1M1D7M1I44M1D1M1D12M1I47M1D8M2D27M1D1M1D35M1D9M1I6M3D52M3I6M1I27M1I8M1I13M1D13M4I16M3I43M1I13M1D31M1D63M1D30M1I6M1D1M1D15M20D18M2D15M9D8M3D16M11D9M1D18M1I27M8I2M3I1M1I11M2D24M2D27M1D2M1D52M1I50M1I4M1D7M7D23M1I6M1D34M2I15M2D11M1I9M1D21M6D1M1D11M2I2M1I7M27D18M1I2M1D10M4D12M3D1M2D15M5D1M1D6M6D6M1D40M5I8M1I8M35I6M1I27M1D15M2I3M18I5M4I2M1I4M4I8M1I39M2I5M6D9M38D3M1I24M1D2M1D17M1D9M2D7M9I12M1I1M1I15M1I10M2D11M1D10M1D19M3I20M1D43M1D8M1I4M3I1M2I2M3I5M3D13M1I9M5I6M1D6M1I2M2D23M1I8M1I19M1D12M1I20M1D5M1I16M2I10M15I5M2D7M1I14M4D13M1D16M1I4M1D5M2D5M2D3M1I14M17I6M1I16M6I13M5D1M1D6M1I4M1D2M2I17M1D33M1I4M1D16M1I44M1I19M1I19M1D10M13D13M1I5M2D12M1D4M1I10M1D15M1D5M1I7M1I8M1D30M1D3M1D6M2I30M1D33M2I7M4I8M1D2M1D16M1D20M1I3M1D35M1I5M1D10M4D5M1D3M1D19M2I5M2I8M5I49M1D14M1I15M1I11M1I4M3D5M1D50M1I11M7I2M4I9M1I18M2I11M1I5M2I13M5I3M2D19M2I11M2I47M4I1M2I7M1I26M1D4M1D6M1D6M1I24M2I5M3D9M1D13M1I9M1I22M1D3M1I12M1I4M4D32M1I2M2I15M3D3M1D10M1D7M1D11M1I4M1D3M7I2M1D11M1I4M1I1M2I9M8I15M1I9M1I44M1D4M2D10M1D15M1I23M5I4M2D7M4I14M1D10M2I35M1I5M3D25M1D17M1I18M5D5M2I15M2D21M1D1M1D55M7I11M1D5M1I13M2I13M1I12M1D18M1I9M3I29M1I5M1D11M2I11M1I4M4I13M1D10M3I83M1D24M1D6M2D4M1I5M1D6M1D34M1D4M2D11M1D4M2D47M10I7M1D40M3D11M2I39M1I19M1I2M1I3M1D22M2I17M2I4M1D2M1I7M1I27M1I7M1I17M1I7M1I15M1D8M1I3M1I1M1I44M1I1M3D4M1I2M1I19M1D15M1I6M4D28M1I8M1D13M1I4M1D11M1D19M2I69M1I43M4D24M1D25M2I13M2I16M1D4M1D8M1D42M1I11M1I7M3D1M2D1M5D14M2D2M1I28M1D5M1I25M1D46M7I8M2I30M1I4M1I19M1D22M1I30M1D10M5I7M1I5M1I3M2I12M11D3M1I7M8D2M6D2M3D7M2D4M1I1M2D5M1D18M2I1M1I1M1I4M1I10M3I18M1I27M2D5M1I6M1D7M2I7M22D30M1D31M1D19M2I46M1I3M1I27M6D13M1I37M1I12M2D14M28I3M1I3M1D18M6I25M1I8M1D9M2D17M1D2M4I10M1I44M1I6M1D14M3I10M2D7M1D10M2I9M15I18M1D13M1I15M1D25M1D13M1I1M1I18M5I17M1D16M1D16M1I29M1I24M1D17M1D15M2I10M1I11M3D3M1I2M1D50M11D2M2D2M1D1M2D1M1D9M1D18M2I41M1I26M1I25M1I22M4D6M2D2M13D23M1D11M1D25M1D7M3I9M1I4M1D16M1I4M1D2M1I6M1I20M1D37M2D42M1I3M1D47M1D11M1D3M1D14M1D7M1D19M7D11M3D10M2I7M1I11M1D48M1I2M1I10M4I2M1I18M1D67M2D4M4D6M1D17M1I6M2I23M1D9M1D1M3D8M1D14M2D2M3I6M4D9M1D5M5D22M1D6M2D25M8D1M2D4M1D2M4D31M2I7M1I11M11D16M2D11M2D14M1D8M2D3M1I21M1I6M2I1M1I6M1D27M1D1M1D33M1D21M2D1M1D8M1D5M2D6M1D8M1I34M1D3M4I7M1I2M1I16M1I1M1I46M1D12M1I7M1I31M6I10M1I1M1I1M1I5M11I10M1I19M1D22M1D10M1D11M1I8M1I24M1D6M2I7M3D2M1D17M1I24M1I2M4D19M1I14M2D17M1D9M3I16M1D10M1D25M1I26M11D3M2D5M1D2M8D30M2I15M2I13M1D6M5D5M3D17M2D17M2I18M2D11M1I11M2I3M1D18M1D9M1I8M1I16M1D2M1D13M3D1M1D10M1D11M1I8M3D3M1I26M1D4M2D8M1D3M2D4M1I4M2I11M1D10M1D4M1D8M6D1M1D5M7D2M1D5M8D3M2D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cg:Z:4M1I16M1I5M3I33M1D14M3D7M1D25M2I5M2I4M1D17M3D11M1D5M3D3M1I15M3I1M2I6M1I2M6D6M2D24M1I3M2D29M1I2M1I3M1I6M1I10M2D8M19D33M1D23M2D9M1D11M1I6M1D5M1D28M1I13M1D5M1I2M1I49M5D6M2I21M1D1M2D2M2D4M4I4M1I5M1I3M1D2M1I4M37D17M2I16M6D5M3D3M6D16M5I4M8I5M4I1M1I52M2D2M1I5M28D33M1D17M2I2M2D31M42I5M1I9M1I7M1D8M1I40M1I39M1I2M1D3M2I11M2I6M2I10M1D14M1I12M1I16M1D6M3I6M2I4M1I1M1I27M1I3M10I3M2D11M3D3M1I35M1I1M3D3M2D19M3D9M4D23M1I3M1I28M1I52M1I28M1D20M2I66M1I3M2I7M1D7M2D9M1D11M1D11M1D7M1I3M1I30M1D11M1D15M2I7M3D3M1I12M6I35M1D4M1D17M1D15M1I5M1D4M1I5M1I3M5D10M1D2M1D8M7I13M5I9M1D4M1I45M6I4M1I19M2D16M1D1M2I23M7I11M1I19M1D13M +ctgA 49186 18309 18754 - ctgA 50001 18559 19001 421 463 60 NM:i:42 ms:i:690 AS:i:668 nn:i:0 tp:A:I cm:i:0 s1:i:0 s2:i:0 de:f:0.0539 rl:i:0 cg:Z:5M1I15M2I30M1D20M1D13M2D2M1D14M8I11M1D18M1I7M1I56M1D33M1D52M2D7M1I19M7D26M1I9M2I10M1I27M1D18M1I15M2I17M +ctgA 49186 1860 2214 - ctgA 50001 1859 2192 321 366 60 NM:i:45 ms:i:501 AS:i:468 nn:i:0 tp:A:I cm:i:0 s1:i:0 s2:i:0 de:f:0.0614 rl:i:0 cg:Z:14M1D4M1D3M1D9M1I12M5D20M2I43M1I10M1I7M2D2M1D8M1I30M1I9M1I2M1I6M15I39M2I16M4I2M1I35M1I2M1I6M1D42M diff --git a/test_data/volvoxhub/config.json b/test_data/volvoxhub/config.json new file mode 100644 index 0000000000..04583515a4 --- /dev/null +++ b/test_data/volvoxhub/config.json @@ -0,0 +1,119 @@ +{ + "assemblies": [ + { + "name": "volvox", + "aliases": ["vvx"], + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "volvox_refseq", + "metadata": { + "date": "2020-08-20" + }, + "formatAbout": { + "hideUris": true, + "config": "jexl:{extraField:'important data'}" + }, + "adapter": { + "type": "TwoBitAdapter", + "twoBitLocation": { + "uri": "volvox.2bit", + "locationType": "UriLocation" + } + } + }, + "refNameAliases": { + "adapter": { + "type": "FromConfigAdapter", + "adapterId": "W6DyPGJ0UU", + "features": [ + { + "refName": "ctgA", + "uniqueId": "alias1", + "aliases": ["A", "contigA"] + }, + { + "refName": "ctgB", + "uniqueId": "alias2", + "aliases": ["B", "contigB"] + } + ] + } + } + }, + { + "name": "volvox2", + "sequence": { + "type": "ReferenceSequenceTrack", + "trackId": "volvox_refseq2", + "adapter": { + "type": "TwoBitAdapter", + "twoBitLocation": { + "uri": "volvox.2bit", + "locationType": "UriLocation" + } + } + } + } + ], + "configuration": {}, + "connections": [ + { + "type": "UCSCTrackHubConnection", + "connectionId": "UCSCTrackHubConnection-volvox-hub1", + "name": "UCSCTrackHubConnection-volvox-hub1", + "hubTxtLocation": { + "uri": "hub1/hub.txt", + "locationType": "UriLocation" + } + }, + { + "type": "UCSCTrackHubConnection", + "connectionId": "UCSCTrackHubConnection-volvox-hub2", + "name": "UCSCTrackHubConnection-volvox-hub2", + "hubTxtLocation": { + "uri": "hub2/hub.txt", + "locationType": "UriLocation" + } + }, + { + "type": "UCSCTrackHubConnection", + "connectionId": "UCSCTrackHubConnection-volvox-remote", + "name": "UCSCTrackHubConnection-volvox-remote", + "hubTxtLocation": { + "uri": "https://s3.amazonaws.com/jbrowse.org/volvoxhub/hub.txt", + "locationType": "UriLocation" + } + } + ], + "defaultSession": { + "name": "Integration test example", + "views": [ + { + "id": "integration_test", + "type": "LinearGenomeView", + "offsetPx": 2000, + "bpPerPx": 0.05, + "displayedRegions": [ + { + "refName": "ctgA", + "start": 0, + "end": 50001, + "assemblyName": "volvox" + } + ] + } + ], + "widgets": { + "hierarchicalTrackSelector": { + "id": "hierarchicalTrackSelector", + "type": "HierarchicalTrackSelectorWidget", + "filterText": "", + "view": "integration_test" + } + }, + "activeWidgets": { + "hierarchicalTrackSelector": "hierarchicalTrackSelector" + } + }, + "tracks": [] +} diff --git a/test_data/volvoxhub/hub1/genomes.txt b/test_data/volvoxhub/hub1/genomes.txt new file mode 100644 index 0000000000..d78064817b --- /dev/null +++ b/test_data/volvoxhub/hub1/genomes.txt @@ -0,0 +1,3 @@ +genome volvox +trackDb volvox/trackDb.txt +twoBitPath volvox/volvox.2bit diff --git a/test_data/volvoxhub/hub1/hub.txt b/test_data/volvoxhub/hub1/hub.txt new file mode 100644 index 0000000000..a6fe62aa85 --- /dev/null +++ b/test_data/volvoxhub/hub1/hub.txt @@ -0,0 +1,5 @@ +hub VolvoxHub +shortLabel Volvox Hub +longLabel Hub with Volvox test data +genomesFile genomes.txt +email stevens.garrett.j@gmail.com diff --git a/test_data/volvoxhub/hub1/volvox/tiny.bam b/test_data/volvoxhub/hub1/volvox/tiny.bam new file mode 100644 index 0000000000..ba6151ad72 Binary files /dev/null and b/test_data/volvoxhub/hub1/volvox/tiny.bam differ diff --git a/test_data/volvoxhub/hub1/volvox/tiny.bam.bai b/test_data/volvoxhub/hub1/volvox/tiny.bam.bai new file mode 100644 index 0000000000..fb1d078d1a Binary files /dev/null and b/test_data/volvoxhub/hub1/volvox/tiny.bam.bai differ diff --git a/test_data/volvoxhub/hub1/volvox/tiny.cram b/test_data/volvoxhub/hub1/volvox/tiny.cram new file mode 100644 index 0000000000..c7cfd75be4 Binary files /dev/null and b/test_data/volvoxhub/hub1/volvox/tiny.cram differ diff --git a/test_data/volvoxhub/hub1/volvox/tiny.cram.crai b/test_data/volvoxhub/hub1/volvox/tiny.cram.crai new file mode 100644 index 0000000000..36d1cd027e Binary files /dev/null and b/test_data/volvoxhub/hub1/volvox/tiny.cram.crai differ diff --git a/test_data/volvoxhub/hub1/volvox/trackDb.txt b/test_data/volvoxhub/hub1/volvox/trackDb.txt new file mode 100644 index 0000000000..daec621b2f --- /dev/null +++ b/test_data/volvoxhub/hub1/volvox/trackDb.txt @@ -0,0 +1,18 @@ +track testgroup +superTrack on +shortLabel Test group +longLabel A grouping of alignment tracks + + track volvoxBamAlignments + parent testgroup + type bam + shortLabel BAM - Volvox Sorted + longLabel BAM alignments of simulated Volvox data + bigDataUrl tiny.bam + + track volvoxCramAlignments + parent testgroup + type bam + shortLabel CRAM - Volvox Sorted + longLabel CRAM alignments of simulated Volvox data + bigDataUrl tiny.cram diff --git a/test_data/volvoxhub/hub2/genomes.txt b/test_data/volvoxhub/hub2/genomes.txt new file mode 100644 index 0000000000..044d3ab8f6 --- /dev/null +++ b/test_data/volvoxhub/hub2/genomes.txt @@ -0,0 +1,3 @@ +genome volvox2 +trackDb volvox2/trackDb.txt +twoBitPath volvox2/volvox.2bit diff --git a/test_data/volvoxhub/hub2/hub.txt b/test_data/volvoxhub/hub2/hub.txt new file mode 100644 index 0000000000..647c158197 --- /dev/null +++ b/test_data/volvoxhub/hub2/hub.txt @@ -0,0 +1,5 @@ +hub Volvox2Hub +shortLabel Volvox2 Hub +longLabel Hub with Volvox2 test data +genomesFile genomes.txt +email stevens.garrett.j@gmail.com diff --git a/test_data/volvoxhub/hub2/volvox2/trackDb.txt b/test_data/volvoxhub/hub2/volvox2/trackDb.txt new file mode 100644 index 0000000000..4affaabb3c --- /dev/null +++ b/test_data/volvoxhub/hub2/volvox2/trackDb.txt @@ -0,0 +1,18 @@ +track testgroup +superTrack on +shortLabel Test group +longLabel A grouping of alignment tracks + + track Volvox2BamAlignments + parent testgroup + type bam + shortLabel BAM - Volvox2 Sorted + longLabel BAM alignments of simulated Volvox2 data + bigDataUrl tiny.bam + + track Volvox2CramAlignments + parent testgroup + type bam + shortLabel CRAM - Volvox2 Sorted + longLabel CRAM alignments of simulated Volvox2 data + bigDataUrl tiny.cram diff --git a/test_data/volvoxhub/volvox.2bit b/test_data/volvoxhub/volvox.2bit new file mode 100644 index 0000000000..0c43b603e3 Binary files /dev/null and b/test_data/volvoxhub/volvox.2bit differ diff --git a/tsconfig.json b/tsconfig.json index fbe3e3826d..429b790071 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -25,7 +25,7 @@ "**/lib/", "**/umd/", "**/tmp/", - "**/demos/", + "**/embedded_demos/", "**/component_tests/", "**/plugin-development-tools/", "**/webpack.config.js" diff --git a/website/README.md b/website/README.md index f0ac140d81..e346521a37 100644 --- a/website/README.md +++ b/website/README.md @@ -16,12 +16,17 @@ We build docusaurus and also create a PDF version with pandoc - We use markdown and not mdx for pandoc compatibility -- We link to images with ../img/file.png in the markdown, which works on both the website and pdf +- We link to images with ../img/file.png in the markdown, which works on both + the website and pdf -- `docs/read_sidebar.js` parses sidebar.json and outputs markdown in order for the pandoc +- `docs/read_sidebar.js` parses sidebar.json and outputs markdown in order for + the pandoc -- `docs/parser.js` parses markdown files and checks their header e.g. the `---\ntitle: My title\ntoplevel: true\n---`. If it does have, as noted there, `toplevel: true` if they are going to be a top level of the table of contents, and if so - outputs a single hash `# ${title}`, otherwise it outputs a double hash `## ${title}` +- `docs/parser.js` parses markdown files and checks their header e.g. the + `---\ntitle: My title\ntoplevel: true\n---`. If it does have, as noted there, + `toplevel: true` if they are going to be a top level of the table of contents, + and if so outputs a single hash `# ${title}`, otherwise it outputs a double + hash `## ${title}` ### Installation @@ -53,4 +58,5 @@ Currently deploys to the jbrowse.org amazon s3 bucket ## Screenshots -See [SCREENSHOTS.md](SCREENSHOTS.md) for info on how various screenshots are generated +See [SCREENSHOTS.md](SCREENSHOTS.md) for info on how various screenshots are +generated diff --git a/website/SCREENSHOTS.md b/website/SCREENSHOTS.md index da947a54b4..61bfc255a1 100644 --- a/website/SCREENSHOTS.md +++ b/website/SCREENSHOTS.md @@ -1,3 +1,4 @@ ## Share links for various screeshots -dotplot.png - http://localhost:3000/?config=test_data%2Fconfig_dotplot.json&session=share-EmATR_zo70&password=GBHfP +dotplot.png - +http://localhost:3000/?config=test_data%2Fconfig_dotplot.json&session=share-EmATR_zo70&password=GBHfP diff --git a/website/blog/2020-07-01-hello-world.md b/website/blog/2020-07-01-hello-world.md index c45280d0b0..340f0b1d9c 100644 --- a/website/blog/2020-07-01-hello-world.md +++ b/website/blog/2020-07-01-hello-world.md @@ -10,8 +10,8 @@ We are happy to now announce the release of JBrowse 2 public beta JBrowse 2 has been in development for almost 2 years at this point, and it has now developed features that offer compelling new functionality -Now, it is finally getting more stable, and we invite interested users to try -it out! +Now, it is finally getting more stable, and we invite interested users to try it +out! To get started diff --git a/website/blog/2020-10-22-jbrowse-web-0.0.1-beta.27-release.md b/website/blog/2020-10-22-jbrowse-web-0.0.1-beta.27-release.md index d1cb1b6d4e..d7437d1826 100644 --- a/website/blog/2020-10-22-jbrowse-web-0.0.1-beta.27-release.md +++ b/website/blog/2020-10-22-jbrowse-web-0.0.1-beta.27-release.md @@ -7,12 +7,13 @@ tags: ['release', 'jbrowse 2'] Hello all, This is the first automated release of JBrowse 2 beta! This includes many -exciting features including a new session sharing system. There are a whole -host of other changes that have not been tracked CHANGELOGs yet but we will be +exciting features including a new session sharing system. There are a whole host +of other changes that have not been tracked CHANGELOGs yet but we will be reporting more granular updates with our later releases! - [@jbrowse/web@0.0.1-beta.27](https://github.com/GMOD/jbrowse-components/releases/tag/@jbrowse/web@0.0.1-beta.27) -To install, you can download the link above, or you can use the jbrowse CLI -tool to automatically download the latest version. See the [jbrowse 2 -quick-start guide](https://jbrowse.org/jb2/docs/quickstart_web) for more info +To install, you can download the link above, or you can use the jbrowse CLI tool +to automatically download the latest version. See the +[jbrowse 2 quick-start guide](https://jbrowse.org/jb2/docs/quickstart_web) for +more info diff --git a/website/blog/2020-10-31-jbrowse-web-0.0.1-beta.28-release.md b/website/blog/2020-10-31-jbrowse-web-0.0.1-beta.28-release.md index 4841f102b0..282b5d35c9 100644 --- a/website/blog/2020-10-31-jbrowse-web-0.0.1-beta.28-release.md +++ b/website/blog/2020-10-31-jbrowse-web-0.0.1-beta.28-release.md @@ -31,6 +31,7 @@ Enjoy! - [@jbrowse/web@0.0.1-beta.28](https://github.com/GMOD/jbrowse-components/releases/tag/@jbrowse/web@0.0.1-beta.28) -To install, you can download the link above, or you can use the jbrowse CLI -tool to automatically download the latest version. See the [jbrowse 2 -quick-start guide](https://jbrowse.org/jb2/docs/quickstart_web) for more info +To install, you can download the link above, or you can use the jbrowse CLI tool +to automatically download the latest version. See the +[jbrowse 2 quick-start guide](https://jbrowse.org/jb2/docs/quickstart_web) for +more info diff --git a/website/blog/2020-11-05-jbrowse-web-1.0.0-release.md b/website/blog/2020-11-05-jbrowse-web-1.0.0-release.md index 668afec6f4..3fedeb8c8a 100644 --- a/website/blog/2020-11-05-jbrowse-web-1.0.0-release.md +++ b/website/blog/2020-11-05-jbrowse-web-1.0.0-release.md @@ -6,33 +6,31 @@ tags: ['release', 'jbrowse 2'] I am pleased to announce the first stable release of JBrowse 2! -This release includes our new "display modes" concept which allows the -same track to be displayed in different view types. For example, the same -synteny track can be used in both a dotplot or a linear synteny view. -Similarly, a SV VCF with breakends can be used in the circular view or a -linear genome view. +This release includes our new "display modes" concept which allows the same +track to be displayed in different view types. For example, the same synteny +track can be used in both a dotplot or a linear synteny view. Similarly, a SV +VCF with breakends can be used in the circular view or a linear genome view. -This has been a massive effort by the team to get us to this 1.0.0 release, -and we greatly thank all the beta users who have helped us with testing. +This has been a massive effort by the team to get us to this 1.0.0 release, and +we greatly thank all the beta users who have helped us with testing. Changes - fixed bug with reference sequences that don't use the alias system - fixed bug with SV inspector having a disabled state stuck on the buttons - added documentation for the `jbrowse admin-server` command -- added display modes, a giant effort to make the same track visible in - multiple contexts +- added display modes, a giant effort to make the same track visible in multiple + contexts - added a splash screen when no default session is in the config file - changed error state of spreadsheet to a volatile - fixed loading state of the RefNameAutocomplete - fixed spreadsheet import of VCF with no FORMAT column -- made a small bundle-size improvement from removing unused crypto-js - resources +- made a small bundle-size improvement from removing unused crypto-js resources - removed savedSessions from config schema - fixed deleting a track when a closed widget references it - fixed crash when live editing an assembly in the assembly manager -- added a simple PAF import form in the DotplotView and LinearSyntenyView - import forms +- added a simple PAF import form in the DotplotView and LinearSyntenyView import + forms - updated @mui/material version - clearer output printed when using admin-server @@ -40,6 +38,7 @@ Enjoy! - [@jbrowse/web@1.0.0](https://github.com/GMOD/jbrowse-components/releases/tag/@jbrowse/web@1.0.0) -To install, you can download the link above, or you can use the jbrowse CLI -tool to automatically download the latest version. See the [jbrowse 2 -quick-start guide](https://jbrowse.org/jb2/docs/quickstart_web) for more info +To install, you can download the link above, or you can use the jbrowse CLI tool +to automatically download the latest version. See the +[jbrowse 2 quick-start guide](https://jbrowse.org/jb2/docs/quickstart_web) for +more info diff --git a/website/blog/2020-11-25-v1.0.1-release.md b/website/blog/2020-11-25-v1.0.1-release.md index 5c2e804531..4e90bce7a2 100644 --- a/website/blog/2020-11-25-v1.0.1-release.md +++ b/website/blog/2020-11-25-v1.0.1-release.md @@ -70,51 +70,107 @@ on NPM. #### :rocket: Enhancement - Other - - [#1462](https://github.com/GMOD/jbrowse-components/pull/1462) Allow importing gzip and bgzip files in the spreadsheet and SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support for more bigBed subtypes and fallback for unsupported types ([@peterkxie](https://github.com/peterkxie)) - - [#1455](https://github.com/GMOD/jbrowse-components/pull/1455) Add the ability to use connection across refreshes in jbrowse-web using session connections ([@peterkxie](https://github.com/peterkxie)) - - [#1439](https://github.com/GMOD/jbrowse-components/pull/1439) 1381 improve assembly add form ([@elliothershberg](https://github.com/elliothershberg)) - - [#1433](https://github.com/GMOD/jbrowse-components/pull/1433) Make add track warning a bit more lenient ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1420](https://github.com/GMOD/jbrowse-components/pull/1420) Add the assembly manager feature to jbrowse-desktop ([@elliothershberg](https://github.com/elliothershberg)) + - [#1462](https://github.com/GMOD/jbrowse-components/pull/1462) Allow + importing gzip and bgzip files in the spreadsheet and SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support + for more bigBed subtypes and fallback for unsupported types + ([@peterkxie](https://github.com/peterkxie)) + - [#1455](https://github.com/GMOD/jbrowse-components/pull/1455) Add the + ability to use connection across refreshes in jbrowse-web using session + connections ([@peterkxie](https://github.com/peterkxie)) + - [#1439](https://github.com/GMOD/jbrowse-components/pull/1439) 1381 improve + assembly add form ([@elliothershberg](https://github.com/elliothershberg)) + - [#1433](https://github.com/GMOD/jbrowse-components/pull/1433) Make add track + warning a bit more lenient + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1420](https://github.com/GMOD/jbrowse-components/pull/1420) Add the + assembly manager feature to jbrowse-desktop + ([@elliothershberg](https://github.com/elliothershberg)) - `core` - - [#1458](https://github.com/GMOD/jbrowse-components/pull/1458) Add three frame translation to the sequence track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1453](https://github.com/GMOD/jbrowse-components/pull/1453) Change "Factory reset" to "Reset session" in jbrowse-web ([@teresam856](https://github.com/teresam856)) - - [#1441](https://github.com/GMOD/jbrowse-components/pull/1441) New icon for the track selector ([@cmdcolin](https://github.com/cmdcolin)) - - [#1438](https://github.com/GMOD/jbrowse-components/pull/1438) Improve assembly loading time by moving to main thread ([@cmdcolin](https://github.com/cmdcolin)) - - [#1434](https://github.com/GMOD/jbrowse-components/pull/1434) Create separate config schema for ReferenceSequenceTrack ([@elliothershberg](https://github.com/elliothershberg)) + - [#1458](https://github.com/GMOD/jbrowse-components/pull/1458) Add three + frame translation to the sequence track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1453](https://github.com/GMOD/jbrowse-components/pull/1453) Change + "Factory reset" to "Reset session" in jbrowse-web + ([@teresam856](https://github.com/teresam856)) + - [#1441](https://github.com/GMOD/jbrowse-components/pull/1441) New icon for + the track selector ([@cmdcolin](https://github.com/cmdcolin)) + - [#1438](https://github.com/GMOD/jbrowse-components/pull/1438) Improve + assembly loading time by moving to main thread + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1434](https://github.com/GMOD/jbrowse-components/pull/1434) Create + separate config schema for ReferenceSequenceTrack + ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - - [#1491](https://github.com/GMOD/jbrowse-components/pull/1491) Fix ability to add a PAF synteny track with add-track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1470](https://github.com/GMOD/jbrowse-components/pull/1470) Avoid rendering the literal string 'null' in the feature details ([@cmdcolin](https://github.com/cmdcolin)) + - [#1491](https://github.com/GMOD/jbrowse-components/pull/1491) Fix ability to + add a PAF synteny track with add-track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1470](https://github.com/GMOD/jbrowse-components/pull/1470) Avoid + rendering the literal string 'null' in the feature details + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1489](https://github.com/GMOD/jbrowse-components/pull/1489) Fix long read vs ref CIGAR rendering for horizontally flipped synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support for more bigBed subtypes and fallback for unsupported types ([@peterkxie](https://github.com/peterkxie)) - - [#1472](https://github.com/GMOD/jbrowse-components/pull/1472) Wait on assemblies that are being tracked by the assemblyManager only ([@cmdcolin](https://github.com/cmdcolin)) - - [#1466](https://github.com/GMOD/jbrowse-components/pull/1466) Avoid rendering the display and renderer settings in the about this track dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#1461](https://github.com/GMOD/jbrowse-components/pull/1461) Fix usage of jbrowse-cli on node 10.9 related to fs.promises ([@cmdcolin](https://github.com/cmdcolin)) - - [#1452](https://github.com/GMOD/jbrowse-components/pull/1452) Bug: search box disappears from LGV header on smaller widths ([@teresam856](https://github.com/teresam856)) - - [#1432](https://github.com/GMOD/jbrowse-components/pull/1432) Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web ([@teresam856](https://github.com/teresam856)) - - [#1431](https://github.com/GMOD/jbrowse-components/pull/1431) Fix connection tracks not showing up in track selector ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1428](https://github.com/GMOD/jbrowse-components/pull/1428) Fix the listVersions behavior of the jbrowse-cli returning duplicate entries ([@cmdcolin](https://github.com/cmdcolin)) - - [#1422](https://github.com/GMOD/jbrowse-components/pull/1422) Fix crash from empty ALT field in VCF ([@cmdcolin](https://github.com/cmdcolin)) - - [#1413](https://github.com/GMOD/jbrowse-components/pull/1413) Fix ability to add CRAM tracks using the web based add-track GUI ([@cmdcolin](https://github.com/cmdcolin)) + - [#1489](https://github.com/GMOD/jbrowse-components/pull/1489) Fix long read + vs ref CIGAR rendering for horizontally flipped synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1460](https://github.com/GMOD/jbrowse-components/pull/1460) Add support + for more bigBed subtypes and fallback for unsupported types + ([@peterkxie](https://github.com/peterkxie)) + - [#1472](https://github.com/GMOD/jbrowse-components/pull/1472) Wait on + assemblies that are being tracked by the assemblyManager only + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1466](https://github.com/GMOD/jbrowse-components/pull/1466) Avoid + rendering the display and renderer settings in the about this track dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1461](https://github.com/GMOD/jbrowse-components/pull/1461) Fix usage of + jbrowse-cli on node 10.9 related to fs.promises + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1452](https://github.com/GMOD/jbrowse-components/pull/1452) Bug: search + box disappears from LGV header on smaller widths + ([@teresam856](https://github.com/teresam856)) + - [#1432](https://github.com/GMOD/jbrowse-components/pull/1432) Make global + variables window.JBrowseSession and window.JBrowseRootModel available in + jbrowse-web ([@teresam856](https://github.com/teresam856)) + - [#1431](https://github.com/GMOD/jbrowse-components/pull/1431) Fix connection + tracks not showing up in track selector + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1428](https://github.com/GMOD/jbrowse-components/pull/1428) Fix the + listVersions behavior of the jbrowse-cli returning duplicate entries + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1422](https://github.com/GMOD/jbrowse-components/pull/1422) Fix crash from + empty ALT field in VCF ([@cmdcolin](https://github.com/cmdcolin)) + - [#1413](https://github.com/GMOD/jbrowse-components/pull/1413) Fix ability to + add CRAM tracks using the web based add-track GUI + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1435](https://github.com/GMOD/jbrowse-components/pull/1435) Updates to quickstart guides ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#1435](https://github.com/GMOD/jbrowse-components/pull/1435) Updates to + quickstart guides ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - Other - - [#1437](https://github.com/GMOD/jbrowse-components/pull/1437) Use lerna-changelog for changelog generation ([@cmdcolin](https://github.com/cmdcolin)) - - [#1465](https://github.com/GMOD/jbrowse-components/pull/1465) Establish minimum node version of 10.4 for using jbrowse-cli tools ([@cmdcolin](https://github.com/cmdcolin)) - - [#1454](https://github.com/GMOD/jbrowse-components/pull/1454) Fix GH workflow build ([@elliothershberg](https://github.com/elliothershberg)) - - [#1448](https://github.com/GMOD/jbrowse-components/pull/1448) Move building and testing from Travis to GitHub Workflow ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1450](https://github.com/GMOD/jbrowse-components/pull/1450) Fix website build ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1437](https://github.com/GMOD/jbrowse-components/pull/1437) Use + lerna-changelog for changelog generation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1465](https://github.com/GMOD/jbrowse-components/pull/1465) Establish + minimum node version of 10.4 for using jbrowse-cli tools + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1454](https://github.com/GMOD/jbrowse-components/pull/1454) Fix GH + workflow build ([@elliothershberg](https://github.com/elliothershberg)) + - [#1448](https://github.com/GMOD/jbrowse-components/pull/1448) Move building + and testing from Travis to GitHub Workflow + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1450](https://github.com/GMOD/jbrowse-components/pull/1450) Fix website + build ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#1468](https://github.com/GMOD/jbrowse-components/pull/1468) Have assembly manager get plugin manager from factory function args ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1468](https://github.com/GMOD/jbrowse-components/pull/1468) Have assembly + manager get plugin manager from factory function args + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 5 diff --git a/website/blog/2020-12-02-v1.0.2-release.md b/website/blog/2020-12-02-v1.0.2-release.md index 78a7146f28..2c82ab410b 100644 --- a/website/blog/2020-12-02-v1.0.2-release.md +++ b/website/blog/2020-12-02-v1.0.2-release.md @@ -69,19 +69,33 @@ on NPM. #### :rocket: Enhancement - `core` - - [#1513](https://github.com/GMOD/jbrowse-components/pull/1513) Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX ([@elliothershberg](https://github.com/elliothershberg)) + - [#1513](https://github.com/GMOD/jbrowse-components/pull/1513) Add a custom + scrollbar that overrides the auto-hiding behavior of scrollbars on OSX + ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - Other - - [#1514](https://github.com/GMOD/jbrowse-components/pull/1514) react-linear-genome-view bug fixes ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1517](https://github.com/GMOD/jbrowse-components/pull/1517) Fix the use of filtering display on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#1512](https://github.com/GMOD/jbrowse-components/pull/1512) Fix setting maxDisplayedBpPerPx for pileup display, helps prevent too large an area from being rendered ([@cmdcolin](https://github.com/cmdcolin)) - - [#1442](https://github.com/GMOD/jbrowse-components/pull/1442) Change track selector togglebutton to normal button ([@cmdcolin](https://github.com/cmdcolin)) - - [#1506](https://github.com/GMOD/jbrowse-components/pull/1506) Fix horizontally flipped translation frames position ([@cmdcolin](https://github.com/cmdcolin)) - - [#1501](https://github.com/GMOD/jbrowse-components/pull/1501) Fix CLI to allow jbrowse create to download newer monorepo tag format ([@cmdcolin](https://github.com/cmdcolin)) + - [#1514](https://github.com/GMOD/jbrowse-components/pull/1514) + react-linear-genome-view bug fixes + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1517](https://github.com/GMOD/jbrowse-components/pull/1517) Fix the use of + filtering display on desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#1512](https://github.com/GMOD/jbrowse-components/pull/1512) Fix setting + maxDisplayedBpPerPx for pileup display, helps prevent too large an area from + being rendered ([@cmdcolin](https://github.com/cmdcolin)) + - [#1442](https://github.com/GMOD/jbrowse-components/pull/1442) Change track + selector togglebutton to normal button + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1506](https://github.com/GMOD/jbrowse-components/pull/1506) Fix + horizontally flipped translation frames position + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1501](https://github.com/GMOD/jbrowse-components/pull/1501) Fix CLI to + allow jbrowse create to download newer monorepo tag format + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#1505](https://github.com/GMOD/jbrowse-components/pull/1505) Fix loading of local files in jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#1505](https://github.com/GMOD/jbrowse-components/pull/1505) Fix loading of + local files in jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 diff --git a/website/blog/2021-01-11-v1.0.3-release.md b/website/blog/2021-01-11-v1.0.3-release.md index 7a923f5873..a6323e41ad 100644 --- a/website/blog/2021-01-11-v1.0.3-release.md +++ b/website/blog/2021-01-11-v1.0.3-release.md @@ -4,13 +4,17 @@ date: 2021-01-11 tags: ['release', 'jbrowse 2'] --- -This release of JBrowse Web includes several improvements and bug fixes, including: +This release of JBrowse Web includes several improvements and bug fixes, +including: -- Search and dropdown combined into single intuitive component on linear genome view +- Search and dropdown combined into single intuitive component on linear genome + view - Big alignment track enhancements - Added sort by tag to sorting options - - Added ability to color by preset options such as "base pair", "mapping quality", and "tag" - - Added ability to filter by preset options such as "read paired" and "read reverse strand" + - Added ability to color by preset options such as "base pair", "mapping + quality", and "tag" + - Added ability to filter by preset options such as "read paired" and "read + reverse strand" - Feature detail widget now shows subfeature details - Added --branch and --nightly flags for create and upgrade CLI commands - Improved admin server GUI @@ -19,9 +23,8 @@ This release of JBrowse Web includes several improvements and bug fixes, includi - Improved build system for external plugins (check out our new plugin template at https://github.com/GMOD/jbrowse-plugin-template) -![](/img/color_by_tag.png) -Figure showing the new feature for "color by tag" and "sort by tag" applied to -a CRAM file +![](/img/color_by_tag.png) Figure showing the new feature for "color by tag" and +"sort by tag" applied to a CRAM file ## Downloads @@ -72,61 +75,143 @@ on NPM. #### :rocket: Enhancement - Other - - [#1560](https://github.com/GMOD/jbrowse-components/pull/1560) Provide a dialog to add extra genomic context for linear read vs. ref visualization ([@elliothershberg](https://github.com/elliothershberg)) - - [#1604](https://github.com/GMOD/jbrowse-components/pull/1604) Add ability to filter for read name to the alignments filter dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#1599](https://github.com/GMOD/jbrowse-components/pull/1599) Replace 'show all regions' with 'show all regions in assembly' ([@cmdcolin](https://github.com/cmdcolin)) - - [#1595](https://github.com/GMOD/jbrowse-components/pull/1595) Admin server GUI enhancements ([@elliothershberg](https://github.com/elliothershberg)) - - [#1584](https://github.com/GMOD/jbrowse-components/pull/1584) Restructure demo page and release cancer demo ([@elliothershberg](https://github.com/elliothershberg)) - - [#1579](https://github.com/GMOD/jbrowse-components/pull/1579) Create --branch and --nightly flags for `jbrowse create` and `jbrowse upgrade` commands ([@cmdcolin](https://github.com/cmdcolin)) - - [#1575](https://github.com/GMOD/jbrowse-components/pull/1575) Improve mobx-state-tree type validation errors ([@cmdcolin](https://github.com/cmdcolin)) - - [#1574](https://github.com/GMOD/jbrowse-components/pull/1574) Make softclip indicator black if no seq available ([@cmdcolin](https://github.com/cmdcolin)) - - [#1554](https://github.com/GMOD/jbrowse-components/pull/1554) Coloring options with simple color for tag ([@peterkxie](https://github.com/peterkxie)) - - [#1565](https://github.com/GMOD/jbrowse-components/pull/1565) Rename jbrowse cli add-track --type to --trackType ([@cmdcolin](https://github.com/cmdcolin)) - - [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) - - [#1533](https://github.com/GMOD/jbrowse-components/pull/1533) Display file headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix package versions ([@cmdcolin](https://github.com/cmdcolin)) - - [#1541](https://github.com/GMOD/jbrowse-components/pull/1541) Add more info about adding a PAF file to the synteny import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#1509](https://github.com/GMOD/jbrowse-components/pull/1509) Combine Search and Dropdown component on LGV ([@teresam856](https://github.com/teresam856)) - - [#1530](https://github.com/GMOD/jbrowse-components/pull/1530) Add spreadsheet filter support for derived columns ([@elliothershberg](https://github.com/elliothershberg)) - - [#1483](https://github.com/GMOD/jbrowse-components/pull/1483) Add session export to and import from file ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1519](https://github.com/GMOD/jbrowse-components/pull/1519) Add autoSql to the bigBed "About this track" dialog ([@cmdcolin](https://github.com/cmdcolin)) + - [#1560](https://github.com/GMOD/jbrowse-components/pull/1560) Provide a + dialog to add extra genomic context for linear read vs. ref visualization + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1604](https://github.com/GMOD/jbrowse-components/pull/1604) Add ability to + filter for read name to the alignments filter dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1599](https://github.com/GMOD/jbrowse-components/pull/1599) Replace 'show + all regions' with 'show all regions in assembly' + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1595](https://github.com/GMOD/jbrowse-components/pull/1595) Admin server + GUI enhancements ([@elliothershberg](https://github.com/elliothershberg)) + - [#1584](https://github.com/GMOD/jbrowse-components/pull/1584) Restructure + demo page and release cancer demo + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1579](https://github.com/GMOD/jbrowse-components/pull/1579) Create + --branch and --nightly flags for `jbrowse create` and `jbrowse upgrade` + commands ([@cmdcolin](https://github.com/cmdcolin)) + - [#1575](https://github.com/GMOD/jbrowse-components/pull/1575) Improve + mobx-state-tree type validation errors + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1574](https://github.com/GMOD/jbrowse-components/pull/1574) Make softclip + indicator black if no seq available + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1554](https://github.com/GMOD/jbrowse-components/pull/1554) Coloring + options with simple color for tag + ([@peterkxie](https://github.com/peterkxie)) + - [#1565](https://github.com/GMOD/jbrowse-components/pull/1565) Rename jbrowse + cli add-track --type to --trackType + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for + sequence track, variant track, launching synteny from dotplot, and add UCSC + plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) + - [#1533](https://github.com/GMOD/jbrowse-components/pull/1533) Display file + headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix + package versions ([@cmdcolin](https://github.com/cmdcolin)) + - [#1541](https://github.com/GMOD/jbrowse-components/pull/1541) Add more info + about adding a PAF file to the synteny import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1509](https://github.com/GMOD/jbrowse-components/pull/1509) Combine Search + and Dropdown component on LGV ([@teresam856](https://github.com/teresam856)) + - [#1530](https://github.com/GMOD/jbrowse-components/pull/1530) Add + spreadsheet filter support for derived columns + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1483](https://github.com/GMOD/jbrowse-components/pull/1483) Add session + export to and import from file + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1519](https://github.com/GMOD/jbrowse-components/pull/1519) Add autoSql to + the bigBed "About this track" dialog + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#1531](https://github.com/GMOD/jbrowse-components/pull/1531) Add track menu options for autoscale, log scale, histogram fill, setting min/max score, and zoom level/resolution for wiggle/snpcoverage tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1473](https://github.com/GMOD/jbrowse-components/pull/1473) Color, filter, and sort options for the alignments ([@cmdcolin](https://github.com/cmdcolin)) - - [#1576](https://github.com/GMOD/jbrowse-components/pull/1576) Add location string to tooltip for wiggle and SNPCoverage tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1529](https://github.com/GMOD/jbrowse-components/pull/1529) Display subfeatures in feature details widget ([@cmdcolin](https://github.com/cmdcolin)) + - [#1531](https://github.com/GMOD/jbrowse-components/pull/1531) Add track menu + options for autoscale, log scale, histogram fill, setting min/max score, and + zoom level/resolution for wiggle/snpcoverage tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1473](https://github.com/GMOD/jbrowse-components/pull/1473) Color, filter, + and sort options for the alignments + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1576](https://github.com/GMOD/jbrowse-components/pull/1576) Add location + string to tooltip for wiggle and SNPCoverage tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1529](https://github.com/GMOD/jbrowse-components/pull/1529) Display + subfeatures in feature details widget + ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `development-tools` - - [#1578](https://github.com/GMOD/jbrowse-components/pull/1578) Update build system for external plugins ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1578](https://github.com/GMOD/jbrowse-components/pull/1578) Update build + system for external plugins + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#1608](https://github.com/GMOD/jbrowse-components/pull/1608) Take into account offsetX of the rubberband on scalebar zooming ([@cmdcolin](https://github.com/cmdcolin)) - - [#1597](https://github.com/GMOD/jbrowse-components/pull/1597) Fix crash when there are undefined references in the state tree e.g. when a track is deleted but still referred to by a session ([@peterkxie](https://github.com/peterkxie)) - - [#1598](https://github.com/GMOD/jbrowse-components/pull/1598) Disable 'copy to clipboard' while share url being generated ([@peterkxie](https://github.com/peterkxie)) - - [#1589](https://github.com/GMOD/jbrowse-components/pull/1589) Fix the display of trackhub registry results ([@cmdcolin](https://github.com/cmdcolin)) - - [#1573](https://github.com/GMOD/jbrowse-components/pull/1573) Update hic-straw to fix error for hic files with many scaffolds ([@cmdcolin](https://github.com/cmdcolin)) - - [#1563](https://github.com/GMOD/jbrowse-components/pull/1563) Remove softclip and hardclip from being counted as SNPs in the SNPCoverage ([@cmdcolin](https://github.com/cmdcolin)) - - [#1559](https://github.com/GMOD/jbrowse-components/pull/1559) Avoid errors from breakpoint split view related to getBoundingClientRect on null track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1540](https://github.com/GMOD/jbrowse-components/pull/1540) Fix memory leak when side scrolling LGV blocks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1534](https://github.com/GMOD/jbrowse-components/pull/1534) Fix breakpoint split view showing too many connections for paired end ends ([@cmdcolin](https://github.com/cmdcolin)) - - [#1524](https://github.com/GMOD/jbrowse-components/pull/1524) Move loading flag for spreadsheet import wizard to volatile to avoid it persisting across refresh ([@cmdcolin](https://github.com/cmdcolin)) - - [#1521](https://github.com/GMOD/jbrowse-components/pull/1521) Add missing dep to react-linear-genome-view ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1608](https://github.com/GMOD/jbrowse-components/pull/1608) Take into + account offsetX of the rubberband on scalebar zooming + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1597](https://github.com/GMOD/jbrowse-components/pull/1597) Fix crash when + there are undefined references in the state tree e.g. when a track is + deleted but still referred to by a session + ([@peterkxie](https://github.com/peterkxie)) + - [#1598](https://github.com/GMOD/jbrowse-components/pull/1598) Disable 'copy + to clipboard' while share url being generated + ([@peterkxie](https://github.com/peterkxie)) + - [#1589](https://github.com/GMOD/jbrowse-components/pull/1589) Fix the + display of trackhub registry results + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1573](https://github.com/GMOD/jbrowse-components/pull/1573) Update + hic-straw to fix error for hic files with many scaffolds + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1563](https://github.com/GMOD/jbrowse-components/pull/1563) Remove + softclip and hardclip from being counted as SNPs in the SNPCoverage + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1559](https://github.com/GMOD/jbrowse-components/pull/1559) Avoid errors + from breakpoint split view related to getBoundingClientRect on null track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1540](https://github.com/GMOD/jbrowse-components/pull/1540) Fix memory + leak when side scrolling LGV blocks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1534](https://github.com/GMOD/jbrowse-components/pull/1534) Fix breakpoint + split view showing too many connections for paired end ends + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1524](https://github.com/GMOD/jbrowse-components/pull/1524) Move loading + flag for spreadsheet import wizard to volatile to avoid it persisting across + refresh ([@cmdcolin](https://github.com/cmdcolin)) + - [#1521](https://github.com/GMOD/jbrowse-components/pull/1521) Add missing + dep to react-linear-genome-view + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#1587](https://github.com/GMOD/jbrowse-components/pull/1587) Fix positioning of scalebar tooltips, overview scalebar plotting, and refName label positioning when displaying many regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#1547](https://github.com/GMOD/jbrowse-components/pull/1547) Fix analytics crashing when using plugins ([@cmdcolin](https://github.com/cmdcolin)) + - [#1587](https://github.com/GMOD/jbrowse-components/pull/1587) Fix + positioning of scalebar tooltips, overview scalebar plotting, and refName + label positioning when displaying many regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1547](https://github.com/GMOD/jbrowse-components/pull/1547) Fix analytics + crashing when using plugins ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1594](https://github.com/GMOD/jbrowse-components/pull/1594) Add GFF3 example to quickstart ([@cmdcolin](https://github.com/cmdcolin)) -- [#1581](https://github.com/GMOD/jbrowse-components/pull/1581) Add some features that are missing from jbrowse 2 to the feature comparison table ([@cmdcolin](https://github.com/cmdcolin)) -- [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) -- [#1537](https://github.com/GMOD/jbrowse-components/pull/1537) Add CONTRIBUTING.md with tips for getting started with codebase ([@cmdcolin](https://github.com/cmdcolin)) +- [#1594](https://github.com/GMOD/jbrowse-components/pull/1594) Add GFF3 example + to quickstart ([@cmdcolin](https://github.com/cmdcolin)) +- [#1581](https://github.com/GMOD/jbrowse-components/pull/1581) Add some + features that are missing from jbrowse 2 to the feature comparison table + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1558](https://github.com/GMOD/jbrowse-components/pull/1558) Add docs for + sequence track, variant track, launching synteny from dotplot, and add UCSC + plugin to demo ([@cmdcolin](https://github.com/cmdcolin)) +- [#1537](https://github.com/GMOD/jbrowse-components/pull/1537) Add + CONTRIBUTING.md with tips for getting started with codebase + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#1606](https://github.com/GMOD/jbrowse-components/pull/1606) Upgrade @testing-library/react and improve test reliability ([@cmdcolin](https://github.com/cmdcolin)) -- [#1555](https://github.com/GMOD/jbrowse-components/pull/1555) Remove the TextDecoder/TextEncoder polyfill ([@cmdcolin](https://github.com/cmdcolin)) -- [#1522](https://github.com/GMOD/jbrowse-components/pull/1522) Update oclif and remove now unnecessary file copy ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#1606](https://github.com/GMOD/jbrowse-components/pull/1606) Upgrade + @testing-library/react and improve test reliability + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1555](https://github.com/GMOD/jbrowse-components/pull/1555) Remove the + TextDecoder/TextEncoder polyfill ([@cmdcolin](https://github.com/cmdcolin)) +- [#1522](https://github.com/GMOD/jbrowse-components/pull/1522) Update oclif and + remove now unnecessary file copy + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 6 diff --git a/website/blog/2021-02-22-JBrowseR-release.md b/website/blog/2021-02-22-JBrowseR-release.md index b2e2a52e47..0c001c3ba3 100644 --- a/website/blog/2021-02-22-JBrowseR-release.md +++ b/website/blog/2021-02-22-JBrowseR-release.md @@ -5,26 +5,26 @@ tags: ['jbrowse 2', 'JBrowseR'] --- We are excited to announce a new JBrowse 2 product: -[JBrowseR](https://gmod.github.io/JBrowseR/). -JBrowseR builds on top of the +[JBrowseR](https://gmod.github.io/JBrowseR/). JBrowseR builds on top of the [React component](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) -that we recently released. -Our React component inherits the general JBrowse 2 philosophy: it is -fully customizable and pluggable, like the core product. +that we recently released. Our React component inherits the general JBrowse 2 +philosophy: it is fully customizable and pluggable, like the core product. -The React component makes it very straightforward to embed a Linear -Genome View into a React app. However, this API can come with a steep -learning curve for bioinformaticians who may not be very familiar with -React. This is where JBrowseR comes in! +The React component makes it very straightforward to embed a Linear Genome View +into a React app. However, this API can come with a steep learning curve for +bioinformaticians who may not be very familiar with React. This is where +JBrowseR comes in! -JBrowseR provides an R interface to the JBrowse 2 LGV React component. -Using JBrowseR, you can: +JBrowseR provides an R interface to the JBrowse 2 LGV React component. Using +JBrowseR, you can: -- Embed the JBrowse 2 genome browser in **R Markdown** documents and **Shiny** applications +- Embed the JBrowse 2 genome browser in **R Markdown** documents and **Shiny** + applications - Deploy a genome browser directly from the R console to view your data - Customize your genome browser to display your own data -With this functionality, you can deploy a first-class genome browser with your data in just a few lines of R code! +With this functionality, you can deploy a first-class genome browser with your +data in just a few lines of R code! For more information on getting started, check out the following resources: diff --git a/website/blog/2021-03-08-v1.0.4-release.md b/website/blog/2021-03-08-v1.0.4-release.md index 7792140e66..f75263bf9a 100644 --- a/website/blog/2021-03-08-v1.0.4-release.md +++ b/website/blog/2021-03-08-v1.0.4-release.md @@ -4,37 +4,49 @@ date: 2021-03-08 tags: ['release', 'jbrowse 2'] --- -This release of JBrowse Web includes a _great_ many small improvements and bug fixes, see the full changelog below. +This release of JBrowse Web includes a _great_ many small improvements and bug +fixes, see the full changelog below. Some particularly salient improvements include: ## Better indications for insertions -The alignments track received a couple updates including "large insertion indicators" for large indels, and also an upside-down count of clipping or insertion events. There is also a triangular indicator plotted when the insertion/clip count exceeds a threshold at that position defaulted to 30% of reads +The alignments track received a couple updates including "large insertion +indicators" for large indels, and also an upside-down count of clipping or +insertion events. There is also a triangular indicator plotted when the +insertion/clip count exceeds a threshold at that position defaulted to 30% of +reads ![](/img/insertion_indicators.png) ## Click and drag the overview bar to "Get sequence" -Users can now download regions of sequence by selecting a region in the linear genome view and clicking "get sequence". See the demonstration video below: +Users can now download regions of sequence by selecting a region in the linear +genome view and clicking "get sequence". See the demonstration video below: -You can also "get sequence" in the read vs reference view, which allows you to "get sequence" for the inserted bases or softclipped bases from a read alignment +You can also "get sequence" in the read vs reference view, which allows you to +"get sequence" for the inserted bases or softclipped bases from a read alignment ![](/img/read_vs_ref_insertion.png) -A long-requested feature, implemented in [#1588](https://github.com/GMOD/jbrowse-components/pull/1588) by [@teresam856](https://github.com/teresam856)! +A long-requested feature, implemented in +[#1588](https://github.com/GMOD/jbrowse-components/pull/1588) by +[@teresam856](https://github.com/teresam856)! ## Enhanced navigation of paired end reads and BND/TRA breakends -Feature detail panels for BND/TRA features, long split-alignments, and paired-end reads have links to navigate or popup of the breakpoint split views with their mates. +Feature detail panels for BND/TRA features, long split-alignments, and +paired-end reads have links to navigate or popup of the breakpoint split views +with their mates. ![](/img/link_to_split_view.png) -Implemented by [@cmdcolin](https://github.com/cmdcolin) in [#1701](https://github.com/GMOD/jbrowse-components/pull/1701). +Implemented by [@cmdcolin](https://github.com/cmdcolin) in +[#1701](https://github.com/GMOD/jbrowse-components/pull/1701). ## Downloads @@ -88,90 +100,213 @@ on NPM. #### :rocket: Enhancement - `core` - - [#1758](https://github.com/GMOD/jbrowse-components/pull/1758) Add ability to get stitched together CDS, protein, and cDNA sequences in feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1721](https://github.com/GMOD/jbrowse-components/pull/1721) Manually adjust feature height and spacing on alignments track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1728](https://github.com/GMOD/jbrowse-components/pull/1728) Add list of loaded plugins to the "About widget" ([@rbuels](https://github.com/rbuels)) - - [#1711](https://github.com/GMOD/jbrowse-components/pull/1711) Add plugin top-level configuration ([@teresam856](https://github.com/teresam856)) - - [#1699](https://github.com/GMOD/jbrowse-components/pull/1699) Add sequence track for both read and reference genome in the "Linear read vs ref" comparison ([@cmdcolin](https://github.com/cmdcolin)) - - [#1701](https://github.com/GMOD/jbrowse-components/pull/1701) Add clickable navigation links to supplementary alignments/paired ends locations and BND/TRA endpoints in detail widgets ([@cmdcolin](https://github.com/cmdcolin)) - - [#1601](https://github.com/GMOD/jbrowse-components/pull/1601) Add ability to color by per-base quality in alignment tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1640](https://github.com/GMOD/jbrowse-components/pull/1640) Move stats calculation to BaseFeatureAdapter ([@cmdcolin](https://github.com/cmdcolin)) - - [#1588](https://github.com/GMOD/jbrowse-components/pull/1588) Add "Get sequence" action to LGV rubber-band ([@teresam856](https://github.com/teresam856)) + - [#1758](https://github.com/GMOD/jbrowse-components/pull/1758) Add ability to + get stitched together CDS, protein, and cDNA sequences in feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1721](https://github.com/GMOD/jbrowse-components/pull/1721) Manually + adjust feature height and spacing on alignments track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1728](https://github.com/GMOD/jbrowse-components/pull/1728) Add list of + loaded plugins to the "About widget" ([@rbuels](https://github.com/rbuels)) + - [#1711](https://github.com/GMOD/jbrowse-components/pull/1711) Add plugin + top-level configuration ([@teresam856](https://github.com/teresam856)) + - [#1699](https://github.com/GMOD/jbrowse-components/pull/1699) Add sequence + track for both read and reference genome in the "Linear read vs ref" + comparison ([@cmdcolin](https://github.com/cmdcolin)) + - [#1701](https://github.com/GMOD/jbrowse-components/pull/1701) Add clickable + navigation links to supplementary alignments/paired ends locations and + BND/TRA endpoints in detail widgets + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1601](https://github.com/GMOD/jbrowse-components/pull/1601) Add ability to + color by per-base quality in alignment tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1640](https://github.com/GMOD/jbrowse-components/pull/1640) Move stats + calculation to BaseFeatureAdapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#1588](https://github.com/GMOD/jbrowse-components/pull/1588) Add "Get + sequence" action to LGV rubber-band + ([@teresam856](https://github.com/teresam856)) - Other - - [#1743](https://github.com/GMOD/jbrowse-components/pull/1743) Add color picker and choice of summary score style for wiggle track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1763](https://github.com/GMOD/jbrowse-components/pull/1763) Add a "CSS reset" to jbrowse-react-linear-genome-view to prevent parent styles from outside the component leaking in ([@cmdcolin](https://github.com/cmdcolin)) - - [#1756](https://github.com/GMOD/jbrowse-components/pull/1756) Split alignments track menu items into "Pileup" and "SNPCoverage" submenus ([@cmdcolin](https://github.com/cmdcolin)) - - [#1742](https://github.com/GMOD/jbrowse-components/pull/1742) Add ability to display crosshatches on the wiggle line/xyplot renderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) - - [#1394](https://github.com/GMOD/jbrowse-components/pull/1394) Add new menu items for show/hide feature labels, set max height, and set compact display mode ([@cmdcolin](https://github.com/cmdcolin)) - - [#1720](https://github.com/GMOD/jbrowse-components/pull/1720) Standardize phred qual scaling between BAM and CRAM and add option to make mismatches render in a lighter color when quality is low ([@cmdcolin](https://github.com/cmdcolin)) - - [#1704](https://github.com/GMOD/jbrowse-components/pull/1704) Add "Show all regions in assembly" to import form and make import form show entire region when refName selected ([@cmdcolin](https://github.com/cmdcolin)) - - [#1687](https://github.com/GMOD/jbrowse-components/pull/1687) Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events ([@cmdcolin](https://github.com/cmdcolin)) - - [#1695](https://github.com/GMOD/jbrowse-components/pull/1695) Improve zoomed-out display of quantitative displays tracks when bicolor pivot is active ([@cmdcolin](https://github.com/cmdcolin)) - - [#1680](https://github.com/GMOD/jbrowse-components/pull/1680) Add on click functionality to quantitative track features ([@teresam856](https://github.com/teresam856)) - - [#1630](https://github.com/GMOD/jbrowse-components/pull/1630) Get column names from BED tabix files and other utils for external jbrowse-plugin-gwas support ([@cmdcolin](https://github.com/cmdcolin)) - - [#1709](https://github.com/GMOD/jbrowse-components/pull/1709) Improve sorting and filtering in variant detail widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#1688](https://github.com/GMOD/jbrowse-components/pull/1688) Bold insertion indicator for large insertions on pileup track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1669](https://github.com/GMOD/jbrowse-components/pull/1669) Allow plain json encoding of the session in the URL ([@cmdcolin](https://github.com/cmdcolin)) - - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable locstring navigation from LGV import form ([@teresam856](https://github.com/teresam856)) - - [#1655](https://github.com/GMOD/jbrowse-components/pull/1655) Add GFF3Tabix and BEDTabix inference to JB1 connection ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1643](https://github.com/GMOD/jbrowse-components/pull/1643) Add an offset that allows all wiggle y-scalebar labels to be visible ([@cmdcolin](https://github.com/cmdcolin)) - - [#1632](https://github.com/GMOD/jbrowse-components/pull/1632) Displays warnings when receiving a session with custom callbacks ([@peterkxie](https://github.com/peterkxie)) - - [#1615](https://github.com/GMOD/jbrowse-components/pull/1615) Increase pileup maxHeight ([@cmdcolin](https://github.com/cmdcolin)) - - [#1624](https://github.com/GMOD/jbrowse-components/pull/1624) GCContent adapter ([@cmdcolin](https://github.com/cmdcolin)) - - [#1614](https://github.com/GMOD/jbrowse-components/pull/1614) Add insertion and clip indicators to SNPCoverage views (part of Alignments tracks) ([@cmdcolin](https://github.com/cmdcolin)) - - [#1610](https://github.com/GMOD/jbrowse-components/pull/1610) Display error message from dynamodb session sharing error ([@cmdcolin](https://github.com/cmdcolin)) + - [#1743](https://github.com/GMOD/jbrowse-components/pull/1743) Add color + picker and choice of summary score style for wiggle track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1763](https://github.com/GMOD/jbrowse-components/pull/1763) Add a "CSS + reset" to jbrowse-react-linear-genome-view to prevent parent styles from + outside the component leaking in ([@cmdcolin](https://github.com/cmdcolin)) + - [#1756](https://github.com/GMOD/jbrowse-components/pull/1756) Split + alignments track menu items into "Pileup" and "SNPCoverage" submenus + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1742](https://github.com/GMOD/jbrowse-components/pull/1742) Add ability to + display crosshatches on the wiggle line/xyplot renderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI + add-track --load inPlace to put exact contents into the config, add better + CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) + - [#1394](https://github.com/GMOD/jbrowse-components/pull/1394) Add new menu + items for show/hide feature labels, set max height, and set compact display + mode ([@cmdcolin](https://github.com/cmdcolin)) + - [#1720](https://github.com/GMOD/jbrowse-components/pull/1720) Standardize + phred qual scaling between BAM and CRAM and add option to make mismatches + render in a lighter color when quality is low + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1704](https://github.com/GMOD/jbrowse-components/pull/1704) Add "Show all + regions in assembly" to import form and make import form show entire region + when refName selected ([@cmdcolin](https://github.com/cmdcolin)) + - [#1687](https://github.com/GMOD/jbrowse-components/pull/1687) Threshold for + indicators on SNPCoverage + inverted bargraph of interbase counts for + sub-threshold events ([@cmdcolin](https://github.com/cmdcolin)) + - [#1695](https://github.com/GMOD/jbrowse-components/pull/1695) Improve + zoomed-out display of quantitative displays tracks when bicolor pivot is + active ([@cmdcolin](https://github.com/cmdcolin)) + - [#1680](https://github.com/GMOD/jbrowse-components/pull/1680) Add on click + functionality to quantitative track features + ([@teresam856](https://github.com/teresam856)) + - [#1630](https://github.com/GMOD/jbrowse-components/pull/1630) Get column + names from BED tabix files and other utils for external jbrowse-plugin-gwas + support ([@cmdcolin](https://github.com/cmdcolin)) + - [#1709](https://github.com/GMOD/jbrowse-components/pull/1709) Improve + sorting and filtering in variant detail widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1688](https://github.com/GMOD/jbrowse-components/pull/1688) Bold insertion + indicator for large insertions on pileup track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1669](https://github.com/GMOD/jbrowse-components/pull/1669) Allow plain + json encoding of the session in the URL + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable + locstring navigation from LGV import form + ([@teresam856](https://github.com/teresam856)) + - [#1655](https://github.com/GMOD/jbrowse-components/pull/1655) Add GFF3Tabix + and BEDTabix inference to JB1 connection + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1643](https://github.com/GMOD/jbrowse-components/pull/1643) Add an offset + that allows all wiggle y-scalebar labels to be visible + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1632](https://github.com/GMOD/jbrowse-components/pull/1632) Displays + warnings when receiving a session with custom callbacks + ([@peterkxie](https://github.com/peterkxie)) + - [#1615](https://github.com/GMOD/jbrowse-components/pull/1615) Increase + pileup maxHeight ([@cmdcolin](https://github.com/cmdcolin)) + - [#1624](https://github.com/GMOD/jbrowse-components/pull/1624) GCContent + adapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#1614](https://github.com/GMOD/jbrowse-components/pull/1614) Add insertion + and clip indicators to SNPCoverage views (part of Alignments tracks) + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1610](https://github.com/GMOD/jbrowse-components/pull/1610) Display error + message from dynamodb session sharing error + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#1777](https://github.com/GMOD/jbrowse-components/pull/1777) Quick fix for block error ([@cmdcolin](https://github.com/cmdcolin)) - - [#1748](https://github.com/GMOD/jbrowse-components/pull/1748) External plugins load after confirming config warning ([@peterkxie](https://github.com/peterkxie)) - - [#1750](https://github.com/GMOD/jbrowse-components/pull/1750) Fix pileup sorting when using string tag ([@cmdcolin](https://github.com/cmdcolin)) - - [#1747](https://github.com/GMOD/jbrowse-components/pull/1747) Fix the position of the popup menu after rubberband select when there is a margin on the component e.g. in embedded ([@cmdcolin](https://github.com/cmdcolin)) - - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) - - [#1731](https://github.com/GMOD/jbrowse-components/pull/1731) Fix alignment track ability to remember the height of the SNPCoverage subtrack on refresh ([@cmdcolin](https://github.com/cmdcolin)) - - [#1719](https://github.com/GMOD/jbrowse-components/pull/1719) Fix for navigation past end of chromosome ([@cmdcolin](https://github.com/cmdcolin)) - - [#1698](https://github.com/GMOD/jbrowse-components/pull/1698) Fix rendering read vs ref comparisons with CIGAR strings that use = sign matches ([@cmdcolin](https://github.com/cmdcolin)) - - [#1697](https://github.com/GMOD/jbrowse-components/pull/1697) Fix softclipping configuration setting causing bases to be missed ([@cmdcolin](https://github.com/cmdcolin)) - - [#1689](https://github.com/GMOD/jbrowse-components/pull/1689) Disable copy/delete menu items for reference sequence track ([@teresam856](https://github.com/teresam856)) - - [#1682](https://github.com/GMOD/jbrowse-components/pull/1682) Fix parsing of BED and BEDPE files with comment header for spreadsheet view ([@cmdcolin](https://github.com/cmdcolin)) - - [#1679](https://github.com/GMOD/jbrowse-components/pull/1679) Fix issue with using launching the add track widget on views that are not displaying any regions ([@teresam856](https://github.com/teresam856)) - - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable locstring navigation from LGV import form ([@teresam856](https://github.com/teresam856)) - - [#1626](https://github.com/GMOD/jbrowse-components/pull/1626) Bug Fix: specify assembly in locstring ([@teresam856](https://github.com/teresam856)) - - [#1619](https://github.com/GMOD/jbrowse-components/pull/1619) Fix overview scale polygon not appearing properly in some cases ([@cmdcolin](https://github.com/cmdcolin)) + - [#1777](https://github.com/GMOD/jbrowse-components/pull/1777) Quick fix for + block error ([@cmdcolin](https://github.com/cmdcolin)) + - [#1748](https://github.com/GMOD/jbrowse-components/pull/1748) External + plugins load after confirming config warning + ([@peterkxie](https://github.com/peterkxie)) + - [#1750](https://github.com/GMOD/jbrowse-components/pull/1750) Fix pileup + sorting when using string tag ([@cmdcolin](https://github.com/cmdcolin)) + - [#1747](https://github.com/GMOD/jbrowse-components/pull/1747) Fix the + position of the popup menu after rubberband select when there is a margin on + the component e.g. in embedded ([@cmdcolin](https://github.com/cmdcolin)) + - [#1736](https://github.com/GMOD/jbrowse-components/pull/1736) Fix CLI + add-track --load inPlace to put exact contents into the config, add better + CLI example docs ([@cmdcolin](https://github.com/cmdcolin)) + - [#1731](https://github.com/GMOD/jbrowse-components/pull/1731) Fix alignment + track ability to remember the height of the SNPCoverage subtrack on refresh + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1719](https://github.com/GMOD/jbrowse-components/pull/1719) Fix for + navigation past end of chromosome ([@cmdcolin](https://github.com/cmdcolin)) + - [#1698](https://github.com/GMOD/jbrowse-components/pull/1698) Fix rendering + read vs ref comparisons with CIGAR strings that use = sign matches + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1697](https://github.com/GMOD/jbrowse-components/pull/1697) Fix + softclipping configuration setting causing bases to be missed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1689](https://github.com/GMOD/jbrowse-components/pull/1689) Disable + copy/delete menu items for reference sequence track + ([@teresam856](https://github.com/teresam856)) + - [#1682](https://github.com/GMOD/jbrowse-components/pull/1682) Fix parsing of + BED and BEDPE files with comment header for spreadsheet view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1679](https://github.com/GMOD/jbrowse-components/pull/1679) Fix issue with + using launching the add track widget on views that are not displaying any + regions ([@teresam856](https://github.com/teresam856)) + - [#1642](https://github.com/GMOD/jbrowse-components/pull/1642) Enable + locstring navigation from LGV import form + ([@teresam856](https://github.com/teresam856)) + - [#1626](https://github.com/GMOD/jbrowse-components/pull/1626) Bug Fix: + specify assembly in locstring ([@teresam856](https://github.com/teresam856)) + - [#1619](https://github.com/GMOD/jbrowse-components/pull/1619) Fix overview + scale polygon not appearing properly in some cases + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#1714](https://github.com/GMOD/jbrowse-components/pull/1714) Fix ability to add a PAF on initial dotplot view creation ([@cmdcolin](https://github.com/cmdcolin)) - - [#1657](https://github.com/GMOD/jbrowse-components/pull/1657) Fix for track using assembly alias not displaying ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1620](https://github.com/GMOD/jbrowse-components/pull/1620) Add error reporting on a worker failure ([@cmdcolin](https://github.com/cmdcolin)) + - [#1714](https://github.com/GMOD/jbrowse-components/pull/1714) Fix ability to + add a PAF on initial dotplot view creation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1657](https://github.com/GMOD/jbrowse-components/pull/1657) Fix for track + using assembly alias not displaying + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1620](https://github.com/GMOD/jbrowse-components/pull/1620) Add error + reporting on a worker failure ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1725](https://github.com/GMOD/jbrowse-components/pull/1725) JBrowseR release ([@elliothershberg](https://github.com/elliothershberg)) -- [#1677](https://github.com/GMOD/jbrowse-components/pull/1677) Config guide updates ([@elliothershberg](https://github.com/elliothershberg)) -- [#1665](https://github.com/GMOD/jbrowse-components/pull/1665) Add Nextstrain COVID storybook ([@elliothershberg](https://github.com/elliothershberg)) -- [#1670](https://github.com/GMOD/jbrowse-components/pull/1670) typo in developer guide docs ([@teresam856](https://github.com/teresam856)) -- [#1592](https://github.com/GMOD/jbrowse-components/pull/1592) Website copy edits ([@rbuels](https://github.com/rbuels)) -- [#1646](https://github.com/GMOD/jbrowse-components/pull/1646) Fix "See code" link in CLI docs ([@garrettjstevens](https://github.com/garrettjstevens)) -- [#1618](https://github.com/GMOD/jbrowse-components/pull/1618) Add whole-genome view and color/sort alignments tutorials to user guide ([@cmdcolin](https://github.com/cmdcolin)) +- [#1725](https://github.com/GMOD/jbrowse-components/pull/1725) JBrowseR release + ([@elliothershberg](https://github.com/elliothershberg)) +- [#1677](https://github.com/GMOD/jbrowse-components/pull/1677) Config guide + updates ([@elliothershberg](https://github.com/elliothershberg)) +- [#1665](https://github.com/GMOD/jbrowse-components/pull/1665) Add Nextstrain + COVID storybook ([@elliothershberg](https://github.com/elliothershberg)) +- [#1670](https://github.com/GMOD/jbrowse-components/pull/1670) typo in + developer guide docs ([@teresam856](https://github.com/teresam856)) +- [#1592](https://github.com/GMOD/jbrowse-components/pull/1592) Website copy + edits ([@rbuels](https://github.com/rbuels)) +- [#1646](https://github.com/GMOD/jbrowse-components/pull/1646) Fix "See code" + link in CLI docs ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#1618](https://github.com/GMOD/jbrowse-components/pull/1618) Add whole-genome + view and color/sort alignments tutorials to user guide + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#1666](https://github.com/GMOD/jbrowse-components/pull/1666) Move "mouseover" config from BaseLinearDisplay to LinearBasicDisplay display ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1751](https://github.com/GMOD/jbrowse-components/pull/1751) Make the variant display derive from the feature display ([@cmdcolin](https://github.com/cmdcolin)) - - [#1716](https://github.com/GMOD/jbrowse-components/pull/1716) Stringify labels before adding to rendering to avoid undefineds on label.length ([@cmdcolin](https://github.com/cmdcolin)) - - [#1713](https://github.com/GMOD/jbrowse-components/pull/1713) Add console.error log in block setError ([@cmdcolin](https://github.com/cmdcolin)) - - [#1663](https://github.com/GMOD/jbrowse-components/pull/1663) Make LGV "initialized" not depend on displayedRegions ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1672](https://github.com/GMOD/jbrowse-components/pull/1672) Fix import forms crashing if there are no assemblies ([@cmdcolin](https://github.com/cmdcolin)) - - [#1644](https://github.com/GMOD/jbrowse-components/pull/1644) Bump electron from 9.3.1 to 9.4.0 ([@dependabot[bot]](https://github.com/apps/dependabot)) - - [#1641](https://github.com/GMOD/jbrowse-components/pull/1641) Remove codecov pr annotations ([@cmdcolin](https://github.com/cmdcolin)) - - [#1609](https://github.com/GMOD/jbrowse-components/pull/1609) Add extra checks for release script ([@peterkxie](https://github.com/peterkxie)) + - [#1666](https://github.com/GMOD/jbrowse-components/pull/1666) Move + "mouseover" config from BaseLinearDisplay to LinearBasicDisplay display + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1751](https://github.com/GMOD/jbrowse-components/pull/1751) Make the + variant display derive from the feature display + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1716](https://github.com/GMOD/jbrowse-components/pull/1716) Stringify + labels before adding to rendering to avoid undefineds on label.length + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1713](https://github.com/GMOD/jbrowse-components/pull/1713) Add + console.error log in block setError + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1663](https://github.com/GMOD/jbrowse-components/pull/1663) Make LGV + "initialized" not depend on displayedRegions + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1672](https://github.com/GMOD/jbrowse-components/pull/1672) Fix import + forms crashing if there are no assemblies + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1644](https://github.com/GMOD/jbrowse-components/pull/1644) Bump electron + from 9.3.1 to 9.4.0 ([@dependabot[bot]](https://github.com/apps/dependabot)) + - [#1641](https://github.com/GMOD/jbrowse-components/pull/1641) Remove codecov + pr annotations ([@cmdcolin](https://github.com/cmdcolin)) + - [#1609](https://github.com/GMOD/jbrowse-components/pull/1609) Add extra + checks for release script ([@peterkxie](https://github.com/peterkxie)) - `core` - - [#1762](https://github.com/GMOD/jbrowse-components/pull/1762) Add requestidlecallback ponyfill in @jbrowse/core/util ([@cmdcolin](https://github.com/cmdcolin)) - - [#1629](https://github.com/GMOD/jbrowse-components/pull/1629) Add RegionsAdapter/SequenceAdapter, reorganize base adapters ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1625](https://github.com/GMOD/jbrowse-components/pull/1625) Make renderArgs consistent and don't duplicate data ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1414](https://github.com/GMOD/jbrowse-components/pull/1414) Typescriptify and MST'ify the add track workflow ([@cmdcolin](https://github.com/cmdcolin)) + - [#1762](https://github.com/GMOD/jbrowse-components/pull/1762) Add + requestidlecallback ponyfill in @jbrowse/core/util + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1629](https://github.com/GMOD/jbrowse-components/pull/1629) Add + RegionsAdapter/SequenceAdapter, reorganize base adapters + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1625](https://github.com/GMOD/jbrowse-components/pull/1625) Make + renderArgs consistent and don't duplicate data + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1414](https://github.com/GMOD/jbrowse-components/pull/1414) Typescriptify + and MST'ify the add track workflow + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 7 diff --git a/website/blog/2021-03-29-v1.1.0-release.md b/website/blog/2021-03-29-v1.1.0-release.md index 218dde3cfb..ab5b93f8bb 100644 --- a/website/blog/2021-03-29-v1.1.0-release.md +++ b/website/blog/2021-03-29-v1.1.0-release.md @@ -8,9 +8,14 @@ We're pleased to announce a new release of JBrowse Web! ## Changed callbacks language from JavaScript to Jexl -To allow users to safely and seamlessly share advanced configurations in sessions, we now use [Jexl](https://github.com/TomFrost/Jexl/blob/master/README.md) to express configuration callbacks. Note that this is a breaking change, `function()`-style callbacks will no longer work. +To allow users to safely and seamlessly share advanced configurations in +sessions, we now use +[Jexl](https://github.com/TomFrost/Jexl/blob/master/README.md) to express +configuration callbacks. Note that this is a breaking change, `function()`-style +callbacks will no longer work. -For details, see the [callbacks section of our configuration guide](/docs/config_guide#configuration-callbacks). +For details, see the +[callbacks section of our configuration guide](/docs/config_guide#configuration-callbacks). ## Fetch intron and upstream/downstream sequences @@ -21,13 +26,16 @@ upstream/downstream sequence in the feature details ## Interactive documentation using Storybook -Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View. -The docs contain live examples of how the LGV component can be used, along with source-code examples. -The site can be found [here](https://jbrowse.org/storybook/lgv/v1.1.0). +Another new update is the first release of our interactive Storybook docs for +the embeddable React Linear Genome View. The docs contain live examples of how +the LGV component can be used, along with source-code examples. The site can be +found [here](https://jbrowse.org/storybook/lgv/v1.1.0). ## Enhanced navigation to drawer widget stack -We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web. +We have added a dropdown to enhance navigation between stack of active widgets. +The update also adds a minimize button to allow quick access to full screen +JBrowse web. See below for demos of the new navigation UI. @@ -86,44 +94,87 @@ on NPM. #### :rocket: Enhancement - `core` - - [#1846](https://github.com/GMOD/jbrowse-components/pull/1846) Improve copy+paste in the data grids for feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1814](https://github.com/GMOD/jbrowse-components/pull/1814) Add ability to get promoter sequence and intron sequence for genes from the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#1816](https://github.com/GMOD/jbrowse-components/pull/1816) Remove some animation effects ([@cmdcolin](https://github.com/cmdcolin)) - - [#1778](https://github.com/GMOD/jbrowse-components/pull/1778) Adds dropdown to show drawer widget stack ([@teresam856](https://github.com/teresam856)) - - [#1685](https://github.com/GMOD/jbrowse-components/pull/1685) Change callbacks language from JavaScript to Jexl ([@peterkxie](https://github.com/peterkxie)) + - [#1846](https://github.com/GMOD/jbrowse-components/pull/1846) Improve + copy+paste in the data grids for feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1814](https://github.com/GMOD/jbrowse-components/pull/1814) Add ability to + get promoter sequence and intron sequence for genes from the feature details + panel ([@cmdcolin](https://github.com/cmdcolin)) + - [#1816](https://github.com/GMOD/jbrowse-components/pull/1816) Remove some + animation effects ([@cmdcolin](https://github.com/cmdcolin)) + - [#1778](https://github.com/GMOD/jbrowse-components/pull/1778) Adds dropdown + to show drawer widget stack ([@teresam856](https://github.com/teresam856)) + - [#1685](https://github.com/GMOD/jbrowse-components/pull/1685) Change + callbacks language from JavaScript to Jexl + ([@peterkxie](https://github.com/peterkxie)) - Other - - [#1831](https://github.com/GMOD/jbrowse-components/pull/1831) Add dialog for launching breakpoint split view from variant feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1803](https://github.com/GMOD/jbrowse-components/pull/1803) Transcript and gene glyphs can now display implied UTRs, active by default ([@cmdcolin](https://github.com/cmdcolin)) - - [#1808](https://github.com/GMOD/jbrowse-components/pull/1808) Add another heuristic for returning gene features from BigBed ([@cmdcolin](https://github.com/cmdcolin)) - - [#1774](https://github.com/GMOD/jbrowse-components/pull/1774) Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view ([@cmdcolin](https://github.com/cmdcolin)) + - [#1831](https://github.com/GMOD/jbrowse-components/pull/1831) Add dialog for + launching breakpoint split view from variant feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1803](https://github.com/GMOD/jbrowse-components/pull/1803) Transcript and + gene glyphs can now display implied UTRs, active by default + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1808](https://github.com/GMOD/jbrowse-components/pull/1808) Add another + heuristic for returning gene features from BigBed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1774](https://github.com/GMOD/jbrowse-components/pull/1774) Add warning + dialog in LGV before returning to import form to prevent accidentally losing + the current view ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#1811](https://github.com/GMOD/jbrowse-components/pull/1811) Check for existence of window more robustly to allow in SSR or node applications ([@elliothershberg](https://github.com/elliothershberg)) - - [#1793](https://github.com/GMOD/jbrowse-components/pull/1793) Fix dotplot rendering outside it's allowed bounds ([@cmdcolin](https://github.com/cmdcolin)) - - [#1783](https://github.com/GMOD/jbrowse-components/pull/1783) Add hic aborting and fix remoteAbort signal propagation ([@cmdcolin](https://github.com/cmdcolin)) - - [#1723](https://github.com/GMOD/jbrowse-components/pull/1723) A few bugfixes ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1811](https://github.com/GMOD/jbrowse-components/pull/1811) Check for + existence of window more robustly to allow in SSR or node applications + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1793](https://github.com/GMOD/jbrowse-components/pull/1793) Fix dotplot + rendering outside it's allowed bounds + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1783](https://github.com/GMOD/jbrowse-components/pull/1783) Add hic + aborting and fix remoteAbort signal propagation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1723](https://github.com/GMOD/jbrowse-components/pull/1723) A few bugfixes + ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - - [#1815](https://github.com/GMOD/jbrowse-components/pull/1815) Clear tracks when using "Return to import form" ([@cmdcolin](https://github.com/cmdcolin)) - - [#1819](https://github.com/GMOD/jbrowse-components/pull/1819) Standardized sentence casing on drawer widget titles ([@cmdcolin](https://github.com/cmdcolin)) - - [#1796](https://github.com/GMOD/jbrowse-components/pull/1796) Bump generic-filehandle for fixing CORS errors from Chrome cache pollution ([@cmdcolin](https://github.com/cmdcolin)) + - [#1815](https://github.com/GMOD/jbrowse-components/pull/1815) Clear tracks + when using "Return to import form" + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1819](https://github.com/GMOD/jbrowse-components/pull/1819) Standardized + sentence casing on drawer widget titles + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1796](https://github.com/GMOD/jbrowse-components/pull/1796) Bump + generic-filehandle for fixing CORS errors from Chrome cache pollution + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1824](https://github.com/GMOD/jbrowse-components/pull/1824) Add storybook docs page for nextjs usage ([@elliothershberg](https://github.com/elliothershberg)) -- [#1770](https://github.com/GMOD/jbrowse-components/pull/1770) 1469 storybook deploy ([@elliothershberg](https://github.com/elliothershberg)) -- [#1807](https://github.com/GMOD/jbrowse-components/pull/1807) Update developer guide to cover displays, and highlight working external plugins ([@cmdcolin](https://github.com/cmdcolin)) -- [#1779](https://github.com/GMOD/jbrowse-components/pull/1779) Collaborative release announcement editing ([@rbuels](https://github.com/rbuels)) -- [#1791](https://github.com/GMOD/jbrowse-components/pull/1791) Add a couple more demos for our live version with MDX ([@cmdcolin](https://github.com/cmdcolin)) +- [#1824](https://github.com/GMOD/jbrowse-components/pull/1824) Add storybook + docs page for nextjs usage + ([@elliothershberg](https://github.com/elliothershberg)) +- [#1770](https://github.com/GMOD/jbrowse-components/pull/1770) 1469 storybook + deploy ([@elliothershberg](https://github.com/elliothershberg)) +- [#1807](https://github.com/GMOD/jbrowse-components/pull/1807) Update developer + guide to cover displays, and highlight working external plugins + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1779](https://github.com/GMOD/jbrowse-components/pull/1779) Collaborative + release announcement editing ([@rbuels](https://github.com/rbuels)) +- [#1791](https://github.com/GMOD/jbrowse-components/pull/1791) Add a couple + more demos for our live version with MDX + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#1820](https://github.com/GMOD/jbrowse-components/pull/1820) Create v1.1.0.md, draft of release announcements ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1823](https://github.com/GMOD/jbrowse-components/pull/1823) Add note about previewing changelog to CONTRIBUTING.md ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1820](https://github.com/GMOD/jbrowse-components/pull/1820) Create + v1.1.0.md, draft of release announcements + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1823](https://github.com/GMOD/jbrowse-components/pull/1823) Add note about + previewing changelog to CONTRIBUTING.md + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#1834](https://github.com/GMOD/jbrowse-components/pull/1834) Change jbrowse-components monorepo default branch from 'master' to 'main' ([@rbuels](https://github.com/rbuels)) + - [#1834](https://github.com/GMOD/jbrowse-components/pull/1834) Change + jbrowse-components monorepo default branch from 'master' to 'main' + ([@rbuels](https://github.com/rbuels)) #### Committers: 6 diff --git a/website/blog/2021-05-03-v1.2.0-release.md b/website/blog/2021-05-03-v1.2.0-release.md index 5cd5514860..1e07400a16 100644 --- a/website/blog/2021-05-03-v1.2.0-release.md +++ b/website/blog/2021-05-03-v1.2.0-release.md @@ -8,21 +8,19 @@ We're excited to announce the v1.2.0 release of JBrowse Web! ## New plugin store added to website -One of the core aspects of JBrowse 2 is that it is an extensible -platform for biological visualization that can be extended with -plugins. We are excited to introduce the first version of our -plugin store, where we list the current external plugins that -are available. Check it out [here](https://jbrowse.org/jb2/plugin_store). -In the coming weeks, we will also be bringing this plugin store directly -into the application, allowing plugin installation with the click of a button. -Stay tuned! +One of the core aspects of JBrowse 2 is that it is an extensible platform for +biological visualization that can be extended with plugins. We are excited to +introduce the first version of our plugin store, where we list the current +external plugins that are available. Check it out +[here](https://jbrowse.org/jb2/plugin_store). In the coming weeks, we will also +be bringing this plugin store directly into the application, allowing plugin +installation with the click of a button. Stay tuned! ## SVG export -We're excited to introduce a new feature to JBrowse Web: built-in -SVG export of track visualizations! This feature currently supports -the linear genome view, and will be extended to more views in future -releases. +We're excited to introduce a new feature to JBrowse Web: built-in SVG export of +track visualizations! This feature currently supports the linear genome view, +and will be extended to more views in future releases. ![](https://raw.githubusercontent.com/cmdcolin/jb2export/6e5486c1939499923045c011b33cfb96b125faba/img/1.png) @@ -37,8 +35,9 @@ selector, enabling it to support arbitrarily large track lists. ## Lazy loading -We have expanded our use of [lazy loading](https://reactjs.org/docs/code-splitting.html#reactlazy), which optimizes app performance and -improves load times. +We have expanded our use of +[lazy loading](https://reactjs.org/docs/code-splitting.html#reactlazy), which +optimizes app performance and improves load times. ## Downloads @@ -95,53 +94,116 @@ on NPM. #### :rocket: Enhancement - `core` - - [#1125](https://github.com/GMOD/jbrowse-components/pull/1125) Export SVG ([@cmdcolin](https://github.com/cmdcolin)) - - [#1867](https://github.com/GMOD/jbrowse-components/pull/1867) Virtualized tree for tracklist to support having thousands of tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1660](https://github.com/GMOD/jbrowse-components/pull/1660) Allow connections to have multiple assemblies ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1864](https://github.com/GMOD/jbrowse-components/pull/1864) Add Material UI's DataGrid to re-exports ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1875](https://github.com/GMOD/jbrowse-components/pull/1875) Make drawer widget titles stay visible when scrolling inside the widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#1877](https://github.com/GMOD/jbrowse-components/pull/1877) Add ability to copy the text produced by the feature details sequence panel to MS Word/Google Docs and preserve styling ([@cmdcolin](https://github.com/cmdcolin)) - - [#1854](https://github.com/GMOD/jbrowse-components/pull/1854) Make "About track" dialog available from tracklist and for non-LGV tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1853](https://github.com/GMOD/jbrowse-components/pull/1853) Add mouseovers in feature details that show field descriptions for VCF fields ([@cmdcolin](https://github.com/cmdcolin)) + - [#1125](https://github.com/GMOD/jbrowse-components/pull/1125) Export SVG + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1867](https://github.com/GMOD/jbrowse-components/pull/1867) Virtualized + tree for tracklist to support having thousands of tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1660](https://github.com/GMOD/jbrowse-components/pull/1660) Allow + connections to have multiple assemblies + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1864](https://github.com/GMOD/jbrowse-components/pull/1864) Add Material + UI's DataGrid to re-exports + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1875](https://github.com/GMOD/jbrowse-components/pull/1875) Make drawer + widget titles stay visible when scrolling inside the widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1877](https://github.com/GMOD/jbrowse-components/pull/1877) Add ability to + copy the text produced by the feature details sequence panel to MS + Word/Google Docs and preserve styling + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1854](https://github.com/GMOD/jbrowse-components/pull/1854) Make "About + track" dialog available from tracklist and for non-LGV tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1853](https://github.com/GMOD/jbrowse-components/pull/1853) Add mouseovers + in feature details that show field descriptions for VCF fields + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1892](https://github.com/GMOD/jbrowse-components/pull/1892) Create new JB2 plugin store ([@elliothershberg](https://github.com/elliothershberg)) - - [#1901](https://github.com/GMOD/jbrowse-components/pull/1901) Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink ([@cmdcolin](https://github.com/cmdcolin)) - - [#1850](https://github.com/GMOD/jbrowse-components/pull/1850) Add true breakend ALT strings to the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete to set-default-session, fix --session ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1861](https://github.com/GMOD/jbrowse-components/pull/1861) Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict ([@cmdcolin](https://github.com/cmdcolin)) + - [#1892](https://github.com/GMOD/jbrowse-components/pull/1892) Create new JB2 + plugin store ([@elliothershberg](https://github.com/elliothershberg)) + - [#1901](https://github.com/GMOD/jbrowse-components/pull/1901) Make using + --out for add-assembly create output directory if it does not exist and fix + outputting to symlink ([@cmdcolin](https://github.com/cmdcolin)) + - [#1850](https://github.com/GMOD/jbrowse-components/pull/1850) Add true + breakend ALT strings to the feature details panel + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete + to set-default-session, fix --session + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1861](https://github.com/GMOD/jbrowse-components/pull/1861) Change + Alignments track "Fade mismatches by quality" setting to a separate config + param and made it less strict ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#1924](https://github.com/GMOD/jbrowse-components/pull/1924) Fix import of BED and navToLocString from spreadsheet views ([@cmdcolin](https://github.com/cmdcolin)) - - [#1918](https://github.com/GMOD/jbrowse-components/pull/1918) Fix issue with some falsy values being hidden in feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#1911](https://github.com/GMOD/jbrowse-components/pull/1911) Fix breakpoint split view visualizations for files that need ref renaming (e.g. chr1 vs 1) ([@cmdcolin](https://github.com/cmdcolin)) - - [#1904](https://github.com/GMOD/jbrowse-components/pull/1904) Fix issue with synteny polygons displaying slightly offset ([@cmdcolin](https://github.com/cmdcolin)) - - [#1884](https://github.com/GMOD/jbrowse-components/pull/1884) Fix rIC ponyfill for use on Safari ([@cmdcolin](https://github.com/cmdcolin)) + - [#1924](https://github.com/GMOD/jbrowse-components/pull/1924) Fix import of + BED and navToLocString from spreadsheet views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1918](https://github.com/GMOD/jbrowse-components/pull/1918) Fix issue with + some falsy values being hidden in feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1911](https://github.com/GMOD/jbrowse-components/pull/1911) Fix breakpoint + split view visualizations for files that need ref renaming (e.g. chr1 vs 1) + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1904](https://github.com/GMOD/jbrowse-components/pull/1904) Fix issue with + synteny polygons displaying slightly offset + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1884](https://github.com/GMOD/jbrowse-components/pull/1884) Fix rIC + ponyfill for use on Safari ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1912](https://github.com/GMOD/jbrowse-components/pull/1912) Fix reloading of local sessions when using React.StrictMode ([@cmdcolin](https://github.com/cmdcolin)) - - [#1900](https://github.com/GMOD/jbrowse-components/pull/1900) Make clicking away from autocomplete popup on track container work ([@cmdcolin](https://github.com/cmdcolin)) - - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete to set-default-session, fix --session ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1871](https://github.com/GMOD/jbrowse-components/pull/1871) Fix crash on dotplot/linear synteny import form and when closing linear synteny track ([@cmdcolin](https://github.com/cmdcolin)) - - [#1860](https://github.com/GMOD/jbrowse-components/pull/1860) Fix alignments read filter jexl syntax ([@cmdcolin](https://github.com/cmdcolin)) + - [#1912](https://github.com/GMOD/jbrowse-components/pull/1912) Fix reloading + of local sessions when using React.StrictMode + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1900](https://github.com/GMOD/jbrowse-components/pull/1900) Make clicking + away from autocomplete popup on track container work + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1878](https://github.com/GMOD/jbrowse-components/pull/1878) Add --delete + to set-default-session, fix --session + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1871](https://github.com/GMOD/jbrowse-components/pull/1871) Fix crash on + dotplot/linear synteny import form and when closing linear synteny track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1860](https://github.com/GMOD/jbrowse-components/pull/1860) Fix alignments + read filter jexl syntax ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#1914](https://github.com/GMOD/jbrowse-components/pull/1914) Use MDX to add proper image captions in web and pdf documentation ([@cmdcolin](https://github.com/cmdcolin)) -- [#1855](https://github.com/GMOD/jbrowse-components/pull/1855) Add download page in website header and new super-quick-start guide ([@cmdcolin](https://github.com/cmdcolin)) +- [#1914](https://github.com/GMOD/jbrowse-components/pull/1914) Use MDX to add + proper image captions in web and pdf documentation + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1855](https://github.com/GMOD/jbrowse-components/pull/1855) Add download + page in website header and new super-quick-start guide + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#1932](https://github.com/GMOD/jbrowse-components/pull/1932) Update analytics and share API URLs to refer to more stable locations ([@peterkxie](https://github.com/peterkxie)) - - [#1888](https://github.com/GMOD/jbrowse-components/pull/1888) More lazy loading of react components to reduce bundle size ([@cmdcolin](https://github.com/cmdcolin)) - - [#1790](https://github.com/GMOD/jbrowse-components/pull/1790) Allow MainThreadRpcDriver to skip serialization during RPC, improving main-thread rendering performance ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1932](https://github.com/GMOD/jbrowse-components/pull/1932) Update + analytics and share API URLs to refer to more stable locations + ([@peterkxie](https://github.com/peterkxie)) + - [#1888](https://github.com/GMOD/jbrowse-components/pull/1888) More lazy + loading of react components to reduce bundle size + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1790](https://github.com/GMOD/jbrowse-components/pull/1790) Allow + MainThreadRpcDriver to skip serialization during RPC, improving main-thread + rendering performance + ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - - [#1926](https://github.com/GMOD/jbrowse-components/pull/1926) Update website to link to demos on cloudfront for better compression ([@cmdcolin](https://github.com/cmdcolin)) - - [#1868](https://github.com/GMOD/jbrowse-components/pull/1868) Export XYPlotRenderer and configSchema ([@elliothershberg](https://github.com/elliothershberg)) - - [#1863](https://github.com/GMOD/jbrowse-components/pull/1863) Update @gmod/indexedfasta ([@cmdcolin](https://github.com/cmdcolin)) - - [#1795](https://github.com/GMOD/jbrowse-components/pull/1795) Make LinearAlignmentsDisplay fully configurable in the UI ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1822](https://github.com/GMOD/jbrowse-components/pull/1822) Let React LGV navigate without setting displayedRegion first ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1926](https://github.com/GMOD/jbrowse-components/pull/1926) Update website + to link to demos on cloudfront for better compression + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1868](https://github.com/GMOD/jbrowse-components/pull/1868) Export + XYPlotRenderer and configSchema + ([@elliothershberg](https://github.com/elliothershberg)) + - [#1863](https://github.com/GMOD/jbrowse-components/pull/1863) Update + @gmod/indexedfasta ([@cmdcolin](https://github.com/cmdcolin)) + - [#1795](https://github.com/GMOD/jbrowse-components/pull/1795) Make + LinearAlignmentsDisplay fully configurable in the UI + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1822](https://github.com/GMOD/jbrowse-components/pull/1822) Let React LGV + navigate without setting displayedRegion first + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 4 diff --git a/website/blog/2021-05-24-v1.3.0-release.md b/website/blog/2021-05-24-v1.3.0-release.md index 8fba41d185..13f6e1c2aa 100644 --- a/website/blog/2021-05-24-v1.3.0-release.md +++ b/website/blog/2021-05-24-v1.3.0-release.md @@ -29,8 +29,8 @@ will be available when we release JBrowse Desktop. The MM and MP/ML tags can be used to color alignments tracks by either base modifications or by methylation. The modifications mode is exciting because it -can show arbitrary DNA/RNA modifications, and the methylation mode uses -specific CpG context to show both modified and unmodified CpGs. +can show arbitrary DNA/RNA modifications, and the methylation mode uses specific +CpG context to show both modified and unmodified CpGs. ![Screenshot of alignments tracks colored by methylation and base modification](https://raw.githubusercontent.com/GMOD/jbrowse-components/7f0c725a929bb15a6adfcf3a155bf9dc5f717af7/website/static/img/alignments/modifications1.png) @@ -92,42 +92,83 @@ on NPM. #### :rocket: Enhancement - Other - - [#2001](https://github.com/GMOD/jbrowse-components/pull/2001) Make tracks added using the add track widget a session track if not in adminMode ([@cmdcolin](https://github.com/cmdcolin)) - - [#1980](https://github.com/GMOD/jbrowse-components/pull/1980) Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist ([@cmdcolin](https://github.com/cmdcolin)) - - [#1977](https://github.com/GMOD/jbrowse-components/pull/1977) Upgrade @material-ui/data-grid ([@cmdcolin](https://github.com/cmdcolin)) + - [#2001](https://github.com/GMOD/jbrowse-components/pull/2001) Make tracks + added using the add track widget a session track if not in adminMode + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1980](https://github.com/GMOD/jbrowse-components/pull/1980) Add popup + confirmation dialog for unknown session plugins, and use plugins.json as a + whitelist ([@cmdcolin](https://github.com/cmdcolin)) + - [#1977](https://github.com/GMOD/jbrowse-components/pull/1977) Upgrade + @material-ui/data-grid ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#1982](https://github.com/GMOD/jbrowse-components/pull/1982) Allow manually specifying adapter type if filename does not match expected pattern ([@cmdcolin](https://github.com/cmdcolin)) - - [#1975](https://github.com/GMOD/jbrowse-components/pull/1975) Allow local files on the users computer to be opened as tracks in jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - - [#1865](https://github.com/GMOD/jbrowse-components/pull/1865) Show modified bases using MM and MP/ML tags in BAM/CRAM ([@cmdcolin](https://github.com/cmdcolin)) - - [#1984](https://github.com/GMOD/jbrowse-components/pull/1984) Better feature details when there are short arrays of json supplied as feature data ([@cmdcolin](https://github.com/cmdcolin)) - - [#1931](https://github.com/GMOD/jbrowse-components/pull/1931) Create in app graphical plugin store ([@elliothershberg](https://github.com/elliothershberg)) + - [#1982](https://github.com/GMOD/jbrowse-components/pull/1982) Allow manually + specifying adapter type if filename does not match expected pattern + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1975](https://github.com/GMOD/jbrowse-components/pull/1975) Allow local + files on the users computer to be opened as tracks in jbrowse-web + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1865](https://github.com/GMOD/jbrowse-components/pull/1865) Show modified + bases using MM and MP/ML tags in BAM/CRAM + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1984](https://github.com/GMOD/jbrowse-components/pull/1984) Better feature + details when there are short arrays of json supplied as feature data + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1931](https://github.com/GMOD/jbrowse-components/pull/1931) Create in app + graphical plugin store + ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - - [#1985](https://github.com/GMOD/jbrowse-components/pull/1985) Avoid error calculating UTR on features that have no exon subfeatures ([@cmdcolin](https://github.com/cmdcolin)) - - [#1954](https://github.com/GMOD/jbrowse-components/pull/1954) Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering ([@cmdcolin](https://github.com/cmdcolin)) - - [#1963](https://github.com/GMOD/jbrowse-components/pull/1963) Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#1945](https://github.com/GMOD/jbrowse-components/pull/1945) Fix hic not being able to render due to incorrect lazy loading ([@cmdcolin](https://github.com/cmdcolin)) + - [#1985](https://github.com/GMOD/jbrowse-components/pull/1985) Avoid error + calculating UTR on features that have no exon subfeatures + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1954](https://github.com/GMOD/jbrowse-components/pull/1954) Add more + environments to configSchema create calls to fix ability to use custom jexl + commands with main thread rendering + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1963](https://github.com/GMOD/jbrowse-components/pull/1963) Fix ability to + use DialogComponent (used for svg export, pileup sort, etc) on embedded + components ([@cmdcolin](https://github.com/cmdcolin)) + - [#1945](https://github.com/GMOD/jbrowse-components/pull/1945) Fix hic not + being able to render due to incorrect lazy loading + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#1956](https://github.com/GMOD/jbrowse-components/pull/1956) Fix connection behavior ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#1966](https://github.com/GMOD/jbrowse-components/pull/1966) Fix ability to use add-track force on symlink tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#1951](https://github.com/GMOD/jbrowse-components/pull/1951) Fix breakpoint split view demo configuration on website ([@cmdcolin](https://github.com/cmdcolin)) + - [#1956](https://github.com/GMOD/jbrowse-components/pull/1956) Fix connection + behavior ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#1966](https://github.com/GMOD/jbrowse-components/pull/1966) Fix ability to + use add-track force on symlink tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1951](https://github.com/GMOD/jbrowse-components/pull/1951) Fix breakpoint + split view demo configuration on website + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2002](https://github.com/GMOD/jbrowse-components/pull/2002) Add @jbrowse/img to homepage ([@cmdcolin](https://github.com/cmdcolin)) -- [#2007](https://github.com/GMOD/jbrowse-components/pull/2007) Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details ([@cmdcolin](https://github.com/cmdcolin)) -- [#1976](https://github.com/GMOD/jbrowse-components/pull/1976) reorganize the demo page to emphasize the cancer sv demo more ([@rbuels](https://github.com/rbuels)) -- [#1952](https://github.com/GMOD/jbrowse-components/pull/1952) Add demo for 1000 genomes extended trio dataset to website ([@cmdcolin](https://github.com/cmdcolin)) -- [#1862](https://github.com/GMOD/jbrowse-components/pull/1862) Add example for using a build-time included plugin to storybook ([@cmdcolin](https://github.com/cmdcolin)) +- [#2002](https://github.com/GMOD/jbrowse-components/pull/2002) Add @jbrowse/img + to homepage ([@cmdcolin](https://github.com/cmdcolin)) +- [#2007](https://github.com/GMOD/jbrowse-components/pull/2007) Update docs for + modifications/methylation coloring, plugin store, and the sequence panel in + feature details ([@cmdcolin](https://github.com/cmdcolin)) +- [#1976](https://github.com/GMOD/jbrowse-components/pull/1976) reorganize the + demo page to emphasize the cancer sv demo more + ([@rbuels](https://github.com/rbuels)) +- [#1952](https://github.com/GMOD/jbrowse-components/pull/1952) Add demo for + 1000 genomes extended trio dataset to website + ([@cmdcolin](https://github.com/cmdcolin)) +- [#1862](https://github.com/GMOD/jbrowse-components/pull/1862) Add example for + using a build-time included plugin to storybook + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#2003](https://github.com/GMOD/jbrowse-components/pull/2003) Make SNPCoverage independently generate the modifications tag-color mapping ([@cmdcolin](https://github.com/cmdcolin)) + - [#2003](https://github.com/GMOD/jbrowse-components/pull/2003) Make + SNPCoverage independently generate the modifications tag-color mapping + ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `development-tools` - - [#1930](https://github.com/GMOD/jbrowse-components/pull/1930) Upgrade react scripts+react to latest versions ([@cmdcolin](https://github.com/cmdcolin)) + - [#1930](https://github.com/GMOD/jbrowse-components/pull/1930) Upgrade react + scripts+react to latest versions ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 diff --git a/website/blog/2021-07-06-v1.3.1-release.md b/website/blog/2021-07-06-v1.3.1-release.md index 01579bf8ea..41d435c518 100644 --- a/website/blog/2021-07-06-v1.3.1-release.md +++ b/website/blog/2021-07-06-v1.3.1-release.md @@ -62,45 +62,91 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2094](https://github.com/GMOD/jbrowse-components/pull/2094) More usage of typography to improve consistent text styling ([@cmdcolin](https://github.com/cmdcolin)) - - [#2068](https://github.com/GMOD/jbrowse-components/pull/2068) Add non-indexed and plaintext VCF Adapter to variants plugin ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2067](https://github.com/GMOD/jbrowse-components/pull/2067) Better error message if a file location has an empty string ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2064](https://github.com/GMOD/jbrowse-components/pull/2064) Export offscreenCanvasPonyfil from core/util ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2060](https://github.com/GMOD/jbrowse-components/pull/2060) Improve performance with large numbers of reference sequences by using MST volatiles ([@cmdcolin](https://github.com/cmdcolin)) - - [#2050](https://github.com/GMOD/jbrowse-components/pull/2050) Configurable app logo for web ([@elliothershberg](https://github.com/elliothershberg)) + - [#2094](https://github.com/GMOD/jbrowse-components/pull/2094) More usage of + typography to improve consistent text styling + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2068](https://github.com/GMOD/jbrowse-components/pull/2068) Add + non-indexed and plaintext VCF Adapter to variants plugin + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2067](https://github.com/GMOD/jbrowse-components/pull/2067) Better error + message if a file location has an empty string + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2064](https://github.com/GMOD/jbrowse-components/pull/2064) Export + offscreenCanvasPonyfil from core/util + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2060](https://github.com/GMOD/jbrowse-components/pull/2060) Improve + performance with large numbers of reference sequences by using MST volatiles + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2050](https://github.com/GMOD/jbrowse-components/pull/2050) Configurable + app logo for web ([@elliothershberg](https://github.com/elliothershberg)) - Other - - [#2104](https://github.com/GMOD/jbrowse-components/pull/2104) Use ScopedCssBaseline to help style the embedded component ([@cmdcolin](https://github.com/cmdcolin)) - - [#2015](https://github.com/GMOD/jbrowse-components/pull/2015) Deprecate ThemeProvider in `@jbrowse/react-linear-genome-view` ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2104](https://github.com/GMOD/jbrowse-components/pull/2104) Use + ScopedCssBaseline to help style the embedded component + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2015](https://github.com/GMOD/jbrowse-components/pull/2015) Deprecate + ThemeProvider in `@jbrowse/react-linear-genome-view` + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#2097](https://github.com/GMOD/jbrowse-components/pull/2097) Improve speed for laying out features for embedded/mainthreadrpc scenarios ([@cmdcolin](https://github.com/cmdcolin)) - - [#2096](https://github.com/GMOD/jbrowse-components/pull/2096) Fix issue with page reload after editing session title ([@cmdcolin](https://github.com/cmdcolin)) - - [#2074](https://github.com/GMOD/jbrowse-components/pull/2074) Fix support for opening local files in spreadsheet/SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#2061](https://github.com/GMOD/jbrowse-components/pull/2061) Fix issue with using --force error when no track was previously loaded ([@cmdcolin](https://github.com/cmdcolin)) - - [#2024](https://github.com/GMOD/jbrowse-components/pull/2024) Flip drawing of negative strand PAF features in linear synteny and dotplot views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2023](https://github.com/GMOD/jbrowse-components/pull/2023) Fix infinite loop in adding some plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2019](https://github.com/GMOD/jbrowse-components/pull/2019) Fix session import to use blob map for opening local files ([@cmdcolin](https://github.com/cmdcolin)) + - [#2097](https://github.com/GMOD/jbrowse-components/pull/2097) Improve speed + for laying out features for embedded/mainthreadrpc scenarios + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2096](https://github.com/GMOD/jbrowse-components/pull/2096) Fix issue with + page reload after editing session title + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2074](https://github.com/GMOD/jbrowse-components/pull/2074) Fix support + for opening local files in spreadsheet/SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2061](https://github.com/GMOD/jbrowse-components/pull/2061) Fix issue with + using --force error when no track was previously loaded + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2024](https://github.com/GMOD/jbrowse-components/pull/2024) Flip drawing + of negative strand PAF features in linear synteny and dotplot views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2023](https://github.com/GMOD/jbrowse-components/pull/2023) Fix infinite + loop in adding some plugins on desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2019](https://github.com/GMOD/jbrowse-components/pull/2019) Fix session + import to use blob map for opening local files + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2071](https://github.com/GMOD/jbrowse-components/pull/2071) Add indicator to the end of ref name dropdown to suggest user to type the searchbox for more ([@teresam856](https://github.com/teresam856)) - - [#2056](https://github.com/GMOD/jbrowse-components/pull/2056) Fix infinite recursion in FromConfigAdaptor by avoiding mutating the passed in data when using SimpleFeature ([@cmdcolin](https://github.com/cmdcolin)) - - [#2018](https://github.com/GMOD/jbrowse-components/pull/2018) Fix 3'UTR in sequence detail panels when no UTRs are in gff ([@cmdcolin](https://github.com/cmdcolin)) + - [#2071](https://github.com/GMOD/jbrowse-components/pull/2071) Add indicator + to the end of ref name dropdown to suggest user to type the searchbox for + more ([@teresam856](https://github.com/teresam856)) + - [#2056](https://github.com/GMOD/jbrowse-components/pull/2056) Fix infinite + recursion in FromConfigAdaptor by avoiding mutating the passed in data when + using SimpleFeature ([@cmdcolin](https://github.com/cmdcolin)) + - [#2018](https://github.com/GMOD/jbrowse-components/pull/2018) Fix 3'UTR in + sequence detail panels when no UTRs are in gff + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#1967](https://github.com/GMOD/jbrowse-components/pull/1967) Omit configurationSchema snapshot when it matches the default ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2078](https://github.com/GMOD/jbrowse-components/pull/2078) Restore eslint rule for no-unused-vars ([@cmdcolin](https://github.com/cmdcolin)) - - [#2051](https://github.com/GMOD/jbrowse-components/pull/2051) Add missing named exports to shared core modules ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2045](https://github.com/GMOD/jbrowse-components/pull/2045) Add basic architecture for text searching ([@teresam856](https://github.com/teresam856)) + - [#1967](https://github.com/GMOD/jbrowse-components/pull/1967) Omit + configurationSchema snapshot when it matches the default + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2078](https://github.com/GMOD/jbrowse-components/pull/2078) Restore eslint + rule for no-unused-vars ([@cmdcolin](https://github.com/cmdcolin)) + - [#2051](https://github.com/GMOD/jbrowse-components/pull/2051) Add missing + named exports to shared core modules + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2045](https://github.com/GMOD/jbrowse-components/pull/2045) Add basic + architecture for text searching + ([@teresam856](https://github.com/teresam856)) - Other - - [#2070](https://github.com/GMOD/jbrowse-components/pull/2070) Remove service worker from jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) - - [#1995](https://github.com/GMOD/jbrowse-components/pull/1995) Pass initialDisplay snapshot via separate param to showTrack ([@cmdcolin](https://github.com/cmdcolin)) + - [#2070](https://github.com/GMOD/jbrowse-components/pull/2070) Remove service + worker from jbrowse-web ([@cmdcolin](https://github.com/cmdcolin)) + - [#1995](https://github.com/GMOD/jbrowse-components/pull/1995) Pass + initialDisplay snapshot via separate param to showTrack + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 5 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) diff --git a/website/blog/2021-07-06-v1.3.2-release.md b/website/blog/2021-07-06-v1.3.2-release.md index 8c581617d7..3373dc7e60 100644 --- a/website/blog/2021-07-06-v1.3.2-release.md +++ b/website/blog/2021-07-06-v1.3.2-release.md @@ -44,14 +44,22 @@ on NPM. #### :rocket: Enhancement - Other - - [#2100](https://github.com/GMOD/jbrowse-components/pull/2100) Improve descriptions on VCF SVs ([@cmdcolin](https://github.com/cmdcolin)) + - [#2100](https://github.com/GMOD/jbrowse-components/pull/2100) Improve + descriptions on VCF SVs ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2106](https://github.com/GMOD/jbrowse-components/pull/2106) Use more accurate estimator for feature label widths ([@cmdcolin](https://github.com/cmdcolin)) + - [#2106](https://github.com/GMOD/jbrowse-components/pull/2106) Use more + accurate estimator for feature label widths + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#2109](https://github.com/GMOD/jbrowse-components/pull/2109) Make sure to wait for assembly to load before downloading canonical refnames in SV inspector ([@cmdcolin](https://github.com/cmdcolin)) -- [#2111](https://github.com/GMOD/jbrowse-components/pull/2111) Fix "Can't resolve '@jbrowse/plugin-legacy-jbrowse'" in `@jbrowse/react-linear-genome-view` ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2109](https://github.com/GMOD/jbrowse-components/pull/2109) Make sure to + wait for assembly to load before downloading canonical refnames in SV + inspector ([@cmdcolin](https://github.com/cmdcolin)) +- [#2111](https://github.com/GMOD/jbrowse-components/pull/2111) Fix "Can't + resolve '@jbrowse/plugin-legacy-jbrowse'" in + `@jbrowse/react-linear-genome-view` + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 diff --git a/website/blog/2021-08-02-v1.3.3.md b/website/blog/2021-08-02-v1.3.3.md index 5d56946ec8..ece23722cc 100644 --- a/website/blog/2021-08-02-v1.3.3.md +++ b/website/blog/2021-08-02-v1.3.3.md @@ -62,30 +62,53 @@ on NPM. #### :rocket: Enhancement - Other - - [#2127](https://github.com/GMOD/jbrowse-components/pull/2127) Add example dataset for COLO829 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2127](https://github.com/GMOD/jbrowse-components/pull/2127) Add example + dataset for COLO829 ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2141](https://github.com/GMOD/jbrowse-components/pull/2141) Update to @mui/material@5.0.0 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2126](https://github.com/GMOD/jbrowse-components/pull/2126) Allow opening plaintext .vcf files from the "Add track" workflow ([@cmdcolin](https://github.com/cmdcolin)) + - [#2141](https://github.com/GMOD/jbrowse-components/pull/2141) Update to + @mui/material@5.0.0 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2126](https://github.com/GMOD/jbrowse-components/pull/2126) Allow opening + plaintext .vcf files from the "Add track" workflow + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2159](https://github.com/GMOD/jbrowse-components/pull/2159) Stop local storage quota-exceeded errors preventing the app from starting ([@cmdcolin](https://github.com/cmdcolin)) - - [#2161](https://github.com/GMOD/jbrowse-components/pull/2161) Remove outline from clicking on SVG chord tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2157](https://github.com/GMOD/jbrowse-components/pull/2157) Fix rendering of negative strand alignment modifications/methylation ([@cmdcolin](https://github.com/cmdcolin)) - - [#2131](https://github.com/GMOD/jbrowse-components/pull/2131) Fix mouseovers/click handlers after "force load" button pressed ([@cmdcolin](https://github.com/cmdcolin)) - - [#2128](https://github.com/GMOD/jbrowse-components/pull/2128) Fix using the "Color by modifications" setting on files that need ref renaming ([@cmdcolin](https://github.com/cmdcolin)) - - [#2115](https://github.com/GMOD/jbrowse-components/pull/2115) Fix bug where sometimes plugin could not be removed from UI ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2119](https://github.com/GMOD/jbrowse-components/pull/2119) Fix loading indicator on the reference sequence selector getting stuck ([@cmdcolin](https://github.com/cmdcolin)) + - [#2159](https://github.com/GMOD/jbrowse-components/pull/2159) Stop local + storage quota-exceeded errors preventing the app from starting + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2161](https://github.com/GMOD/jbrowse-components/pull/2161) Remove outline + from clicking on SVG chord tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2157](https://github.com/GMOD/jbrowse-components/pull/2157) Fix rendering + of negative strand alignment modifications/methylation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2131](https://github.com/GMOD/jbrowse-components/pull/2131) Fix + mouseovers/click handlers after "force load" button pressed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2128](https://github.com/GMOD/jbrowse-components/pull/2128) Fix using the + "Color by modifications" setting on files that need ref renaming + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2115](https://github.com/GMOD/jbrowse-components/pull/2115) Fix bug where + sometimes plugin could not be removed from UI + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2119](https://github.com/GMOD/jbrowse-components/pull/2119) Fix loading + indicator on the reference sequence selector getting stuck + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2101](https://github.com/GMOD/jbrowse-components/pull/2101) Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item ([@teresam856](https://github.com/teresam856)) + - [#2101](https://github.com/GMOD/jbrowse-components/pull/2101) Fix behavior + of the end-of-list indicator in refNameAutocomplete to always display as a + disabled item ([@teresam856](https://github.com/teresam856)) #### :house: Internal - Other - - [#2152](https://github.com/GMOD/jbrowse-components/pull/2152) Remove storybook symlink workaround ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2152](https://github.com/GMOD/jbrowse-components/pull/2152) Remove + storybook symlink workaround + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2099](https://github.com/GMOD/jbrowse-components/pull/2099) Use rbush data structure for layout of feature tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2099](https://github.com/GMOD/jbrowse-components/pull/2099) Use rbush data + structure for layout of feature tracks + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 diff --git a/website/blog/2021-08-23-v1.3.4.md b/website/blog/2021-08-23-v1.3.4.md index 43248dec08..f5f419670b 100644 --- a/website/blog/2021-08-23-v1.3.4.md +++ b/website/blog/2021-08-23-v1.3.4.md @@ -88,47 +88,89 @@ on NPM. #### :rocket: Enhancement - Other - - [#2163](https://github.com/GMOD/jbrowse-components/pull/2163) Add new embeddable React Circular Genome View ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2229](https://github.com/GMOD/jbrowse-components/pull/2229) Use extendPluggableElement for context menu items ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2233](https://github.com/GMOD/jbrowse-components/pull/2233) Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs ([@cmdcolin](https://github.com/cmdcolin)) - - [#2199](https://github.com/GMOD/jbrowse-components/pull/2199) Make the BED parser not interpret general tab delimited data as BED12 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2241](https://github.com/GMOD/jbrowse-components/pull/2241) Restore previous window location when re-opening on desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2203](https://github.com/GMOD/jbrowse-components/pull/2203) Add a helpful message if there is a 404 on config.json error ([@cmdcolin](https://github.com/cmdcolin)) - - [#2204](https://github.com/GMOD/jbrowse-components/pull/2204) Hide reads with unmapped flag by default in alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2198](https://github.com/GMOD/jbrowse-components/pull/2198) Add better inversion visualization to read vs reference visualizations ([@cmdcolin](https://github.com/cmdcolin)) - - [#2154](https://github.com/GMOD/jbrowse-components/pull/2154) Add UMD build of react-linear-genome-view for plain-js use ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2163](https://github.com/GMOD/jbrowse-components/pull/2163) Add new + embeddable React Circular Genome View + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2229](https://github.com/GMOD/jbrowse-components/pull/2229) Use + extendPluggableElement for context menu items + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2233](https://github.com/GMOD/jbrowse-components/pull/2233) Add optional + chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files + with many refseqs ([@cmdcolin](https://github.com/cmdcolin)) + - [#2199](https://github.com/GMOD/jbrowse-components/pull/2199) Make the BED + parser not interpret general tab delimited data as BED12 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2241](https://github.com/GMOD/jbrowse-components/pull/2241) Restore + previous window location when re-opening on desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2203](https://github.com/GMOD/jbrowse-components/pull/2203) Add a helpful + message if there is a 404 on config.json error + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2204](https://github.com/GMOD/jbrowse-components/pull/2204) Hide reads + with unmapped flag by default in alignments tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2198](https://github.com/GMOD/jbrowse-components/pull/2198) Add better + inversion visualization to read vs reference visualizations + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2154](https://github.com/GMOD/jbrowse-components/pull/2154) Add UMD build + of react-linear-genome-view for plain-js use + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2236](https://github.com/GMOD/jbrowse-components/pull/2236) Detect assembly loading error and encapsulate error instead of failing at app level ([@cmdcolin](https://github.com/cmdcolin)) - - [#2029](https://github.com/GMOD/jbrowse-components/pull/2029) Polish desktop builds ([@elliothershberg](https://github.com/elliothershberg)) - - [#2140](https://github.com/GMOD/jbrowse-components/pull/2140) New core plugin that adds a "bookmarked regions" list widget, new extension points system ([@elliothershberg](https://github.com/elliothershberg)) + - [#2236](https://github.com/GMOD/jbrowse-components/pull/2236) Detect + assembly loading error and encapsulate error instead of failing at app level + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2029](https://github.com/GMOD/jbrowse-components/pull/2029) Polish desktop + builds ([@elliothershberg](https://github.com/elliothershberg)) + - [#2140](https://github.com/GMOD/jbrowse-components/pull/2140) New core + plugin that adds a "bookmarked regions" list widget, new extension points + system ([@elliothershberg](https://github.com/elliothershberg)) #### :bug: Bug Fix - `core` - - [#2245](https://github.com/GMOD/jbrowse-components/pull/2245) Fix missing regenerator runtime dependency in core ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2202](https://github.com/GMOD/jbrowse-components/pull/2202) Fixed a crash when an incompatible adapter is selected for provided data in 'open track' ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2197](https://github.com/GMOD/jbrowse-components/pull/2197) Fix handle leak for killed worker checker ([@cmdcolin](https://github.com/cmdcolin)) + - [#2245](https://github.com/GMOD/jbrowse-components/pull/2245) Fix missing + regenerator runtime dependency in core + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2202](https://github.com/GMOD/jbrowse-components/pull/2202) Fixed a crash + when an incompatible adapter is selected for provided data in 'open track' + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2197](https://github.com/GMOD/jbrowse-components/pull/2197) Fix handle + leak for killed worker checker ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2208](https://github.com/GMOD/jbrowse-components/pull/2208) Fix issue where collapsed categories were not remembered after toggling a track ([@cmdcolin](https://github.com/cmdcolin)) + - [#2208](https://github.com/GMOD/jbrowse-components/pull/2208) Fix issue + where collapsed categories were not remembered after toggling a track + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2192](https://github.com/GMOD/jbrowse-components/pull/2192) Update Linear Genome View embedding docs ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2192](https://github.com/GMOD/jbrowse-components/pull/2192) Update Linear + Genome View embedding docs + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :house: Internal - `core` - - [#2057](https://github.com/GMOD/jbrowse-components/pull/2057) Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance ([@cmdcolin](https://github.com/cmdcolin)) - - [#2231](https://github.com/GMOD/jbrowse-components/pull/2231) Export offscreenCanvasUtils ([@cmdcolin](https://github.com/cmdcolin)) - - [#2226](https://github.com/GMOD/jbrowse-components/pull/2226) Use superRenderProps and superTrackMenuItems for better simulated inheritance model ([@cmdcolin](https://github.com/cmdcolin)) - - [#1874](https://github.com/GMOD/jbrowse-components/pull/1874) Add aborting to CoreGetFeatures rpcManager call ([@cmdcolin](https://github.com/cmdcolin)) + - [#2057](https://github.com/GMOD/jbrowse-components/pull/2057) Use idMaker + for dataAdapterCache key for faster FromConfigAdapter performance + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2231](https://github.com/GMOD/jbrowse-components/pull/2231) Export + offscreenCanvasUtils ([@cmdcolin](https://github.com/cmdcolin)) + - [#2226](https://github.com/GMOD/jbrowse-components/pull/2226) Use + superRenderProps and superTrackMenuItems for better simulated inheritance + model ([@cmdcolin](https://github.com/cmdcolin)) + - [#1874](https://github.com/GMOD/jbrowse-components/pull/1874) Add aborting + to CoreGetFeatures rpcManager call + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2232](https://github.com/GMOD/jbrowse-components/pull/2232) Remove filtering display type from core ([@cmdcolin](https://github.com/cmdcolin)) - - [#2234](https://github.com/GMOD/jbrowse-components/pull/2234) Add rootModel setError on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#2232](https://github.com/GMOD/jbrowse-components/pull/2232) Remove + filtering display type from core ([@cmdcolin](https://github.com/cmdcolin)) + - [#2234](https://github.com/GMOD/jbrowse-components/pull/2234) Add rootModel + setError on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Elliot Hershberg ([@elliothershberg](https://github.com/elliothershberg)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) diff --git a/website/blog/2021-09-14-v1.4.4-release.md b/website/blog/2021-09-14-v1.4.4-release.md index c210ef02bb..42dce99fb5 100644 --- a/website/blog/2021-09-14-v1.4.4-release.md +++ b/website/blog/2021-09-14-v1.4.4-release.md @@ -11,19 +11,31 @@ include: Finally, we have added the ability to search by gene name! -Users will now be able to create their own text indexes with the `jbrowse text-index` command, which creates an index for searching by gene names, identifiers and descriptions. +Users will now be able to create their own text indexes with the +`jbrowse text-index` command, which creates an index for searching by gene +names, identifiers and descriptions. ![searching in lgv](https://user-images.githubusercontent.com/45598764/132396329-f3fa9ed4-ace4-40b6-8eff-8289bbd3d2ca.gif) -GIF showing the process of searching via the location search box of the Linear Genome View. Try it out yourself here, type your favorite gene name e.g. HER2, PTEN, or others in the search box https://jbrowse.org/code/jb2/v1.4.4/?config=test_data%2Fconfig_demo.json&session=share-H3vwqh1BKa&password=xYz9Z +GIF showing the process of searching via the location search box of the Linear +Genome View. Try it out yourself here, type your favorite gene name e.g. HER2, +PTEN, or others in the search box +https://jbrowse.org/code/jb2/v1.4.4/?config=test_data%2Fconfig_demo.json&session=share-H3vwqh1BKa&password=xYz9Z -For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this [quick start](/docs/quickstart_cli#indexing-feature-names-for-searching) +For a quick introduction and a tutorial on how to add this feature to your +JBrowse instance, check out this +[quick start](/docs/quickstart_web#indexing-feature-names-for-searching) -Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases. +Like most parts of JBrowse, the text searching system is pluggable. Plugin +developers can add new text index adapters to connect JBrowse to other types of +text search services, indexes, or databases. -Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page +Users of the @jbrowse/react-linear-genome-view can also enable text searching +functionality, see +https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page -Note that 1.4.0-1.4.3 had issues during publish, so we moved all release notes for them to here. Thanks to @bbimber for letting us know about these issues. +Note that 1.4.0-1.4.3 had issues during publish, so we moved all release notes +for them to here. Thanks to @bbimber for letting us know about these issues. ## Downloads @@ -58,35 +70,66 @@ on NPM. #### :rocket: Enhancement - Other - - [#2287](https://github.com/GMOD/jbrowse-components/pull/2287) Use react-popper to reduce tooltip lag on pages with many elements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2294](https://github.com/GMOD/jbrowse-components/pull/2294) Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2272](https://github.com/GMOD/jbrowse-components/pull/2272) Auto adjust box RefNameAutocomplete width based on refName length ([@cmdcolin](https://github.com/cmdcolin)) - - [#2243](https://github.com/GMOD/jbrowse-components/pull/2243) Import bookmarks functionality for grid bookmark widget ([@cmdcolin](https://github.com/cmdcolin)) + - [#2287](https://github.com/GMOD/jbrowse-components/pull/2287) Use + react-popper to reduce tooltip lag on pages with many elements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2294](https://github.com/GMOD/jbrowse-components/pull/2294) Don't rely on + SVTYPE=BND for breakend split view options and thicker mouseover chords on + circular views ([@cmdcolin](https://github.com/cmdcolin)) + - [#2272](https://github.com/GMOD/jbrowse-components/pull/2272) Auto adjust + box RefNameAutocomplete width based on refName length + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2243](https://github.com/GMOD/jbrowse-components/pull/2243) Import + bookmarks functionality for grid bookmark widget + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2247](https://github.com/GMOD/jbrowse-components/pull/2247) New jbrowse-desktop start screen design ([@cmdcolin](https://github.com/cmdcolin)) - - [#2254](https://github.com/GMOD/jbrowse-components/pull/2254) Better error reporting from web worker and chrom sizes adapter errors ([@cmdcolin](https://github.com/cmdcolin)) - - [#1881](https://github.com/GMOD/jbrowse-components/pull/1881) Add new text searching functionality to core, with `jbrowse text-index` CLI command to generate trix index ([@teresam856](https://github.com/teresam856)) + - [#2247](https://github.com/GMOD/jbrowse-components/pull/2247) New + jbrowse-desktop start screen design + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2254](https://github.com/GMOD/jbrowse-components/pull/2254) Better error + reporting from web worker and chrom sizes adapter errors + ([@cmdcolin](https://github.com/cmdcolin)) + - [#1881](https://github.com/GMOD/jbrowse-components/pull/1881) Add new text + searching functionality to core, with `jbrowse text-index` CLI command to + generate trix index ([@teresam856](https://github.com/teresam856)) #### :bug: Bug Fix - `core` - - [#2320](https://github.com/GMOD/jbrowse-components/pull/2320) Fix issue where add track widget doesn't infer adapters on second usage ([@cmdcolin](https://github.com/cmdcolin)) - - [#2250](https://github.com/GMOD/jbrowse-components/pull/2250) Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available ([@cmdcolin](https://github.com/cmdcolin)) + - [#2320](https://github.com/GMOD/jbrowse-components/pull/2320) Fix issue + where add track widget doesn't infer adapters on second usage + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2250](https://github.com/GMOD/jbrowse-components/pull/2250) Prevent the + ToggleButton for the FileSelector toggling to local file when only URL + should be available ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2309](https://github.com/GMOD/jbrowse-components/pull/2309) Fix mouseover selection appearing across unrelated blocks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2283](https://github.com/GMOD/jbrowse-components/pull/2283) Fix ability for the variant detail panel to create breakpoint split view for \ elements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2268](https://github.com/GMOD/jbrowse-components/pull/2268) Fix autocomplete height on small displays ([@cmdcolin](https://github.com/cmdcolin)) + - [#2309](https://github.com/GMOD/jbrowse-components/pull/2309) Fix mouseover + selection appearing across unrelated blocks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2283](https://github.com/GMOD/jbrowse-components/pull/2283) Fix ability + for the variant detail panel to create breakpoint split view for \ + elements ([@cmdcolin](https://github.com/cmdcolin)) + - [#2268](https://github.com/GMOD/jbrowse-components/pull/2268) Fix + autocomplete height on small displays + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2300](https://github.com/GMOD/jbrowse-components/pull/2300) Release announcement draft v1.4.0 ([@teresam856](https://github.com/teresam856)) -- [#2310](https://github.com/GMOD/jbrowse-components/pull/2310) Add cancer demos to the demos page on website ([@cmdcolin](https://github.com/cmdcolin)) -- [#2253](https://github.com/GMOD/jbrowse-components/pull/2253) Add note about legacy-peer-deps to embedded component readme ([@cmdcolin](https://github.com/cmdcolin)) -- [#2262](https://github.com/GMOD/jbrowse-components/pull/2262) Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks ([@cmdcolin](https://github.com/cmdcolin)) +- [#2300](https://github.com/GMOD/jbrowse-components/pull/2300) Release + announcement draft v1.4.0 ([@teresam856](https://github.com/teresam856)) +- [#2310](https://github.com/GMOD/jbrowse-components/pull/2310) Add cancer demos + to the demos page on website ([@cmdcolin](https://github.com/cmdcolin)) +- [#2253](https://github.com/GMOD/jbrowse-components/pull/2253) Add note about + legacy-peer-deps to embedded component readme + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2262](https://github.com/GMOD/jbrowse-components/pull/2262) Add more MDX + documentation pages to @jbrowse/react-linear-genome-view storybooks + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#2263](https://github.com/GMOD/jbrowse-components/pull/2263) Force publish all packages on release ([@cmdcolin](https://github.com/cmdcolin)) +- [#2263](https://github.com/GMOD/jbrowse-components/pull/2263) Force publish + all packages on release ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 diff --git a/website/blog/2021-10-18-v1.5.0-release.md b/website/blog/2021-10-18-v1.5.0-release.md index 00a4919c4a..0b45858792 100644 --- a/website/blog/2021-10-18-v1.5.0-release.md +++ b/website/blog/2021-10-18-v1.5.0-release.md @@ -4,8 +4,8 @@ date: 2021-10-18 14:02:19 tags: ['release', 'jbrowse 2'] --- -We are pleased to present the release of v1.5.0! We have some major new -features to announce with this version! +We are pleased to present the release of v1.5.0! We have some major new features +to announce with this version! ## JBrowse Desktop @@ -22,8 +22,10 @@ JBrowse Desktop features a new landing page designed to help you manage your work. Here's a few things you can do with it: - re-visit saved sessions using the recent session panel -- launch new sessions easily from the quick start panel (e.g. hg19 and hg38 are built-in) -- create a new entries in the quick start panel (e.g. quick launch your favorite organism) +- launch new sessions easily from the quick start panel (e.g. hg19 and hg38 are + built-in) +- create a new entries in the quick start panel (e.g. quick launch your favorite + organism) - quickly rename or delete sessions from the landing page ![JBrowse Desktop landing page](/img/desktop-landing.png) @@ -97,50 +99,98 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2413](https://github.com/GMOD/jbrowse-components/pull/2413) Bundle size savings ([@cmdcolin](https://github.com/cmdcolin)) - - [#2390](https://github.com/GMOD/jbrowse-components/pull/2390) Support plain text (non-tabix'ed) GFF files with new Gff3Adapter ([@teresam856](https://github.com/teresam856)) - - [#2384](https://github.com/GMOD/jbrowse-components/pull/2384) Allow docking the drawer on the left side of the screen ([@cmdcolin](https://github.com/cmdcolin)) - - [#2387](https://github.com/GMOD/jbrowse-components/pull/2387) Add bulk delete of sessions on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2279](https://github.com/GMOD/jbrowse-components/pull/2279) Add ability to access authenticated resources using pluggable internet accounts framework ([@peterkxie](https://github.com/peterkxie)) + - [#2413](https://github.com/GMOD/jbrowse-components/pull/2413) Bundle size + savings ([@cmdcolin](https://github.com/cmdcolin)) + - [#2390](https://github.com/GMOD/jbrowse-components/pull/2390) Support plain + text (non-tabix'ed) GFF files with new Gff3Adapter + ([@teresam856](https://github.com/teresam856)) + - [#2384](https://github.com/GMOD/jbrowse-components/pull/2384) Allow docking + the drawer on the left side of the screen + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2387](https://github.com/GMOD/jbrowse-components/pull/2387) Add bulk + delete of sessions on jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2279](https://github.com/GMOD/jbrowse-components/pull/2279) Add ability to + access authenticated resources using pluggable internet accounts framework + ([@peterkxie](https://github.com/peterkxie)) - Other - - [#2388](https://github.com/GMOD/jbrowse-components/pull/2388) Create "quickstart list" on jbrowse-desktop which users can add to ([@cmdcolin](https://github.com/cmdcolin)) - - [#2385](https://github.com/GMOD/jbrowse-components/pull/2385) Ensure all dependencies are properly specified in package.json files using eslint-plugin-import ([@cmdcolin](https://github.com/cmdcolin)) - - [#2373](https://github.com/GMOD/jbrowse-components/pull/2373) Add auto update functionality for jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2369](https://github.com/GMOD/jbrowse-components/pull/2369) Add tooltip with track description to track selector ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2258](https://github.com/GMOD/jbrowse-components/pull/2258) Update admin-server to accept value from ?config= so that multiple configs could be edited ([@cmdcolin](https://github.com/cmdcolin)) - - [#2321](https://github.com/GMOD/jbrowse-components/pull/2321) Add show descriptions toggle box to most feature tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2388](https://github.com/GMOD/jbrowse-components/pull/2388) Create + "quickstart list" on jbrowse-desktop which users can add to + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2385](https://github.com/GMOD/jbrowse-components/pull/2385) Ensure all + dependencies are properly specified in package.json files using + eslint-plugin-import ([@cmdcolin](https://github.com/cmdcolin)) + - [#2373](https://github.com/GMOD/jbrowse-components/pull/2373) Add auto + update functionality for jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2369](https://github.com/GMOD/jbrowse-components/pull/2369) Add tooltip + with track description to track selector + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2258](https://github.com/GMOD/jbrowse-components/pull/2258) Update + admin-server to accept value from ?config= so that multiple configs could be + edited ([@cmdcolin](https://github.com/cmdcolin)) + - [#2321](https://github.com/GMOD/jbrowse-components/pull/2321) Add show + descriptions toggle box to most feature tracks + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2355](https://github.com/GMOD/jbrowse-components/pull/2355) Allow prefix and exact matches jb1 text search ([@cmdcolin](https://github.com/cmdcolin)) - - [#2348](https://github.com/GMOD/jbrowse-components/pull/2348) Fix ability to use JB1 backcompat text search adapter ([@teresam856](https://github.com/teresam856)) - - [#2322](https://github.com/GMOD/jbrowse-components/pull/2322) Fix install plugin workflow and error handling on desktop, update to electron 15 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2329](https://github.com/GMOD/jbrowse-components/pull/2329) Fix bugs preventing embedded circular genome view from rendering in some circumstances ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2355](https://github.com/GMOD/jbrowse-components/pull/2355) Allow prefix + and exact matches jb1 text search ([@cmdcolin](https://github.com/cmdcolin)) + - [#2348](https://github.com/GMOD/jbrowse-components/pull/2348) Fix ability to + use JB1 backcompat text search adapter + ([@teresam856](https://github.com/teresam856)) + - [#2322](https://github.com/GMOD/jbrowse-components/pull/2322) Fix install + plugin workflow and error handling on desktop, update to electron 15 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2329](https://github.com/GMOD/jbrowse-components/pull/2329) Fix bugs + preventing embedded circular genome view from rendering in some + circumstances ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2352](https://github.com/GMOD/jbrowse-components/pull/2352) Better keyboard navigations on text search autocomplete component ([@cmdcolin](https://github.com/cmdcolin)) - - [#2332](https://github.com/GMOD/jbrowse-components/pull/2332) Fix ability to use LocalFile on nodejs-based apps e.g. @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) + - [#2352](https://github.com/GMOD/jbrowse-components/pull/2352) Better + keyboard navigations on text search autocomplete component + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2332](https://github.com/GMOD/jbrowse-components/pull/2332) Fix ability to + use LocalFile on nodejs-based apps e.g. @jbrowse/img + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2407](https://github.com/GMOD/jbrowse-components/pull/2407) Update website for jbrowse-desktop release ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) -- [#2328](https://github.com/GMOD/jbrowse-components/pull/2328) Use ../ for all doc links and use trailing slash to fix links ([@cmdcolin](https://github.com/cmdcolin)) +- [#2407](https://github.com/GMOD/jbrowse-components/pull/2407) Update website + for jbrowse-desktop release + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#2328](https://github.com/GMOD/jbrowse-components/pull/2328) Use ../ for all + doc links and use trailing slash to fix links + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - Other - - [#2382](https://github.com/GMOD/jbrowse-components/pull/2382) Export RefNameAutocomplete and ViewModel from LinearGenomeView for downstream usage ([@hextraza](https://github.com/hextraza)) - - [#2336](https://github.com/GMOD/jbrowse-components/pull/2336) Add jbrowse-img to monorepo ([@cmdcolin](https://github.com/cmdcolin)) - - [#2324](https://github.com/GMOD/jbrowse-components/pull/2324) Remove unused wrapForRpc functionality ([@cmdcolin](https://github.com/cmdcolin)) + - [#2382](https://github.com/GMOD/jbrowse-components/pull/2382) Export + RefNameAutocomplete and ViewModel from LinearGenomeView for downstream usage + ([@hextraza](https://github.com/hextraza)) + - [#2336](https://github.com/GMOD/jbrowse-components/pull/2336) Add + jbrowse-img to monorepo ([@cmdcolin](https://github.com/cmdcolin)) + - [#2324](https://github.com/GMOD/jbrowse-components/pull/2324) Remove unused + wrapForRpc functionality ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2379](https://github.com/GMOD/jbrowse-components/pull/2379) Bump typescript to 4.4.3 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2363](https://github.com/GMOD/jbrowse-components/pull/2363) Add some typescripting of some MST models and components ([@cmdcolin](https://github.com/cmdcolin)) - - [#2351](https://github.com/GMOD/jbrowse-components/pull/2351) Use main "module" field instead of "browser" from dependency package json files electron builds ([@cmdcolin](https://github.com/cmdcolin)) - - [#2323](https://github.com/GMOD/jbrowse-components/pull/2323) Remove session related menu items from jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#2379](https://github.com/GMOD/jbrowse-components/pull/2379) Bump + typescript to 4.4.3 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2363](https://github.com/GMOD/jbrowse-components/pull/2363) Add some + typescripting of some MST models and components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2351](https://github.com/GMOD/jbrowse-components/pull/2351) Use main + "module" field instead of "browser" from dependency package json files + electron builds ([@cmdcolin](https://github.com/cmdcolin)) + - [#2323](https://github.com/GMOD/jbrowse-components/pull/2323) Remove session + related menu items from jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 6 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) diff --git a/website/blog/2021-11-04-v1.5.1-release.md b/website/blog/2021-11-04-v1.5.1-release.md index 346703b660..aee3e173c1 100644 --- a/website/blog/2021-11-04-v1.5.1-release.md +++ b/website/blog/2021-11-04-v1.5.1-release.md @@ -31,8 +31,8 @@ with the Core-guessAdapterForLocation ## Open plaintext FASTA file on JBrowse desktop -Users can now open a plain FASTA instead of an indexed FASTA on JBrowse -desktop, and it will create a .fai index on the fly +Users can now open a plain FASTA instead of an indexed FASTA on JBrowse desktop, +and it will create a .fai index on the fly ## Downloads @@ -88,48 +88,91 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2488](https://github.com/GMOD/jbrowse-components/pull/2488) Improve usability of the search result autocomplete when typing in via keyboard ([@cmdcolin](https://github.com/cmdcolin)) - - [#2267](https://github.com/GMOD/jbrowse-components/pull/2267) Add cytoband to overview scale bar in LGV ([@cmdcolin](https://github.com/cmdcolin)) - - [#2447](https://github.com/GMOD/jbrowse-components/pull/2447) Drawer widget tooltips and use position: fixed on fab ([@cmdcolin](https://github.com/cmdcolin)) - - [#2299](https://github.com/GMOD/jbrowse-components/pull/2299) Add new pluggable element type and properties to adapter type for registering adapter association with 'add track' workflow ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2488](https://github.com/GMOD/jbrowse-components/pull/2488) Improve + usability of the search result autocomplete when typing in via keyboard + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2267](https://github.com/GMOD/jbrowse-components/pull/2267) Add cytoband + to overview scale bar in LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2447](https://github.com/GMOD/jbrowse-components/pull/2447) Drawer widget + tooltips and use position: fixed on fab + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2299](https://github.com/GMOD/jbrowse-components/pull/2299) Add new + pluggable element type and properties to adapter type for registering + adapter association with 'add track' workflow + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Other - - [#2484](https://github.com/GMOD/jbrowse-components/pull/2484) "Add custom plugin" dialog improvements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2389](https://github.com/GMOD/jbrowse-components/pull/2389) Create plaintext GtfAdapter in plugins/gtf ([@teresam856](https://github.com/teresam856)) - - [#2443](https://github.com/GMOD/jbrowse-components/pull/2443) Support plaintext fasta on desktop by dynamically creating a FAI file on the fly ([@cmdcolin](https://github.com/cmdcolin)) - - [#2479](https://github.com/GMOD/jbrowse-components/pull/2479) Allow gzipped Gff3Adapter input and use 512MB limit ([@cmdcolin](https://github.com/cmdcolin)) - - [#2467](https://github.com/GMOD/jbrowse-components/pull/2467) Set default session dialog redesign ([@cmdcolin](https://github.com/cmdcolin)) - - [#2461](https://github.com/GMOD/jbrowse-components/pull/2461) Add assembly manager back into tools menu on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2442](https://github.com/GMOD/jbrowse-components/pull/2442) Add simple loading screen for LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2484](https://github.com/GMOD/jbrowse-components/pull/2484) "Add custom + plugin" dialog improvements ([@cmdcolin](https://github.com/cmdcolin)) + - [#2389](https://github.com/GMOD/jbrowse-components/pull/2389) Create + plaintext GtfAdapter in plugins/gtf + ([@teresam856](https://github.com/teresam856)) + - [#2443](https://github.com/GMOD/jbrowse-components/pull/2443) Support + plaintext fasta on desktop by dynamically creating a FAI file on the fly + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2479](https://github.com/GMOD/jbrowse-components/pull/2479) Allow gzipped + Gff3Adapter input and use 512MB limit + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2467](https://github.com/GMOD/jbrowse-components/pull/2467) Set default + session dialog redesign ([@cmdcolin](https://github.com/cmdcolin)) + - [#2461](https://github.com/GMOD/jbrowse-components/pull/2461) Add assembly + manager back into tools menu on jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2442](https://github.com/GMOD/jbrowse-components/pull/2442) Add simple + loading screen for LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2494](https://github.com/GMOD/jbrowse-components/pull/2494) Add polyfill for text-index compatibility with node 10 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2492](https://github.com/GMOD/jbrowse-components/pull/2492) Fix ability to open breakpoint split view from a BEDPE row in SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#2480](https://github.com/GMOD/jbrowse-components/pull/2480) Fix refName renaming on VcfAdapter for files that don't have ##contig lines ([@cmdcolin](https://github.com/cmdcolin)) - - [#2469](https://github.com/GMOD/jbrowse-components/pull/2469) Fix embedded crash when opening dialogs ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2451](https://github.com/GMOD/jbrowse-components/pull/2451) Fix issue with intermittent text-index failures and improve speed ([@cmdcolin](https://github.com/cmdcolin)) - - [#2439](https://github.com/GMOD/jbrowse-components/pull/2439) Fix adding plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2426](https://github.com/GMOD/jbrowse-components/pull/2426) Fix CLI create/upgrade failing to find the latest release ([@cmdcolin](https://github.com/cmdcolin)) + - [#2494](https://github.com/GMOD/jbrowse-components/pull/2494) Add polyfill + for text-index compatibility with node 10 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2492](https://github.com/GMOD/jbrowse-components/pull/2492) Fix ability to + open breakpoint split view from a BEDPE row in SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2480](https://github.com/GMOD/jbrowse-components/pull/2480) Fix refName + renaming on VcfAdapter for files that don't have ##contig lines + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2469](https://github.com/GMOD/jbrowse-components/pull/2469) Fix embedded + crash when opening dialogs + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2451](https://github.com/GMOD/jbrowse-components/pull/2451) Fix issue with + intermittent text-index failures and improve speed + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2439](https://github.com/GMOD/jbrowse-components/pull/2439) Fix adding + plugins on desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#2426](https://github.com/GMOD/jbrowse-components/pull/2426) Fix CLI + create/upgrade failing to find the latest release + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2457](https://github.com/GMOD/jbrowse-components/pull/2457) Fix linear synteny view import form failure ([@cmdcolin](https://github.com/cmdcolin)) - - [#2444](https://github.com/GMOD/jbrowse-components/pull/2444) Fix crash when chromSizesLocation not specified when loading TwoBitAdapter in GUI ([@cmdcolin](https://github.com/cmdcolin)) + - [#2457](https://github.com/GMOD/jbrowse-components/pull/2457) Fix linear + synteny view import form failure ([@cmdcolin](https://github.com/cmdcolin)) + - [#2444](https://github.com/GMOD/jbrowse-components/pull/2444) Fix crash when + chromSizesLocation not specified when loading TwoBitAdapter in GUI + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2446](https://github.com/GMOD/jbrowse-components/pull/2446) Improve some CLI --help messages ([@cmdcolin](https://github.com/cmdcolin)) -- [#2437](https://github.com/GMOD/jbrowse-components/pull/2437) Add example of defining and using a plugin with the embedded component ([@cmdcolin](https://github.com/cmdcolin)) -- [#2430](https://github.com/GMOD/jbrowse-components/pull/2430) Website optimize for less layout shift ([@cmdcolin](https://github.com/cmdcolin)) +- [#2446](https://github.com/GMOD/jbrowse-components/pull/2446) Improve some CLI + --help messages ([@cmdcolin](https://github.com/cmdcolin)) +- [#2437](https://github.com/GMOD/jbrowse-components/pull/2437) Add example of + defining and using a plugin with the embedded component + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2430](https://github.com/GMOD/jbrowse-components/pull/2430) Website optimize + for less layout shift ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2445](https://github.com/GMOD/jbrowse-components/pull/2445) Create core snapshot error message component ([@cmdcolin](https://github.com/cmdcolin)) - - [#2288](https://github.com/GMOD/jbrowse-components/pull/2288) Add extra re-exports for default modules ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2445](https://github.com/GMOD/jbrowse-components/pull/2445) Create core + snapshot error message component ([@cmdcolin](https://github.com/cmdcolin)) + - [#2288](https://github.com/GMOD/jbrowse-components/pull/2288) Add extra + re-exports for default modules + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 4 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Teresa Martinez ([@teresam856](https://github.com/teresam856)) diff --git a/website/blog/2021-12-20-v1.5.2-release.md b/website/blog/2021-12-20-v1.5.2-release.md index c5b6e959ec..9d7b61d50a 100644 --- a/website/blog/2021-12-20-v1.5.2-release.md +++ b/website/blog/2021-12-20-v1.5.2-release.md @@ -4,8 +4,8 @@ date: 2021-12-20 13:31:18 tags: ['release', 'jbrowse 2'] --- -We're excited to present some great new features and performance improvements -in v1.5.2! +We're excited to present some great new features and performance improvements in +v1.5.2! ## New arc display type @@ -23,7 +23,8 @@ work, but if you want to check out how the new template works, check out the ## Storybook docs added for Circular Genome View React component -Find them linked under `@jbrowse/react-circular-genome-view` [here](https://jbrowse.org/jb2/download/#embedded-components). +Find them linked under `@jbrowse/react-circular-genome-view` +[here](https://jbrowse.org/jb2/download/#embedded-components). ## Performance improvements @@ -87,55 +88,115 @@ on NPM. #### :rocket: Enhancement - Other - - [#2579](https://github.com/GMOD/jbrowse-components/pull/2579) Add help text and help dialog for the RefNameAutocomplete ([@cmdcolin](https://github.com/cmdcolin)) - - [#2553](https://github.com/GMOD/jbrowse-components/pull/2553) Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display ([@cmdcolin](https://github.com/cmdcolin)) - - [#2552](https://github.com/GMOD/jbrowse-components/pull/2552) Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill ([@cmdcolin](https://github.com/cmdcolin)) - - [#2509](https://github.com/GMOD/jbrowse-components/pull/2509) Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer ([@hextraza](https://github.com/hextraza)) - - [#2485](https://github.com/GMOD/jbrowse-components/pull/2485) Only use one button, "Go", in text search ambiguous results dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2501](https://github.com/GMOD/jbrowse-components/pull/2501) Add a tooltip to desktop session path so you can see the full path if it's cut off ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2579](https://github.com/GMOD/jbrowse-components/pull/2579) Add help text + and help dialog for the RefNameAutocomplete + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2553](https://github.com/GMOD/jbrowse-components/pull/2553) Add + sashimi-style arcs for RNA-seq type skips on SNPCoverage display + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2552](https://github.com/GMOD/jbrowse-components/pull/2552) Change border + on non-cytoband OverviewScaleBar visible region back to blue and cytoband + OverviewScaleBar to a little lighter fill + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2509](https://github.com/GMOD/jbrowse-components/pull/2509) Implement prop + interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer + ([@hextraza](https://github.com/hextraza)) + - [#2485](https://github.com/GMOD/jbrowse-components/pull/2485) Only use one + button, "Go", in text search ambiguous results dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2501](https://github.com/GMOD/jbrowse-components/pull/2501) Add a tooltip + to desktop session path so you can see the full path if it's cut off + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2580](https://github.com/GMOD/jbrowse-components/pull/2580) Make core snackbar notifications module with auto-dismissing info/success level notifications ([@cmdcolin](https://github.com/cmdcolin)) - - [#2534](https://github.com/GMOD/jbrowse-components/pull/2534) New display type for drawing arcs ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2590](https://github.com/GMOD/jbrowse-components/pull/2590) Add more exports that can be used by plugins ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2578](https://github.com/GMOD/jbrowse-components/pull/2578) Add layouts code to core re-exports ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2523](https://github.com/GMOD/jbrowse-components/pull/2523) Performance optimizations for alignments tracks, particularly those with many short reads ([@cmdcolin](https://github.com/cmdcolin)) - - [#2500](https://github.com/GMOD/jbrowse-components/pull/2500) Add RenderProps to core/pluggableElementTypes export ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2580](https://github.com/GMOD/jbrowse-components/pull/2580) Make core + snackbar notifications module with auto-dismissing info/success level + notifications ([@cmdcolin](https://github.com/cmdcolin)) + - [#2534](https://github.com/GMOD/jbrowse-components/pull/2534) New display + type for drawing arcs + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2590](https://github.com/GMOD/jbrowse-components/pull/2590) Add more + exports that can be used by plugins + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2578](https://github.com/GMOD/jbrowse-components/pull/2578) Add layouts + code to core re-exports + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2523](https://github.com/GMOD/jbrowse-components/pull/2523) Performance + optimizations for alignments tracks, particularly those with many short + reads ([@cmdcolin](https://github.com/cmdcolin)) + - [#2500](https://github.com/GMOD/jbrowse-components/pull/2500) Add + RenderProps to core/pluggableElementTypes export + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core`, `development-tools` - - [#2487](https://github.com/GMOD/jbrowse-components/pull/2487) Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2487](https://github.com/GMOD/jbrowse-components/pull/2487) Add support + for additional types of plugin formats (commonjs, esm) to allow access to + node modules on jbrowse desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#2594](https://github.com/GMOD/jbrowse-components/pull/2594) Fix infinite loop bug while searching certain strings and handle multi-word searches better ([@cmdcolin](https://github.com/cmdcolin)) - - [#2589](https://github.com/GMOD/jbrowse-components/pull/2589) Fix occasional failures observed from running text-index command ([@cmdcolin](https://github.com/cmdcolin)) - - [#2583](https://github.com/GMOD/jbrowse-components/pull/2583) Fix for alignments track base modifications display regarding skipped bases on Mm tag ([@cmdcolin](https://github.com/cmdcolin)) - - [#2556](https://github.com/GMOD/jbrowse-components/pull/2556) Fix ability to access BigWig tracks on http basic auth for some cases ([@cmdcolin](https://github.com/cmdcolin)) - - [#2577](https://github.com/GMOD/jbrowse-components/pull/2577) Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2521](https://github.com/GMOD/jbrowse-components/pull/2521) Fix ability to search for tracks with parentheses in tracklist ([@cmdcolin](https://github.com/cmdcolin)) - - [#2512](https://github.com/GMOD/jbrowse-components/pull/2512) Fix [object Window] issue in alignment read vs reference dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2499](https://github.com/GMOD/jbrowse-components/pull/2499) Add missing dependency to CLI ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2594](https://github.com/GMOD/jbrowse-components/pull/2594) Fix infinite + loop bug while searching certain strings and handle multi-word searches + better ([@cmdcolin](https://github.com/cmdcolin)) + - [#2589](https://github.com/GMOD/jbrowse-components/pull/2589) Fix occasional + failures observed from running text-index command + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2583](https://github.com/GMOD/jbrowse-components/pull/2583) Fix for + alignments track base modifications display regarding skipped bases on Mm + tag ([@cmdcolin](https://github.com/cmdcolin)) + - [#2556](https://github.com/GMOD/jbrowse-components/pull/2556) Fix ability to + access BigWig tracks on http basic auth for some cases + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2577](https://github.com/GMOD/jbrowse-components/pull/2577) Fix ability to + use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, + GTF support to add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) + - [#2521](https://github.com/GMOD/jbrowse-components/pull/2521) Fix ability to + search for tracks with parentheses in tracklist + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2512](https://github.com/GMOD/jbrowse-components/pull/2512) Fix [object + Window] issue in alignment read vs reference dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2499](https://github.com/GMOD/jbrowse-components/pull/2499) Add missing + dependency to CLI ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#2585](https://github.com/GMOD/jbrowse-components/pull/2585) Fix ability to use "Color by methylation" on files that require refname renaming ([@cmdcolin](https://github.com/cmdcolin)) - - [#2517](https://github.com/GMOD/jbrowse-components/pull/2517) Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state ([@cmdcolin](https://github.com/cmdcolin)) - - [#2564](https://github.com/GMOD/jbrowse-components/pull/2564) Start looking for parents with parent, not self in findParentThat ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2563](https://github.com/GMOD/jbrowse-components/pull/2563) Restore ability to load plugins from relative URL ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2533](https://github.com/GMOD/jbrowse-components/pull/2533) Fix drawer widget minimized button being unclickable when overlapping with a view ([@cmdcolin](https://github.com/cmdcolin)) + - [#2585](https://github.com/GMOD/jbrowse-components/pull/2585) Fix ability to + use "Color by methylation" on files that require refname renaming + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2517](https://github.com/GMOD/jbrowse-components/pull/2517) Remove + aborting on adapter loading process to fix some tracks getting stuck in + infinite loading state ([@cmdcolin](https://github.com/cmdcolin)) + - [#2564](https://github.com/GMOD/jbrowse-components/pull/2564) Start looking + for parents with parent, not self in findParentThat + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2563](https://github.com/GMOD/jbrowse-components/pull/2563) Restore + ability to load plugins from relative URL + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2533](https://github.com/GMOD/jbrowse-components/pull/2533) Fix drawer + widget minimized button being unclickable when overlapping with a view + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2522](https://github.com/GMOD/jbrowse-components/pull/2522) Add circular genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) -- [#2508](https://github.com/GMOD/jbrowse-components/pull/2508) Update docs for embedded components ([@teresam856](https://github.com/teresam856)) -- [#2495](https://github.com/GMOD/jbrowse-components/pull/2495) Improve organization on docs landing page ([@cmdcolin](https://github.com/cmdcolin)) +- [#2522](https://github.com/GMOD/jbrowse-components/pull/2522) Add circular + genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) +- [#2508](https://github.com/GMOD/jbrowse-components/pull/2508) Update docs for + embedded components ([@teresam856](https://github.com/teresam856)) +- [#2495](https://github.com/GMOD/jbrowse-components/pull/2495) Improve + organization on docs landing page ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2597](https://github.com/GMOD/jbrowse-components/pull/2597) Fix flaky tests related to auth and canvas image snapshots ([@cmdcolin](https://github.com/cmdcolin)) - - [#2504](https://github.com/GMOD/jbrowse-components/pull/2504) Spreadsheet change jbrequire to es6 imports ([@cmdcolin](https://github.com/cmdcolin)) + - [#2597](https://github.com/GMOD/jbrowse-components/pull/2597) Fix flaky + tests related to auth and canvas image snapshots + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2504](https://github.com/GMOD/jbrowse-components/pull/2504) Spreadsheet + change jbrequire to es6 imports ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 6 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - Peter Xie ([@peterkxie](https://github.com/peterkxie)) diff --git a/website/blog/2021-12-21-v1.5.3-release.md b/website/blog/2021-12-21-v1.5.3-release.md index 3516dc922b..1b72341ef8 100644 --- a/website/blog/2021-12-21-v1.5.3-release.md +++ b/website/blog/2021-12-21-v1.5.3-release.md @@ -36,7 +36,9 @@ on NPM. #### :bug: Bug Fix - `development-tools` - - [#2600](https://github.com/GMOD/jbrowse-components/pull/2600) Fix broken published build of jbrowse/development-tools ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2600](https://github.com/GMOD/jbrowse-components/pull/2600) Fix broken + published build of jbrowse/development-tools + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 1 diff --git a/website/blog/2022-01-07-v1.5.5-release.md b/website/blog/2022-01-07-v1.5.5-release.md index 6a31f35375..5c233cffb1 100644 --- a/website/blog/2022-01-07-v1.5.5-release.md +++ b/website/blog/2022-01-07-v1.5.5-release.md @@ -12,7 +12,7 @@ It also adds some better layout in the feature details panel, improved typescript interfaces, and allows users to open multiple genome assemblies from the start screen in JBrowse Desktop -This release also supercedes v1.5.4 which failed to upload to npm properly +This release also supersedes v1.5.4 which failed to upload to npm properly ## Downloads @@ -44,27 +44,43 @@ on NPM. #### :rocket: Enhancement - Other - - [#2601](https://github.com/GMOD/jbrowse-components/pull/2601) Allow opening multiple sequences from the desktop start screen ([@cmdcolin](https://github.com/cmdcolin)) + - [#2601](https://github.com/GMOD/jbrowse-components/pull/2601) Allow opening + multiple sequences from the desktop start screen + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2623](https://github.com/GMOD/jbrowse-components/pull/2623) Adjust label width on base feature detail to enforce better alignment ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2623](https://github.com/GMOD/jbrowse-components/pull/2623) Adjust label + width on base feature detail to enforce better alignment + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :bug: Bug Fix - Other - - [#2612](https://github.com/GMOD/jbrowse-components/pull/2612) Fix ability to remove plugins ([@cmdcolin](https://github.com/cmdcolin)) - - [#2622](https://github.com/GMOD/jbrowse-components/pull/2622) Fix GUI color editor rgba string format ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2607](https://github.com/GMOD/jbrowse-components/pull/2607) Fix wiggle tooltip crash on non-numerical inputs ([@cmdcolin](https://github.com/cmdcolin)) + - [#2612](https://github.com/GMOD/jbrowse-components/pull/2612) Fix ability to + remove plugins ([@cmdcolin](https://github.com/cmdcolin)) + - [#2622](https://github.com/GMOD/jbrowse-components/pull/2622) Fix GUI color + editor rgba string format + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2607](https://github.com/GMOD/jbrowse-components/pull/2607) Fix wiggle + tooltip crash on non-numerical inputs + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2626](https://github.com/GMOD/jbrowse-components/pull/2626) Fix bad layout resulting in features being unable to be clicked in embedded mode ([@cmdcolin](https://github.com/cmdcolin)) + - [#2626](https://github.com/GMOD/jbrowse-components/pull/2626) Fix bad layout + resulting in features being unable to be clicked in embedded mode + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2595](https://github.com/GMOD/jbrowse-components/pull/2595) Use some newly available TypeScript types ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2576](https://github.com/GMOD/jbrowse-components/pull/2576) Use TypeScript parameter properties ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2595](https://github.com/GMOD/jbrowse-components/pull/2595) Use some newly + available TypeScript types + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2576](https://github.com/GMOD/jbrowse-components/pull/2576) Use TypeScript + parameter properties + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) diff --git a/website/blog/2022-01-13-v1.5.8-release.md b/website/blog/2022-01-13-v1.5.8-release.md index 9fc4fc0e3f..a9fef47963 100644 --- a/website/blog/2022-01-13-v1.5.8-release.md +++ b/website/blog/2022-01-13-v1.5.8-release.md @@ -8,12 +8,12 @@ This release fixes an important issue where @jbrowse/react-linear-genome-view and other embedded packages did not work with v1.5.5 due to a babel misconfiguration apologies to all affected! -Also we now can access the parent feature in jexl callbacks with -parent(feature) or get(feature, 'parent') which is often needed when coloring -subfeatures like exon/CDS features +Also we now can access the parent feature in jexl callbacks with parent(feature) +or get(feature, 'parent') which is often needed when coloring subfeatures like +exon/CDS features -This release also was made because v1.5.6 and v1.5.7 only were half-published -to npm, so v1.5.8 fixes it here +This release also was made because v1.5.6 and v1.5.7 only were half-published to +npm, so v1.5.8 fixes it here ## Downloads @@ -45,8 +45,11 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2629](https://github.com/GMOD/jbrowse-components/pull/2629) Add ability to get parent feature in jexl syntax with either parent(feature) or get(feature,'parent') ([@cmdcolin](https://github.com/cmdcolin)) - - [#2632](https://github.com/GMOD/jbrowse-components/pull/2632) Add vertical resize handle to dotplot view ([@cmdcolin](https://github.com/cmdcolin)) + - [#2629](https://github.com/GMOD/jbrowse-components/pull/2629) Add ability to + get parent feature in jexl syntax with either parent(feature) or + get(feature,'parent') ([@cmdcolin](https://github.com/cmdcolin)) + - [#2632](https://github.com/GMOD/jbrowse-components/pull/2632) Add vertical + resize handle to dotplot view ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 diff --git a/website/blog/2022-01-13-v1.5.9-release.md b/website/blog/2022-01-13-v1.5.9-release.md index 95fee2b003..9cea3f56ce 100644 --- a/website/blog/2022-01-13-v1.5.9-release.md +++ b/website/blog/2022-01-13-v1.5.9-release.md @@ -4,7 +4,8 @@ date: 2022-01-13 15:23:06 tags: ['release', 'jbrowse 2'] --- -This fixes a babel misconfiguration in v1.5.8 that prevented embedded packages from working +This fixes a babel misconfiguration in v1.5.8 that prevented embedded packages +from working ## Downloads @@ -37,7 +38,9 @@ on NPM. #### :bug: Bug Fix -- [#2645](https://github.com/GMOD/jbrowse-components/pull/2645) Fix core by not using absolute runtime in babel ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2645](https://github.com/GMOD/jbrowse-components/pull/2645) Fix core by not + using absolute runtime in babel + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 1 diff --git a/website/blog/2022-01-29-v1.6.4-release.md b/website/blog/2022-01-29-v1.6.4-release.md index 1f9707f2f8..9c4d87ed81 100644 --- a/website/blog/2022-01-29-v1.6.4-release.md +++ b/website/blog/2022-01-29-v1.6.4-release.md @@ -8,9 +8,9 @@ This release has a couple long awaited features! - Ability to load a session from a URL in JBrowse Web, for example, https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:2000-40000&assembly=volvox&tracks=gff3tabix_genes,volvox_filtered_vcf,volvox_microarray,volvox_cram - Note: the embedded components do not make any assumptions about the URL, so - do not have this functionality. Just the JBrowse Web package. See [the URL - params API docs](/docs/urlparams) for more info + Note: the embedded components do not make any assumptions about the URL, so do + not have this functionality. Just the JBrowse Web package. See + [the URL params API docs](/docs/urlparams) for more info - Stats estimation, tracks will try to estimate how much data they have to load and hide themselves if it is determined to be too much @@ -21,11 +21,13 @@ also vertically resize the linear synteny view panel allowing for a taller or shorter view! The rendering has also been sped up in both linear synteny and dotplot views with certain code paths being up to 40x faster. -Also check out the recording and notes from our [PAG 2022 tutorial -session](/docs/tutorials/archive/pag2022_synteny_tutorial/)! +Also check out the recording and notes from our +[PAG 2022 tutorial session](/docs/archive/pag2022_synteny_tutorial/)! ![](https://user-images.githubusercontent.com/6511937/151449824-8993a755-cc44-440f-bd98-8d251f144c58.png) -Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.4/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj +Screenshot showing the new curvy lines of the synteny view with the grape vs +peach demo +http://jbrowse.org/code/jb2/v1.6.4/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj note that 1.6.0-1.6.3 were slightly buggy and collected into 1.6.4 here @@ -54,40 +56,74 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations and usability improvements to synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) - - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to display curved lines and to square the dotplot and synteny views ([@cmdcolin](https://github.com/cmdcolin)) - - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot plot rendering ([@cmdcolin](https://github.com/cmdcolin)) + - [#2679](https://github.com/GMOD/jbrowse-components/pull/2679) Optimizations + and usability improvements to synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2677](https://github.com/GMOD/jbrowse-components/pull/2677) Save user + settings from LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#2571](https://github.com/GMOD/jbrowse-components/pull/2571) Add stats + estimation to JB2 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2666](https://github.com/GMOD/jbrowse-components/pull/2666) Add option to + display curved lines and to square the dotplot and synteny views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2672](https://github.com/GMOD/jbrowse-components/pull/2672) Optimize dot + plot rendering ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error handling on jbrowse desktop open sequence dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap PAF support ([@cmdcolin](https://github.com/cmdcolin)) - - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of deletion on reads in alignments track ([@cmdcolin](https://github.com/cmdcolin)) + - [#2680](https://github.com/GMOD/jbrowse-components/pull/2680) Improve error + handling on jbrowse desktop open sequence dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2670](https://github.com/GMOD/jbrowse-components/pull/2670) Add mashmap + PAF support ([@cmdcolin](https://github.com/cmdcolin)) + - [#2659](https://github.com/GMOD/jbrowse-components/pull/2659) Draw size of + deletion on reads in alignments track + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to create new sessions solely from a "session spec" in the URL ([@cmdcolin](https://github.com/cmdcolin)) + - [#2165](https://github.com/GMOD/jbrowse-components/pull/2165) Add ability to + create new sessions solely from a "session spec" in the URL + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix adapterType dropdown in add track widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken @jbrowse/img by adding babel config back to core ([@cmdcolin](https://github.com/cmdcolin)) + - [#2688](https://github.com/GMOD/jbrowse-components/pull/2688) Fix + adapterType dropdown in add track widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2654](https://github.com/GMOD/jbrowse-components/pull/2654) Fix broken + @jbrowse/img by adding babel config back to core + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use path.resolve to fix --load symlink in jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom glyphs to apply to features without subfeatures ([@bbimber](https://github.com/bbimber)) - - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" of embedded React views ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2686](https://github.com/GMOD/jbrowse-components/pull/2686) Use + path.resolve to fix --load symlink in jbrowse CLI + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2660](https://github.com/GMOD/jbrowse-components/pull/2660) Fix custom + glyphs to apply to features without subfeatures + ([@bbimber](https://github.com/bbimber)) + - [#2652](https://github.com/GMOD/jbrowse-components/pull/2652) Fix "module" + of embedded React views + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation -- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add documentation for URL params and session spec ([@cmdcolin](https://github.com/cmdcolin)) -- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG 2022 youtube tutorial on demos page and course archive ([@cmdcolin](https://github.com/cmdcolin)) +- [#2663](https://github.com/GMOD/jbrowse-components/pull/2663) Add + documentation for URL params and session spec + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2655](https://github.com/GMOD/jbrowse-components/pull/2655) Add link to PAG + 2022 youtube tutorial on demos page and course archive + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress test of package that uses embedded components ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid console.warns in tests due to writing to MST nodes that are not alive ([@cmdcolin](https://github.com/cmdcolin)) + - [#2649](https://github.com/GMOD/jbrowse-components/pull/2649) Add Cypress + test of package that uses embedded components + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2648](https://github.com/GMOD/jbrowse-components/pull/2648) Avoid + console.warns in tests due to writing to MST nodes that are not alive + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload using yarn resolution on react-error-overlay ([@cmdcolin](https://github.com/cmdcolin)) + - [#2657](https://github.com/GMOD/jbrowse-components/pull/2657) Fix hot reload + using yarn resolution on react-error-overlay + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 diff --git a/website/blog/2022-02-18-v1.6.5-release.md b/website/blog/2022-02-18-v1.6.5-release.md index a65f7ac8b8..0240a2776b 100644 --- a/website/blog/2022-02-18-v1.6.5-release.md +++ b/website/blog/2022-02-18-v1.6.5-release.md @@ -59,36 +59,70 @@ on NPM. #### :rocket: Enhancement -- [#2736](https://github.com/GMOD/jbrowse-components/pull/2736) Add better display of error state in dotplot view and load gzipped PAF files ([@cmdcolin](https://github.com/cmdcolin)) -- [#2705](https://github.com/GMOD/jbrowse-components/pull/2705) Increase admin-server payload limit ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2736](https://github.com/GMOD/jbrowse-components/pull/2736) Add better + display of error state in dotplot view and load gzipped PAF files + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2705](https://github.com/GMOD/jbrowse-components/pull/2705) Increase + admin-server payload limit + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#2758](https://github.com/GMOD/jbrowse-components/pull/2758) Use VariantTrack for plaintext VCF type ([@cmdcolin](https://github.com/cmdcolin)) - - [#2738](https://github.com/GMOD/jbrowse-components/pull/2738) Add better catch for XS and TS tag detection from CRAM ([@cmdcolin](https://github.com/cmdcolin)) - - [#2733](https://github.com/GMOD/jbrowse-components/pull/2733) Use sparse array for alignments coverage to fix bug viewing large sparse regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2734](https://github.com/GMOD/jbrowse-components/pull/2734) Use node fetch instead of follow-redirects in cli ([@cmdcolin](https://github.com/cmdcolin)) - - [#2726](https://github.com/GMOD/jbrowse-components/pull/2726) Handle .bgz file extension for text-index ([@cmdcolin](https://github.com/cmdcolin)) - - [#2727](https://github.com/GMOD/jbrowse-components/pull/2727) Add engines 16 to @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) - - [#2723](https://github.com/GMOD/jbrowse-components/pull/2723) Make jbrowse desktop more robust to errors when reading recent sessions file ([@cmdcolin](https://github.com/cmdcolin)) - - [#2715](https://github.com/GMOD/jbrowse-components/pull/2715) Change --target to --root for jbrowse CLI admin-server ([@cmdcolin](https://github.com/cmdcolin)) + - [#2758](https://github.com/GMOD/jbrowse-components/pull/2758) Use + VariantTrack for plaintext VCF type + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2738](https://github.com/GMOD/jbrowse-components/pull/2738) Add better + catch for XS and TS tag detection from CRAM + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2733](https://github.com/GMOD/jbrowse-components/pull/2733) Use sparse + array for alignments coverage to fix bug viewing large sparse regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2734](https://github.com/GMOD/jbrowse-components/pull/2734) Use node fetch + instead of follow-redirects in cli + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2726](https://github.com/GMOD/jbrowse-components/pull/2726) Handle .bgz + file extension for text-index ([@cmdcolin](https://github.com/cmdcolin)) + - [#2727](https://github.com/GMOD/jbrowse-components/pull/2727) Add engines 16 + to @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) + - [#2723](https://github.com/GMOD/jbrowse-components/pull/2723) Make jbrowse + desktop more robust to errors when reading recent sessions file + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2715](https://github.com/GMOD/jbrowse-components/pull/2715) Change + --target to --root for jbrowse CLI admin-server + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2757](https://github.com/GMOD/jbrowse-components/pull/2757) Fix type confusion with stats estimation causing BAM files to fail byte size calculation ([@cmdcolin](https://github.com/cmdcolin)) - - [#2750](https://github.com/GMOD/jbrowse-components/pull/2750) Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox ([@cmdcolin](https://github.com/cmdcolin)) - - [#2719](https://github.com/GMOD/jbrowse-components/pull/2719) Avoid uninitialized state during stats estimation ([@cmdcolin](https://github.com/cmdcolin)) - - [#2707](https://github.com/GMOD/jbrowse-components/pull/2707) Fix ability to use authenticated assembly files ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2695](https://github.com/GMOD/jbrowse-components/pull/2695) Fix disabled state on the linear genome view track labels dropdown menu ([@cmdcolin](https://github.com/cmdcolin)) + - [#2757](https://github.com/GMOD/jbrowse-components/pull/2757) Fix type + confusion with stats estimation causing BAM files to fail byte size + calculation ([@cmdcolin](https://github.com/cmdcolin)) + - [#2750](https://github.com/GMOD/jbrowse-components/pull/2750) Add + bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in + alignments track in webkit and firefox + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2719](https://github.com/GMOD/jbrowse-components/pull/2719) Avoid + uninitialized state during stats estimation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2707](https://github.com/GMOD/jbrowse-components/pull/2707) Fix ability to + use authenticated assembly files + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2695](https://github.com/GMOD/jbrowse-components/pull/2695) Fix disabled + state on the linear genome view track labels dropdown menu + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2716](https://github.com/GMOD/jbrowse-components/pull/2716) Update to node12 requirement for @jbrowse/cli ([@cmdcolin](https://github.com/cmdcolin)) -- [#2605](https://github.com/GMOD/jbrowse-components/pull/2605) Developer guide reorganization and create new API document ([@cmdcolin](https://github.com/cmdcolin)) +- [#2716](https://github.com/GMOD/jbrowse-components/pull/2716) Update to node12 + requirement for @jbrowse/cli ([@cmdcolin](https://github.com/cmdcolin)) +- [#2605](https://github.com/GMOD/jbrowse-components/pull/2605) Developer guide + reorganization and create new API document + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2664](https://github.com/GMOD/jbrowse-components/pull/2664) Use babel config from core in root ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2664](https://github.com/GMOD/jbrowse-components/pull/2664) Use babel + config from core in root + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 diff --git a/website/blog/2022-03-15-v1.6.6-release.md b/website/blog/2022-03-15-v1.6.6-release.md index 6e2f407dd6..3d50d89d06 100644 --- a/website/blog/2022-03-15-v1.6.6-release.md +++ b/website/blog/2022-03-15-v1.6.6-release.md @@ -11,7 +11,8 @@ This contains several updated synteny features, including: - load .chain files from UCSC - load .delta files from mummer - load .anchors and .anchors.simple files from MCScan from the GUI -- ability to "rectangularize" the dotplot view and improved dotplot view overviews (shows total bp of selected regions) +- ability to "rectangularize" the dotplot view and improved dotplot view + overviews (shows total bp of selected regions) ![](https://user-images.githubusercontent.com/6511937/157131973-1c8962cb-bea2-4bde-a4ee-a5a874d5f370.png) @@ -34,10 +35,10 @@ We also have an updated configuration editor GUI with collapsible sections Screenshot showing new collapsible (turquoise) sections in the config editor A number of alignments track look and feel improvements were also added. The -scale bar was made to just list the min and max values when the height is -small, clip indicator position when horizontally flipped was fixed, and the -headroom was removed making the snpcoverage take up the full height of the -small area it uses. +scale bar was made to just list the min and max values when the height is small, +clip indicator position when horizontally flipped was fixed, and the headroom +was removed making the snpcoverage take up the full height of the small area it +uses. ![](https://user-images.githubusercontent.com/6511937/158481635-142063b3-0cba-424e-8e06-de6a89b9ef9f.png) @@ -110,40 +111,83 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2796](https://github.com/GMOD/jbrowse-components/pull/2796) Add collapsible accordion sections in configuration editor ([@cmdcolin](https://github.com/cmdcolin)) - - [#2791](https://github.com/GMOD/jbrowse-components/pull/2791) Add new coloring options for dotplot and ability to "rectangularize" dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2741](https://github.com/GMOD/jbrowse-components/pull/2741) Allow ability to enter a space-separated locstring to open a list of regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2725](https://github.com/GMOD/jbrowse-components/pull/2725) Refactor InternetAccounts, add standard getFetcher ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2787](https://github.com/GMOD/jbrowse-components/pull/2787) Display the total bp viewed in the header of the dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2767](https://github.com/GMOD/jbrowse-components/pull/2767) Wiggle and SNPCoverage look and feel improvements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2746](https://github.com/GMOD/jbrowse-components/pull/2746) Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view ([@cmdcolin](https://github.com/cmdcolin)) + - [#2796](https://github.com/GMOD/jbrowse-components/pull/2796) Add + collapsible accordion sections in configuration editor + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2791](https://github.com/GMOD/jbrowse-components/pull/2791) Add new + coloring options for dotplot and ability to "rectangularize" dotplot view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2741](https://github.com/GMOD/jbrowse-components/pull/2741) Allow ability + to enter a space-separated locstring to open a list of regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2725](https://github.com/GMOD/jbrowse-components/pull/2725) Refactor + InternetAccounts, add standard getFetcher + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2787](https://github.com/GMOD/jbrowse-components/pull/2787) Display the + total bp viewed in the header of the dotplot view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2767](https://github.com/GMOD/jbrowse-components/pull/2767) Wiggle and + SNPCoverage look and feel improvements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2746](https://github.com/GMOD/jbrowse-components/pull/2746) Add .delta and + .chain format adapters, fix ref name aliasing in synteny/dotplot views, and + optimize very long CIGAR string in synteny view + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2799](https://github.com/GMOD/jbrowse-components/pull/2799) Exit process after rendering to speed up jb2export ([@cmdcolin](https://github.com/cmdcolin)) - - [#2793](https://github.com/GMOD/jbrowse-components/pull/2793) Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2761](https://github.com/GMOD/jbrowse-components/pull/2761) Add a --clean argument to `jbrowse upgrade` to clean up old files ([@cmdcolin](https://github.com/cmdcolin)) - - [#2760](https://github.com/GMOD/jbrowse-components/pull/2760) Make a configurable refNameColumn in RefNameAliasAdapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#2799](https://github.com/GMOD/jbrowse-components/pull/2799) Exit process + after rendering to speed up jb2export + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2793](https://github.com/GMOD/jbrowse-components/pull/2793) Add + abortcontroller polyfill to jbrowse-img to allow it to run under node 14 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2761](https://github.com/GMOD/jbrowse-components/pull/2761) Add a --clean + argument to `jbrowse upgrade` to clean up old files + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2760](https://github.com/GMOD/jbrowse-components/pull/2760) Make a + configurable refNameColumn in RefNameAliasAdapter + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#2798](https://github.com/GMOD/jbrowse-components/pull/2798) Fix bug where web worker would sometimes be called before it was ready ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2798](https://github.com/GMOD/jbrowse-components/pull/2798) Fix bug where + web worker would sometimes be called before it was ready + ([@garrettjstevens](https://github.com/garrettjstevens)) - Other - - [#2797](https://github.com/GMOD/jbrowse-components/pull/2797) Fix crash plotting methylation in sparse regions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2782](https://github.com/GMOD/jbrowse-components/pull/2782) Fix display of cytobands when horizontally flipped ([@cmdcolin](https://github.com/cmdcolin)) - - [#2678](https://github.com/GMOD/jbrowse-components/pull/2678) Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads ([@cmdcolin](https://github.com/cmdcolin)) - - [#2774](https://github.com/GMOD/jbrowse-components/pull/2774) Fix overwriting broken symlink with --force in add-track CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#2773](https://github.com/GMOD/jbrowse-components/pull/2773) Fix using global stats autoscale on wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2766](https://github.com/GMOD/jbrowse-components/pull/2766) Add a check for empty content blocks to fix rare empty stats estimation ([@cmdcolin](https://github.com/cmdcolin)) + - [#2797](https://github.com/GMOD/jbrowse-components/pull/2797) Fix crash + plotting methylation in sparse regions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2782](https://github.com/GMOD/jbrowse-components/pull/2782) Fix display of + cytobands when horizontally flipped + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2678](https://github.com/GMOD/jbrowse-components/pull/2678) Preserve + double border line when using trackLabel offset and use smaller gap between + snpcoverage and reads ([@cmdcolin](https://github.com/cmdcolin)) + - [#2774](https://github.com/GMOD/jbrowse-components/pull/2774) Fix + overwriting broken symlink with --force in add-track CLI + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2773](https://github.com/GMOD/jbrowse-components/pull/2773) Fix using + global stats autoscale on wiggle tracks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2766](https://github.com/GMOD/jbrowse-components/pull/2766) Add a check + for empty content blocks to fix rare empty stats estimation + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2804](https://github.com/GMOD/jbrowse-components/pull/2804) Add note about additional pre-requisites to README ([@cmdcolin](https://github.com/cmdcolin)) -- [#2762](https://github.com/GMOD/jbrowse-components/pull/2762) Add bookmark widget docs to user guide ([@cmdcolin](https://github.com/cmdcolin)) +- [#2804](https://github.com/GMOD/jbrowse-components/pull/2804) Add note about + additional pre-requisites to README ([@cmdcolin](https://github.com/cmdcolin)) +- [#2762](https://github.com/GMOD/jbrowse-components/pull/2762) Add bookmark + widget docs to user guide ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#2813](https://github.com/GMOD/jbrowse-components/pull/2813) Create codeVerifierPKCE only when needed ([@garrettjstevens](https://github.com/garrettjstevens)) -- [#2808](https://github.com/GMOD/jbrowse-components/pull/2808) Polyfill window.crypto.getRandomValues in tests ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2813](https://github.com/GMOD/jbrowse-components/pull/2813) Create + codeVerifierPKCE only when needed + ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2808](https://github.com/GMOD/jbrowse-components/pull/2808) Polyfill + window.crypto.getRandomValues in tests + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 diff --git a/website/blog/2022-03-16-v1.6.7-release.md b/website/blog/2022-03-16-v1.6.7-release.md index 9c49a7dc7f..7b0d43a37d 100644 --- a/website/blog/2022-03-16-v1.6.7-release.md +++ b/website/blog/2022-03-16-v1.6.7-release.md @@ -51,12 +51,17 @@ on NPM. #### :rocket: Enhancement -- [#2820](https://github.com/GMOD/jbrowse-components/pull/2820) Add optimization for BAM and unzip operations ([@cmdcolin](https://github.com/cmdcolin)) +- [#2820](https://github.com/GMOD/jbrowse-components/pull/2820) Add optimization + for BAM and unzip operations ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#2821](https://github.com/GMOD/jbrowse-components/pull/2821) Fixup scroll on wiggle tracks with trackLabels->offset ([@cmdcolin](https://github.com/cmdcolin)) -- [#2819](https://github.com/GMOD/jbrowse-components/pull/2819) Fix bug in desktop where first track gets stuck loading ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2821](https://github.com/GMOD/jbrowse-components/pull/2821) Fixup scroll on + wiggle tracks with trackLabels->offset + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2819](https://github.com/GMOD/jbrowse-components/pull/2819) Fix bug in + desktop where first track gets stuck loading + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 diff --git a/website/blog/2022-03-25-v1.6.8-release.md b/website/blog/2022-03-25-v1.6.8-release.md index c0fbe29eb7..10d8e18792 100644 --- a/website/blog/2022-03-25-v1.6.8-release.md +++ b/website/blog/2022-03-25-v1.6.8-release.md @@ -6,7 +6,8 @@ tags: ['release', 'jbrowse 2'] We are pleased to announce the v1.6.8 release! -This release includes a change to the default gene style to use boxes instead of "chevron" features, with a directional arrowhead +This release includes a change to the default gene style to use boxes instead of +"chevron" features, with a directional arrowhead Before @@ -64,29 +65,57 @@ on NPM. #### :rocket: Enhancement - Other - - [#2847](https://github.com/GMOD/jbrowse-components/pull/2847) Add option to color all the letters on all the reads to the pileup renderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#2849](https://github.com/GMOD/jbrowse-components/pull/2849) Avoid drawing intron subfeatures for gene glyphs ([@cmdcolin](https://github.com/cmdcolin)) - - [#2835](https://github.com/GMOD/jbrowse-components/pull/2835) Hide add track and connection menu items when using embedded component ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#2836](https://github.com/GMOD/jbrowse-components/pull/2836) Display low-quality modifications in SNPCoverage renderer for MM tag ([@cmdcolin](https://github.com/cmdcolin)) + - [#2847](https://github.com/GMOD/jbrowse-components/pull/2847) Add option to + color all the letters on all the reads to the pileup renderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2849](https://github.com/GMOD/jbrowse-components/pull/2849) Avoid drawing + intron subfeatures for gene glyphs + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2835](https://github.com/GMOD/jbrowse-components/pull/2835) Hide add track + and connection menu items when using embedded component + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#2836](https://github.com/GMOD/jbrowse-components/pull/2836) Display + low-quality modifications in SNPCoverage renderer for MM tag + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2809](https://github.com/GMOD/jbrowse-components/pull/2809) Optimizations for alignments tracks and BAM parsing ([@cmdcolin](https://github.com/cmdcolin)) - - [#2828](https://github.com/GMOD/jbrowse-components/pull/2828) Change calculation for number of webworkers for web/desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to specify number of workers ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#2775](https://github.com/GMOD/jbrowse-components/pull/2775) New SVG gene glyph with directional arrows ([@cmdcolin](https://github.com/cmdcolin)) + - [#2809](https://github.com/GMOD/jbrowse-components/pull/2809) Optimizations + for alignments tracks and BAM parsing + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2828](https://github.com/GMOD/jbrowse-components/pull/2828) Change + calculation for number of webworkers for web/desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to + specify number of workers + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2775](https://github.com/GMOD/jbrowse-components/pull/2775) New SVG gene + glyph with directional arrows ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#2852](https://github.com/GMOD/jbrowse-components/pull/2852) Fix misaligned features under breakpoint split view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2844](https://github.com/GMOD/jbrowse-components/pull/2844) Fix layout of small features without labels for SvgFeatureRenderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#2839](https://github.com/GMOD/jbrowse-components/pull/2839) Fix the drawing of SNP height when the SNPCoverage track is using log scale ([@cmdcolin](https://github.com/cmdcolin)) - - [#2825](https://github.com/GMOD/jbrowse-components/pull/2825) Fix tracklabels positioning not updating in UI after user selection ([@cmdcolin](https://github.com/cmdcolin)) + - [#2852](https://github.com/GMOD/jbrowse-components/pull/2852) Fix misaligned + features under breakpoint split view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2844](https://github.com/GMOD/jbrowse-components/pull/2844) Fix layout of + small features without labels for SvgFeatureRenderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2839](https://github.com/GMOD/jbrowse-components/pull/2839) Fix the + drawing of SNP height when the SNPCoverage track is using log scale + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2825](https://github.com/GMOD/jbrowse-components/pull/2825) Fix + tracklabels positioning not updating in UI after user selection + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2841](https://github.com/GMOD/jbrowse-components/pull/2841) Fix alignments tracks loading excessive data on chromosomes where no features exist ([@cmdcolin](https://github.com/cmdcolin)) - - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to specify number of workers ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2841](https://github.com/GMOD/jbrowse-components/pull/2841) Fix alignments + tracks loading excessive data on chromosomes where no features exist + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2829](https://github.com/GMOD/jbrowse-components/pull/2829) Allow user to + specify number of workers + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) diff --git a/website/blog/2022-04-14-v1.7.0-release.md b/website/blog/2022-04-14-v1.7.0-release.md index a867a5c869..df35f30743 100644 --- a/website/blog/2022-04-14-v1.7.0-release.md +++ b/website/blog/2022-04-14-v1.7.0-release.md @@ -10,8 +10,8 @@ features including 1. Floating feature labels, so if you are zoomed into the middle of a gene, the feature label hangs out alongside it on the left side of the screen! The results may not be pixel perfect in all cases (reverse complement labels can - end up overlapping other features for example) but we hope this helps you - see the labels for features that extend off the screen! + end up overlapping other features for example) but we hope this helps you see + the labels for features that extend off the screen! ![](https://user-images.githubusercontent.com/6511937/163470981-cfbd4464-bd5a-4421-8d9c-c8e6bb2d19bc.png) @@ -19,11 +19,11 @@ features including zoomed into the feature 2. Upgraded build system for jbrowse-web and jbrowse-desktop to webpack 5, and - added examples of using webpack 5 with embedded components. Webpack 5 - results in smaller build sizes for jbrowse-web. For a typical session, - amount of .js downloaded with gzip enabled in v1.6.9 is ~1.4MB, in v1.7.0 - ~900kb (-500kb smaller). Without gzip enabled v1.6.9 4.8MB, v1.7.0 2.5MB - (-2MB smaller). The result is largely due to better webworker bundling. See + added examples of using webpack 5 with embedded components. Webpack 5 results + in smaller build sizes for jbrowse-web. For a typical session, amount of .js + downloaded with gzip enabled in v1.6.9 is ~1.4MB, in v1.7.0 ~900kb (-500kb + smaller). Without gzip enabled v1.6.9 4.8MB, v1.7.0 2.5MB (-2MB smaller). The + result is largely due to better webworker bundling. See https://jbrowse.org/jb2/docs/embedded_components/ for webpack 5 examples in embedded components @@ -102,44 +102,85 @@ on NPM. #### :rocket: Enhancement - Other - - [#2909](https://github.com/GMOD/jbrowse-components/pull/2909) Add --prefixSize flag to @jbrowse/cli text-index ([@cmdcolin](https://github.com/cmdcolin)) - - [#2887](https://github.com/GMOD/jbrowse-components/pull/2887) Optimize filtering on alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#2879](https://github.com/GMOD/jbrowse-components/pull/2879) Multi-level synteny rubberband ([@cmdcolin](https://github.com/cmdcolin)) - - [#2874](https://github.com/GMOD/jbrowse-components/pull/2874) Optimizations for rendering long syntenic alignments e.g. CHM13 vs GRCh38 ([@cmdcolin](https://github.com/cmdcolin)) - - [#2872](https://github.com/GMOD/jbrowse-components/pull/2872) Better connection between paired-end alignments in breakpoint split view and optimizations ([@cmdcolin](https://github.com/cmdcolin)) + - [#2909](https://github.com/GMOD/jbrowse-components/pull/2909) Add + --prefixSize flag to @jbrowse/cli text-index + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2887](https://github.com/GMOD/jbrowse-components/pull/2887) Optimize + filtering on alignments tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#2879](https://github.com/GMOD/jbrowse-components/pull/2879) Multi-level + synteny rubberband ([@cmdcolin](https://github.com/cmdcolin)) + - [#2874](https://github.com/GMOD/jbrowse-components/pull/2874) Optimizations + for rendering long syntenic alignments e.g. CHM13 vs GRCh38 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2872](https://github.com/GMOD/jbrowse-components/pull/2872) Better + connection between paired-end alignments in breakpoint split view and + optimizations ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2902](https://github.com/GMOD/jbrowse-components/pull/2902) Standardize heights of widgets in LGV import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#2781](https://github.com/GMOD/jbrowse-components/pull/2781) Add floating labels to SVG features ([@cmdcolin](https://github.com/cmdcolin)) - - [#2875](https://github.com/GMOD/jbrowse-components/pull/2875) Make assembly selector remember your last selected assembly ([@cmdcolin](https://github.com/cmdcolin)) - - [#2860](https://github.com/GMOD/jbrowse-components/pull/2860) Avoid performing many peekTransferables to optimize RPC serialization ([@rbuels](https://github.com/rbuels)) + - [#2902](https://github.com/GMOD/jbrowse-components/pull/2902) Standardize + heights of widgets in LGV import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2781](https://github.com/GMOD/jbrowse-components/pull/2781) Add floating + labels to SVG features ([@cmdcolin](https://github.com/cmdcolin)) + - [#2875](https://github.com/GMOD/jbrowse-components/pull/2875) Make assembly + selector remember your last selected assembly + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2860](https://github.com/GMOD/jbrowse-components/pull/2860) Avoid + performing many peekTransferables to optimize RPC serialization + ([@rbuels](https://github.com/rbuels)) #### :bug: Bug Fix - Other - - [#2908](https://github.com/GMOD/jbrowse-components/pull/2908) Fix AboutDialog under vite for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#2900](https://github.com/GMOD/jbrowse-components/pull/2900) Fix the 'Open assembly' menu item in jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#2882](https://github.com/GMOD/jbrowse-components/pull/2882) Add padding at the bottom of the configuration editor to help color editing popup being cutoff ([@cmdcolin](https://github.com/cmdcolin)) - - [#2877](https://github.com/GMOD/jbrowse-components/pull/2877) Fix strand on arrows in horizontally flipped mode ([@cmdcolin](https://github.com/cmdcolin)) + - [#2908](https://github.com/GMOD/jbrowse-components/pull/2908) Fix + AboutDialog under vite for embedded components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2900](https://github.com/GMOD/jbrowse-components/pull/2900) Fix the 'Open + assembly' menu item in jbrowse desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2882](https://github.com/GMOD/jbrowse-components/pull/2882) Add padding at + the bottom of the configuration editor to help color editing popup being + cutoff ([@cmdcolin](https://github.com/cmdcolin)) + - [#2877](https://github.com/GMOD/jbrowse-components/pull/2877) Fix strand on + arrows in horizontally flipped mode + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components ([@cmdcolin](https://github.com/cmdcolin)) + - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a + user-supplied fetchESM callback to import ESM plugins to fix 'Critical + dependency...' errors from embedded components + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2894](https://github.com/GMOD/jbrowse-components/pull/2894) Add create-react-app v5 embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) -- [#2830](https://github.com/GMOD/jbrowse-components/pull/2830) Documentation comparing main app with embedded components ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#2894](https://github.com/GMOD/jbrowse-components/pull/2894) Add + create-react-app v5 embedded component demos + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2830](https://github.com/GMOD/jbrowse-components/pull/2830) Documentation + comparing main app with embedded components + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - `core` - - [#2904](https://github.com/GMOD/jbrowse-components/pull/2904) Use a user-supplied fetchCJS callback to import CJS plugins ([@cmdcolin](https://github.com/cmdcolin)) - - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#2857](https://github.com/GMOD/jbrowse-components/pull/2857) Refactor and improve types of OffscreenCanvas shim and ponyfill ([@rbuels](https://github.com/rbuels)) + - [#2904](https://github.com/GMOD/jbrowse-components/pull/2904) Use a + user-supplied fetchCJS callback to import CJS plugins + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2891](https://github.com/GMOD/jbrowse-components/pull/2891) Use a + user-supplied fetchESM callback to import ESM plugins to fix 'Critical + dependency...' errors from embedded components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2857](https://github.com/GMOD/jbrowse-components/pull/2857) Refactor and + improve types of OffscreenCanvas shim and ponyfill + ([@rbuels](https://github.com/rbuels)) - `__mocks__`, `core` - - [#2905](https://github.com/GMOD/jbrowse-components/pull/2905) Use react-use-measure instead of react-use-dimensions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2646](https://github.com/GMOD/jbrowse-components/pull/2646) Upgrade repository to use webpack 5/CRA 5 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2905](https://github.com/GMOD/jbrowse-components/pull/2905) Use + react-use-measure instead of react-use-dimensions + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2646](https://github.com/GMOD/jbrowse-components/pull/2646) Upgrade + repository to use webpack 5/CRA 5 ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Robert Buels ([@rbuels](https://github.com/rbuels)) diff --git a/website/blog/2022-04-15-v1.7.3-release.md b/website/blog/2022-04-15-v1.7.3-release.md index 7d23c0ff73..55d0f4d4a4 100644 --- a/website/blog/2022-04-15-v1.7.3-release.md +++ b/website/blog/2022-04-15-v1.7.3-release.md @@ -4,9 +4,11 @@ date: 2022-04-15 04:46:50 tags: ['release', 'jbrowse 2'] --- -This is a release fixed some small issues with using typescript in the embedded components +This is a release fixed some small issues with using typescript in the embedded +components -See https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0 for the latest feature-set +See https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0 for the +latest feature-set ## Downloads diff --git a/website/blog/2022-04-19-v1.7.4-release.md b/website/blog/2022-04-19-v1.7.4-release.md index 076dd38d73..a9fd615c6f 100644 --- a/website/blog/2022-04-19-v1.7.4-release.md +++ b/website/blog/2022-04-19-v1.7.4-release.md @@ -69,9 +69,13 @@ on NPM. #### :bug: Bug Fix - Other - - [#2925](https://github.com/GMOD/jbrowse-components/pull/2925) Fix embedded vanillaJS/script tag usage of embedded components ([@cmdcolin](https://github.com/cmdcolin)) + - [#2925](https://github.com/GMOD/jbrowse-components/pull/2925) Fix embedded + vanillaJS/script tag usage of embedded components + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2923](https://github.com/GMOD/jbrowse-components/pull/2923) Add babel/runtime to dependencies ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#2923](https://github.com/GMOD/jbrowse-components/pull/2923) Add + babel/runtime to dependencies + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 diff --git a/website/blog/2022-04-26-v1.7.5-release.md b/website/blog/2022-04-26-v1.7.5-release.md index 33658047e8..fc62aecd4d 100644 --- a/website/blog/2022-04-26-v1.7.5-release.md +++ b/website/blog/2022-04-26-v1.7.5-release.md @@ -9,8 +9,8 @@ We are pleased to present the release of v1.7.5 This release includes two major improvements - Ability to index tracks for searching by gene names in JBrowse Desktop. This - let's users choose per-track indexes in the add track widget interactively, - or index them after-the-fact using the track menu. + let's users choose per-track indexes in the add track widget interactively, or + index them after-the-fact using the track menu. - Removed serialization of BAM/CRAM features for pileup tracks which brings large performance benefits for jbrowse-web and jbrowse-desktop. Previously, all the BAM/CRAM features were serialized across the RPC boundary in @@ -34,7 +34,8 @@ Figure showing performance improvement of the noserialize improvement compared with v1.7.4, which brings the webworker performance in line with the embedded app (which does no serialization) -This release also fixes a bug with using trix indexes created by `jbrowse text-index` in v1.7.0-v1.7.4 (with the adjustable prefix size) +This release also fixes a bug with using trix indexes created by +`jbrowse text-index` in v1.7.0-v1.7.4 (with the adjustable prefix size) ## Downloads @@ -83,19 +84,32 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2885](https://github.com/GMOD/jbrowse-components/pull/2885) Reduce serialization overhead on alignments tracks and access feature details asynchronously ([@cmdcolin](https://github.com/cmdcolin)) + - [#2885](https://github.com/GMOD/jbrowse-components/pull/2885) Reduce + serialization overhead on alignments tracks and access feature details + asynchronously ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2935](https://github.com/GMOD/jbrowse-components/pull/2935) Use the name "Read Sequence" for the read vs ref view ([@cmdcolin](https://github.com/cmdcolin)) - - [#2916](https://github.com/GMOD/jbrowse-components/pull/2916) Add vite setup to our embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) - - [#2927](https://github.com/GMOD/jbrowse-components/pull/2927) Optimize gtf by only parsing lazily per-refName ([@cmdcolin](https://github.com/cmdcolin)) - - [#2928](https://github.com/GMOD/jbrowse-components/pull/2928) Add vanillajs/script tag loading embedded components demos ([@cmdcolin](https://github.com/cmdcolin)) + - [#2935](https://github.com/GMOD/jbrowse-components/pull/2935) Use the name + "Read Sequence" for the read vs ref view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2916](https://github.com/GMOD/jbrowse-components/pull/2916) Add vite setup + to our embedded component demos ([@cmdcolin](https://github.com/cmdcolin)) + - [#2927](https://github.com/GMOD/jbrowse-components/pull/2927) Optimize gtf + by only parsing lazily per-refName + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2928](https://github.com/GMOD/jbrowse-components/pull/2928) Add + vanillajs/script tag loading embedded components demos + ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `text-indexing` - - [#2684](https://github.com/GMOD/jbrowse-components/pull/2684) Text-indexing in desktop ([@teresam856](https://github.com/teresam856)) + - [#2684](https://github.com/GMOD/jbrowse-components/pull/2684) Text-indexing + in desktop ([@teresam856](https://github.com/teresam856)) #### :bug: Bug Fix -- [#2863](https://github.com/GMOD/jbrowse-components/pull/2863) Render gene with CDS subfeatures properly ([@cmdcolin](https://github.com/cmdcolin)) -- [#2934](https://github.com/GMOD/jbrowse-components/pull/2934) Bump @gmod/trix to fix prefix size calculation and searching first word in index ([@cmdcolin](https://github.com/cmdcolin)) +- [#2863](https://github.com/GMOD/jbrowse-components/pull/2863) Render gene with + CDS subfeatures properly ([@cmdcolin](https://github.com/cmdcolin)) +- [#2934](https://github.com/GMOD/jbrowse-components/pull/2934) Bump @gmod/trix + to fix prefix size calculation and searching first word in index + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 diff --git a/website/blog/2022-04-26-v1.7.6-release.md b/website/blog/2022-04-26-v1.7.6-release.md index 0e1fe522a4..1a58b0537b 100644 --- a/website/blog/2022-04-26-v1.7.6-release.md +++ b/website/blog/2022-04-26-v1.7.6-release.md @@ -34,7 +34,9 @@ on NPM. #### :bug: Bug Fix -- [#2939](https://github.com/GMOD/jbrowse-components/pull/2939) Fix loading CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) +- [#2939](https://github.com/GMOD/jbrowse-components/pull/2939) Fix loading + CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse + desktop ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 diff --git a/website/blog/2022-05-04-v1.7.7-release.md b/website/blog/2022-05-04-v1.7.7-release.md index 65075e5806..3583ad1106 100644 --- a/website/blog/2022-05-04-v1.7.7-release.md +++ b/website/blog/2022-05-04-v1.7.7-release.md @@ -39,12 +39,15 @@ on NPM. #### :bug: Bug Fix -- [#2941](https://github.com/GMOD/jbrowse-components/pull/2941) Fix linear read vs ref hanging in v1.7.5 ([@cmdcolin](https://github.com/cmdcolin)) +- [#2941](https://github.com/GMOD/jbrowse-components/pull/2941) Fix linear read + vs ref hanging in v1.7.5 ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#2944](https://github.com/GMOD/jbrowse-components/pull/2944) Avoid stalling on undefined assemblyName during ref name renaming ([@cmdcolin](https://github.com/cmdcolin)) + - [#2944](https://github.com/GMOD/jbrowse-components/pull/2944) Avoid stalling + on undefined assemblyName during ref name renaming + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 diff --git a/website/blog/2022-05-20-v1.7.8-release.md b/website/blog/2022-05-20-v1.7.8-release.md index 4adc09b474..721f6a8384 100644 --- a/website/blog/2022-05-20-v1.7.8-release.md +++ b/website/blog/2022-05-20-v1.7.8-release.md @@ -10,10 +10,14 @@ Some highlights include - ~20% speed improvement for CRAM data - bugfix for filter-by being broken on alignments tracks in v1.7.0-v1.7.7 -- bugfix for certain methylation/modifications being drawn incorrectly on alignments tracks -- bugfix for the "Open" button not navigating to the correct location on the LGV import form -- improved visualization of indels in methylation/modifications mode on alignments tracks -- skip text index query if the input is a loc string, resulting in quicker navigation +- bugfix for certain methylation/modifications being drawn incorrectly on + alignments tracks +- bugfix for the "Open" button not navigating to the correct location on the LGV + import form +- improved visualization of indels in methylation/modifications mode on + alignments tracks +- skip text index query if the input is a loc string, resulting in quicker + navigation Screenshots showing the new viewing of indels when viewing methylation @@ -63,28 +67,48 @@ on NPM. #### :rocket: Enhancement -- [#2970](https://github.com/GMOD/jbrowse-components/pull/2970) Draw indels in modifications/methylation mode ([@cmdcolin](https://github.com/cmdcolin)) -- [#2961](https://github.com/GMOD/jbrowse-components/pull/2961) Add more visible pileup mismatches when zoomed out ([@cmdcolin](https://github.com/cmdcolin)) -- [#2960](https://github.com/GMOD/jbrowse-components/pull/2960) Avoid performing a text index search if input looks like a locstring ([@cmdcolin](https://github.com/cmdcolin)) -- [#2954](https://github.com/GMOD/jbrowse-components/pull/2954) Support in-memory GFF3 and GTF in JBrowse 1 connection ([@garrettjstevens](https://github.com/garrettjstevens)) -- [#2947](https://github.com/GMOD/jbrowse-components/pull/2947) Optimization for SNPCoverageAdapter and CRAM parsing ([@cmdcolin](https://github.com/cmdcolin)) +- [#2970](https://github.com/GMOD/jbrowse-components/pull/2970) Draw indels in + modifications/methylation mode ([@cmdcolin](https://github.com/cmdcolin)) +- [#2961](https://github.com/GMOD/jbrowse-components/pull/2961) Add more visible + pileup mismatches when zoomed out ([@cmdcolin](https://github.com/cmdcolin)) +- [#2960](https://github.com/GMOD/jbrowse-components/pull/2960) Avoid performing + a text index search if input looks like a locstring + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2954](https://github.com/GMOD/jbrowse-components/pull/2954) Support + in-memory GFF3 and GTF in JBrowse 1 connection + ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2947](https://github.com/GMOD/jbrowse-components/pull/2947) Optimization for + SNPCoverageAdapter and CRAM parsing ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#2969](https://github.com/GMOD/jbrowse-components/pull/2969) Fix link on yeast synteny demo and fix CIGAR rendering on dotplot ([@cmdcolin](https://github.com/cmdcolin)) -- [#2964](https://github.com/GMOD/jbrowse-components/pull/2964) Fix crash displaying modifications called on softclipped regions of reads ([@cmdcolin](https://github.com/cmdcolin)) -- [#2965](https://github.com/GMOD/jbrowse-components/pull/2965) Fix filter functionality on pileup tracks ([@cmdcolin](https://github.com/cmdcolin)) -- [#2953](https://github.com/GMOD/jbrowse-components/pull/2953) Fix "Open" button on LGV ImportForm ([@cmdcolin](https://github.com/cmdcolin)) -- [#2952](https://github.com/GMOD/jbrowse-components/pull/2952) Fix read vs ref not finding primary alignment on certain CRAM files ([@cmdcolin](https://github.com/cmdcolin)) -- [#2951](https://github.com/GMOD/jbrowse-components/pull/2951) Fix viewing soft/hardclip indicator in some regions ([@cmdcolin](https://github.com/cmdcolin)) +- [#2969](https://github.com/GMOD/jbrowse-components/pull/2969) Fix link on + yeast synteny demo and fix CIGAR rendering on dotplot + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2964](https://github.com/GMOD/jbrowse-components/pull/2964) Fix crash + displaying modifications called on softclipped regions of reads + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2965](https://github.com/GMOD/jbrowse-components/pull/2965) Fix filter + functionality on pileup tracks ([@cmdcolin](https://github.com/cmdcolin)) +- [#2953](https://github.com/GMOD/jbrowse-components/pull/2953) Fix "Open" + button on LGV ImportForm ([@cmdcolin](https://github.com/cmdcolin)) +- [#2952](https://github.com/GMOD/jbrowse-components/pull/2952) Fix read vs ref + not finding primary alignment on certain CRAM files + ([@cmdcolin](https://github.com/cmdcolin)) +- [#2951](https://github.com/GMOD/jbrowse-components/pull/2951) Fix viewing + soft/hardclip indicator in some regions + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2946](https://github.com/GMOD/jbrowse-components/pull/2946) Small doc updates ([@cmdcolin](https://github.com/cmdcolin)) +- [#2946](https://github.com/GMOD/jbrowse-components/pull/2946) Small doc + updates ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#2955](https://github.com/GMOD/jbrowse-components/pull/2955) Re-enable eslint autofix for prettier rules ([@garrettjstevens](https://github.com/garrettjstevens)) +- [#2955](https://github.com/GMOD/jbrowse-components/pull/2955) Re-enable eslint + autofix for prettier rules + ([@garrettjstevens](https://github.com/garrettjstevens)) #### Committers: 2 diff --git a/website/blog/2022-06-02-v1.7.9-release.md b/website/blog/2022-06-02-v1.7.9-release.md index d34252edf2..5513e58f7f 100644 --- a/website/blog/2022-06-02-v1.7.9-release.md +++ b/website/blog/2022-06-02-v1.7.9-release.md @@ -62,24 +62,39 @@ on NPM. #### :rocket: Enhancement - `core` - - [#2991](https://github.com/GMOD/jbrowse-components/pull/2991) Use canvas2svg for SVG export, fixes non-rasterized usage of bezier, arcs, and more ([@cmdcolin](https://github.com/cmdcolin)) - - [#2483](https://github.com/GMOD/jbrowse-components/pull/2483) Add setting to color by query score per alignment for dotplot, support HTML in config slot descriptions ([@cmdcolin](https://github.com/cmdcolin)) - - [#2983](https://github.com/GMOD/jbrowse-components/pull/2983) Set target=\_blank by default in user HTML links ([@cmdcolin](https://github.com/cmdcolin)) + - [#2991](https://github.com/GMOD/jbrowse-components/pull/2991) Use canvas2svg + for SVG export, fixes non-rasterized usage of bezier, arcs, and more + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2483](https://github.com/GMOD/jbrowse-components/pull/2483) Add setting to + color by query score per alignment for dotplot, support HTML in config slot + descriptions ([@cmdcolin](https://github.com/cmdcolin)) + - [#2983](https://github.com/GMOD/jbrowse-components/pull/2983) Set + target=\_blank by default in user HTML links + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2994](https://github.com/GMOD/jbrowse-components/pull/2994) Allow choosing filename for svg export ([@cmdcolin](https://github.com/cmdcolin)) - - [#2968](https://github.com/GMOD/jbrowse-components/pull/2968) Add FASTA metadata location to BgzipFastaAdapter and IndexFastaAdapter configuration ([@adamjohnwright](https://github.com/adamjohnwright)) + - [#2994](https://github.com/GMOD/jbrowse-components/pull/2994) Allow choosing + filename for svg export ([@cmdcolin](https://github.com/cmdcolin)) + - [#2968](https://github.com/GMOD/jbrowse-components/pull/2968) Add FASTA + metadata location to BgzipFastaAdapter and IndexFastaAdapter configuration + ([@adamjohnwright](https://github.com/adamjohnwright)) #### :bug: Bug Fix - `core` - - [#2989](https://github.com/GMOD/jbrowse-components/pull/2989) Fix bezierCurveTo ponyfill on firefox ([@cmdcolin](https://github.com/cmdcolin)) + - [#2989](https://github.com/GMOD/jbrowse-components/pull/2989) Fix + bezierCurveTo ponyfill on firefox ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#2977](https://github.com/GMOD/jbrowse-components/pull/2977) Respect --indexFile option when adding VCF and BED tracks ([@heavywatal](https://github.com/heavywatal)) - - [#2974](https://github.com/GMOD/jbrowse-components/pull/2974) Fix track indexing being ignored after first add track widget usage ([@teresam856](https://github.com/teresam856)) + - [#2977](https://github.com/GMOD/jbrowse-components/pull/2977) Respect + --indexFile option when adding VCF and BED tracks + ([@heavywatal](https://github.com/heavywatal)) + - [#2974](https://github.com/GMOD/jbrowse-components/pull/2974) Fix track + indexing being ignored after first add track widget usage + ([@teresam856](https://github.com/teresam856)) #### :house: Internal -- [#2980](https://github.com/GMOD/jbrowse-components/pull/2980) Remove errors related to test coverage in CI ([@cmdcolin](https://github.com/cmdcolin)) +- [#2980](https://github.com/GMOD/jbrowse-components/pull/2980) Remove errors + related to test coverage in CI ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 diff --git a/website/blog/2022-06-13-v1.7.10-release.md b/website/blog/2022-06-13-v1.7.10-release.md index 31c935094d..8563ca7724 100644 --- a/website/blog/2022-06-13-v1.7.10-release.md +++ b/website/blog/2022-06-13-v1.7.10-release.md @@ -13,15 +13,16 @@ This has some great new features including https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info) - Session URL formats for loading spreadsheet, SV inspector, and linear and - dotplot synteny views (see https://jbrowse.org/jb2/docs/urlparams/ for details) + dotplot synteny views (see https://jbrowse.org/jb2/docs/urlparams/ for + details) - You can enter "chr1 100 200" to navigate to "chr1:100-200" as a simple way to copy from a bed file or similar ### Feature detail formatter -Here is an example which adds a link to the "Name" panel in the feature -details. It uses the jexl callback that returns an object with keys for each -field to modify (e.g. the key name is used here). See +Here is an example which adds a link to the "Name" panel in the feature details. +It uses the jexl callback that returns an object with keys for each field to +modify (e.g. the key name is used here). See ```json { @@ -50,7 +51,9 @@ Example screenshot ![](https://user-images.githubusercontent.com/6511937/173461279-1afebb28-5928-47c1-8157-ecd2427a7fb2.png) -See https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info +See +https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels +for more info ### Clearer configuration panel with explicit "Add item" button with "OK"/"Cancel" to confirm @@ -118,34 +121,69 @@ on NPM. #### :rocket: Enhancement - Other - - [#3025](https://github.com/GMOD/jbrowse-components/pull/3025) Add dotplot session spec ([@cmdcolin](https://github.com/cmdcolin)) - - [#2975](https://github.com/GMOD/jbrowse-components/pull/2975) Add simplified URL format for loading synteny views ([@cmdcolin](https://github.com/cmdcolin)) - - [#3023](https://github.com/GMOD/jbrowse-components/pull/3023) Add error handling in case of invalid OAuth2 configuration used. ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) - - [#3020](https://github.com/GMOD/jbrowse-components/pull/3020) Allow choosing trackId when using text-index with --file with --fileId ([@cmdcolin](https://github.com/cmdcolin)) - - [#3016](https://github.com/GMOD/jbrowse-components/pull/3016) Allow whitespace separated refname,start,end type locstring ([@cmdcolin](https://github.com/cmdcolin)) - - [#3006](https://github.com/GMOD/jbrowse-components/pull/3006) Add string array configuration slot UI improvements ([@cmdcolin](https://github.com/cmdcolin)) - - [#2998](https://github.com/GMOD/jbrowse-components/pull/2998) Avoid rendering offscreen contents in pileup renderer ([@cmdcolin](https://github.com/cmdcolin)) - - [#3000](https://github.com/GMOD/jbrowse-components/pull/3000) Add reference base and correct percentage calculations to tooltip on SNPCoverage display ([@cmdcolin](https://github.com/cmdcolin)) + - [#3025](https://github.com/GMOD/jbrowse-components/pull/3025) Add dotplot + session spec ([@cmdcolin](https://github.com/cmdcolin)) + - [#2975](https://github.com/GMOD/jbrowse-components/pull/2975) Add simplified + URL format for loading synteny views + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3023](https://github.com/GMOD/jbrowse-components/pull/3023) Add error + handling in case of invalid OAuth2 configuration used. + ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) + - [#3020](https://github.com/GMOD/jbrowse-components/pull/3020) Allow choosing + trackId when using text-index with --file with --fileId + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3016](https://github.com/GMOD/jbrowse-components/pull/3016) Allow + whitespace separated refname,start,end type locstring + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3006](https://github.com/GMOD/jbrowse-components/pull/3006) Add string + array configuration slot UI improvements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2998](https://github.com/GMOD/jbrowse-components/pull/2998) Avoid + rendering offscreen contents in pileup renderer + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3000](https://github.com/GMOD/jbrowse-components/pull/3000) Add reference + base and correct percentage calculations to tooltip on SNPCoverage display + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#2981](https://github.com/GMOD/jbrowse-components/pull/2981) Add simplified URL format for loading spreadsheet and SV inspector ([@cmdcolin](https://github.com/cmdcolin)) - - [#2990](https://github.com/GMOD/jbrowse-components/pull/2990) Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#3003](https://github.com/GMOD/jbrowse-components/pull/3003) Add ability to run field formatters on the feature details panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#3017](https://github.com/GMOD/jbrowse-components/pull/3017) Add button to copy track config in About track dialog ([@cmdcolin](https://github.com/cmdcolin)) - - [#2999](https://github.com/GMOD/jbrowse-components/pull/2999) Generate clickable links to track data in about track dialog ([@cmdcolin](https://github.com/cmdcolin)) + - [#2981](https://github.com/GMOD/jbrowse-components/pull/2981) Add simplified + URL format for loading spreadsheet and SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2990](https://github.com/GMOD/jbrowse-components/pull/2990) Use shortened + megabases (M) display when zoomed out, and option to hide the "open track + selector" button + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#3003](https://github.com/GMOD/jbrowse-components/pull/3003) Add ability to + run field formatters on the feature details panel + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3017](https://github.com/GMOD/jbrowse-components/pull/3017) Add button to + copy track config in About track dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#2999](https://github.com/GMOD/jbrowse-components/pull/2999) Generate + clickable links to track data in about track dialog + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core` - - [#3005](https://github.com/GMOD/jbrowse-components/pull/3005) Use cascading menu helper library for track menu to avoid menu going offscreen ([@cmdcolin](https://github.com/cmdcolin)) + - [#3005](https://github.com/GMOD/jbrowse-components/pull/3005) Use cascading + menu helper library for track menu to avoid menu going offscreen + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3021](https://github.com/GMOD/jbrowse-components/pull/3021) Fix mouseover display of read name to alignments track ([@cmdcolin](https://github.com/cmdcolin)) - - [#3012](https://github.com/GMOD/jbrowse-components/pull/3012) Small fix to rankSearchResults logic ([@cmdcolin](https://github.com/cmdcolin)) - - [#3009](https://github.com/GMOD/jbrowse-components/pull/3009) Add jsdom to jbrowse-img to fix --noRasterize option ([@cmdcolin](https://github.com/cmdcolin)) + - [#3021](https://github.com/GMOD/jbrowse-components/pull/3021) Fix mouseover + display of read name to alignments track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3012](https://github.com/GMOD/jbrowse-components/pull/3012) Small fix to + rankSearchResults logic ([@cmdcolin](https://github.com/cmdcolin)) + - [#3009](https://github.com/GMOD/jbrowse-components/pull/3009) Add jsdom to + jbrowse-img to fix --noRasterize option + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3007](https://github.com/GMOD/jbrowse-components/pull/3007) Fix read vs ref dotplot view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3007](https://github.com/GMOD/jbrowse-components/pull/3007) Fix read vs + ref dotplot view ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - [@andrzejgrzelak](https://github.com/andrzejgrzelak) diff --git a/website/blog/2022-06-22-v1.7.11-release.md b/website/blog/2022-06-22-v1.7.11-release.md index efad886356..a89b57677b 100644 --- a/website/blog/2022-06-22-v1.7.11-release.md +++ b/website/blog/2022-06-22-v1.7.11-release.md @@ -78,27 +78,43 @@ on NPM. #### :rocket: Enhancement - `core` - - [#3044](https://github.com/GMOD/jbrowse-components/pull/3044) Remove node-canvas from @jbrowse/core dependencies ([@cmdcolin](https://github.com/cmdcolin)) - - [#3041](https://github.com/GMOD/jbrowse-components/pull/3041) Fix ability to search and load data files using lower case refName aliases ([@cmdcolin](https://github.com/cmdcolin)) + - [#3044](https://github.com/GMOD/jbrowse-components/pull/3044) Remove + node-canvas from @jbrowse/core dependencies + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3041](https://github.com/GMOD/jbrowse-components/pull/3041) Fix ability to + search and load data files using lower case refName aliases + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3042](https://github.com/GMOD/jbrowse-components/pull/3042) Add fetch with proxy support to jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) - - [#3038](https://github.com/GMOD/jbrowse-components/pull/3038) Display coordinates in overview scalebar when no cytoband available ([@cmdcolin](https://github.com/cmdcolin)) - - [#3015](https://github.com/GMOD/jbrowse-components/pull/3015) Add plaintext bed support with BedAdapter ([@cmdcolin](https://github.com/cmdcolin)) + - [#3042](https://github.com/GMOD/jbrowse-components/pull/3042) Add fetch with + proxy support to jbrowse CLI ([@cmdcolin](https://github.com/cmdcolin)) + - [#3038](https://github.com/GMOD/jbrowse-components/pull/3038) Display + coordinates in overview scalebar when no cytoband available + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3015](https://github.com/GMOD/jbrowse-components/pull/3015) Add plaintext + bed support with BedAdapter ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix -- [#3049](https://github.com/GMOD/jbrowse-components/pull/3049) Fix ability to use callbacks for the linear arc renderer ([@cmdcolin](https://github.com/cmdcolin)) +- [#3049](https://github.com/GMOD/jbrowse-components/pull/3049) Fix ability to + use callbacks for the linear arc renderer + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#2831](https://github.com/GMOD/jbrowse-components/pull/2831) Update commands for sorting GFF3 for tabix ([@cmdcolin](https://github.com/cmdcolin)) -- [#3018](https://github.com/GMOD/jbrowse-components/pull/3018) Add desktop specific plugin example ([@cmdcolin](https://github.com/cmdcolin)) -- [#3022](https://github.com/GMOD/jbrowse-components/pull/3022) Add example using embedded components with next.js ([@cmdcolin](https://github.com/cmdcolin)) +- [#2831](https://github.com/GMOD/jbrowse-components/pull/2831) Update commands + for sorting GFF3 for tabix ([@cmdcolin](https://github.com/cmdcolin)) +- [#3018](https://github.com/GMOD/jbrowse-components/pull/3018) Add desktop + specific plugin example ([@cmdcolin](https://github.com/cmdcolin)) +- [#3022](https://github.com/GMOD/jbrowse-components/pull/3022) Add example + using embedded components with next.js + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#3035](https://github.com/GMOD/jbrowse-components/pull/3035) Add typescripting to hierarchical track selector ([@cmdcolin](https://github.com/cmdcolin)) + - [#3035](https://github.com/GMOD/jbrowse-components/pull/3035) Add + typescripting to hierarchical track selector + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 diff --git a/website/blog/2022-07-07-v2.0.0-release.md b/website/blog/2022-07-07-v2.0.0-release.md index 409371c065..ebf541e3e9 100644 --- a/website/blog/2022-07-07-v2.0.0-release.md +++ b/website/blog/2022-07-07-v2.0.0-release.md @@ -4,9 +4,9 @@ date: 2022-07-07 20:21:51 tags: ['release', 'jbrowse 2'] --- -We are pleased to release v2.0.0! This is a major version milestone, but it -does not have a huge number of changes. Instead, the major change that resulted -in becoming v2.0.0 was the upgrade of many of our dependencies including +We are pleased to release v2.0.0! This is a major version milestone, but it does +not have a huge number of changes. Instead, the major change that resulted in +becoming v2.0.0 was the upgrade of many of our dependencies including - material-ui v4 -> v5 - mobx-state-tree v3.14.1 -> v5 @@ -19,9 +19,9 @@ with this upgrade, let us know and we can help Some notable improvements: -- This release improves bundle sizes for users of embedded components, by - adding ESM builds to NPM. This can reduce the initial load of a webpage using - e.g. @jbrowse/react-linear-genome-view by about 55% (1.4MB gzipped js->770kb +- This release improves bundle sizes for users of embedded components, by adding + ESM builds to NPM. This can reduce the initial load of a webpage using e.g. + @jbrowse/react-linear-genome-view by about 55% (1.4MB gzipped js->770kb gzipped js) ## Downloads @@ -89,28 +89,49 @@ on NPM. #### :rocket: Enhancement - Other - - [#3001](https://github.com/GMOD/jbrowse-components/pull/3001) Draw SNPs in modifications/methylation views ([@cmdcolin](https://github.com/cmdcolin)) - - [#3068](https://github.com/GMOD/jbrowse-components/pull/3068) Allow HTML in feature tooltips, remove react-simple-code-editor ([@cmdcolin](https://github.com/cmdcolin)) - - [#3065](https://github.com/GMOD/jbrowse-components/pull/3065) Allow changing between xyplot,line,density for linear wiggle tracks and other small fixes ([@cmdcolin](https://github.com/cmdcolin)) + - [#3001](https://github.com/GMOD/jbrowse-components/pull/3001) Draw SNPs in + modifications/methylation views ([@cmdcolin](https://github.com/cmdcolin)) + - [#3068](https://github.com/GMOD/jbrowse-components/pull/3068) Allow HTML in + feature tooltips, remove react-simple-code-editor + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3065](https://github.com/GMOD/jbrowse-components/pull/3065) Allow changing + between xyplot,line,density for linear wiggle tracks and other small fixes + ([@cmdcolin](https://github.com/cmdcolin)) - `text-indexing` - - [#3058](https://github.com/GMOD/jbrowse-components/pull/3058) Improve bundle size and code splitting on embedded builds (v2) ([@cmdcolin](https://github.com/cmdcolin)) + - [#3058](https://github.com/GMOD/jbrowse-components/pull/3058) Improve bundle + size and code splitting on embedded builds (v2) + ([@cmdcolin](https://github.com/cmdcolin)) - `__mocks__`, `core`, `text-indexing` - - [#2949](https://github.com/GMOD/jbrowse-components/pull/2949) Upgrade to MUI v5, mobx-state-tree v5, mobx-react v6, mobx-react v7 ([@cmdcolin](https://github.com/cmdcolin)) + - [#2949](https://github.com/GMOD/jbrowse-components/pull/2949) Upgrade to MUI + v5, mobx-state-tree v5, mobx-react v6, mobx-react v7 + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3072](https://github.com/GMOD/jbrowse-components/pull/3072) Fix the display of inversions for MCScan alignments ([@cmdcolin](https://github.com/cmdcolin)) - - [#3074](https://github.com/GMOD/jbrowse-components/pull/3074) Fix the display of deletions vs insertions being backwards in synteny view with CIGAR strings ([@cmdcolin](https://github.com/cmdcolin)) - - [#3057](https://github.com/GMOD/jbrowse-components/pull/3057) Fix export SVG crash on some BigWig tracks ([@cmdcolin](https://github.com/cmdcolin)) - - [#3052](https://github.com/GMOD/jbrowse-components/pull/3052) Fix negative value quantitative display in svg exports ([@cmdcolin](https://github.com/cmdcolin)) + - [#3072](https://github.com/GMOD/jbrowse-components/pull/3072) Fix the + display of inversions for MCScan alignments + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3074](https://github.com/GMOD/jbrowse-components/pull/3074) Fix the + display of deletions vs insertions being backwards in synteny view with + CIGAR strings ([@cmdcolin](https://github.com/cmdcolin)) + - [#3057](https://github.com/GMOD/jbrowse-components/pull/3057) Fix export SVG + crash on some BigWig tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#3052](https://github.com/GMOD/jbrowse-components/pull/3052) Fix negative + value quantitative display in svg exports + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3064](https://github.com/GMOD/jbrowse-components/pull/3064) Fix opening link in new tab by default in feature details ([@cmdcolin](https://github.com/cmdcolin)) - - [#3053](https://github.com/GMOD/jbrowse-components/pull/3053) Avoid displaying [object Object] on deeply nested data in base feature details ([@cmdcolin](https://github.com/cmdcolin)) + - [#3064](https://github.com/GMOD/jbrowse-components/pull/3064) Fix opening + link in new tab by default in feature details + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3053](https://github.com/GMOD/jbrowse-components/pull/3053) Avoid + displaying [object Object] on deeply nested data in base feature details + ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal -- [#3067](https://github.com/GMOD/jbrowse-components/pull/3067) Typescriptify some integration tests ([@cmdcolin](https://github.com/cmdcolin)) +- [#3067](https://github.com/GMOD/jbrowse-components/pull/3067) Typescriptify + some integration tests ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 diff --git a/website/blog/2022-07-13-v2.0.1-release.md b/website/blog/2022-07-13-v2.0.1-release.md index 52caa24a64..218e79d708 100644 --- a/website/blog/2022-07-13-v2.0.1-release.md +++ b/website/blog/2022-07-13-v2.0.1-release.md @@ -12,14 +12,15 @@ the linear synteny view ![](https://user-images.githubusercontent.com/6511937/178566572-6fb7600b-172f-4317-8a6d-1318310d2baf.png) If there are base level alignments, either from the read vs ref view or e.g. a -PAF file generated with minimap -c (outputs CIGAR), then you can also mouse -over to get information about the particular part of that alignment e.g. the -CIGAR string +PAF file generated with minimap -c (outputs CIGAR), then you can also mouse over +to get information about the particular part of that alignment e.g. the CIGAR +string ![](https://user-images.githubusercontent.com/6511937/178847662-9c915393-91c8-4d04-be91-9d7987b5e1a9.png) Figure showing a mouseover inside a deletion in the read vs ref view -This release also has some other small fixes and improvements, see release notes! +This release also has some other small fixes and improvements, see release +notes! ## Downloads @@ -85,21 +86,38 @@ on NPM. #### :rocket: Enhancement - `core` - - [#3089](https://github.com/GMOD/jbrowse-components/pull/3089) Clarify error message when adapter has no features ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3084](https://github.com/GMOD/jbrowse-components/pull/3084) Show a descriptive error if an adapter doesn't provide a sequence ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3071](https://github.com/GMOD/jbrowse-components/pull/3071) Add ability to mouseover/click on synteny feature polygons in the linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3089](https://github.com/GMOD/jbrowse-components/pull/3089) Clarify error + message when adapter has no features + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3084](https://github.com/GMOD/jbrowse-components/pull/3084) Show a + descriptive error if an adapter doesn't provide a sequence + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3071](https://github.com/GMOD/jbrowse-components/pull/3071) Add ability to + mouseover/click on synteny feature polygons in the linear synteny view + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3081](https://github.com/GMOD/jbrowse-components/pull/3081) Add ability to toggle gridlines on the LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#3081](https://github.com/GMOD/jbrowse-components/pull/3081) Add ability to + toggle gridlines on the LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3088](https://github.com/GMOD/jbrowse-components/pull/3088) Fix labels being cut-off in SVG features by rendering feature labels on main thread ([@cmdcolin](https://github.com/cmdcolin)) - - [#3085](https://github.com/GMOD/jbrowse-components/pull/3085) Fix zoom to behavior being inaccurate with many displayed regions visible ([@cmdcolin](https://github.com/cmdcolin)) - - [#3082](https://github.com/GMOD/jbrowse-components/pull/3082) Fix negative strand CIGAR renderings on linear synteny view ([@cmdcolin](https://github.com/cmdcolin)) - - [#3077](https://github.com/GMOD/jbrowse-components/pull/3077) Fix crash opening multiple synteny track selectors launched from dotplot view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3088](https://github.com/GMOD/jbrowse-components/pull/3088) Fix labels + being cut-off in SVG features by rendering feature labels on main thread + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3085](https://github.com/GMOD/jbrowse-components/pull/3085) Fix zoom to + behavior being inaccurate with many displayed regions visible + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3082](https://github.com/GMOD/jbrowse-components/pull/3082) Fix negative + strand CIGAR renderings on linear synteny view + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3077](https://github.com/GMOD/jbrowse-components/pull/3077) Fix crash + opening multiple synteny track selectors launched from dotplot view + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3086](https://github.com/GMOD/jbrowse-components/pull/3086) Fix pxToBp and bpToPx calculations when there are many displayed regions ([@cmdcolin](https://github.com/cmdcolin)) + - [#3086](https://github.com/GMOD/jbrowse-components/pull/3086) Fix pxToBp and + bpToPx calculations when there are many displayed regions + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 diff --git a/website/blog/2022-07-28-v2.1.0-release.md b/website/blog/2022-07-28-v2.1.0-release.md index 524b8216d6..59b9587873 100644 --- a/website/blog/2022-07-28-v2.1.0-release.md +++ b/website/blog/2022-07-28-v2.1.0-release.md @@ -4,8 +4,8 @@ date: 2022-07-28 22:05:11 tags: ['release', 'jbrowse 2'] --- -We are pleased to present 2.1.0! This release adds some significant new -features including: +We are pleased to present 2.1.0! This release adds some significant new features +including: - Multi-wiggle tracks - This allows, for example, multiple bigwig files to be displayed in a single track with synchronized scalebar settings. See @@ -19,9 +19,11 @@ features including: Example links for multi-bigwig sessions -- ENCODE bigWigs https://jbrowse.org/code/jb2/v2.1.0/?config=test_data%2Fconfig_demo.json&session=share-Pw7kOjagSF&password=e0SuE +- ENCODE bigWigs + https://jbrowse.org/code/jb2/v2.1.0/?config=test_data%2Fconfig_demo.json&session=share-Pw7kOjagSF&password=e0SuE -- COLO829 Tumor vs Normal coverage bigWigs https://jbrowse.org/code/jb2/v2.1.0/?config=test_data%2Fconfig_demo.json&session=share-J4owOIkT0F&password=orr2h +- COLO829 Tumor vs Normal coverage bigWigs + https://jbrowse.org/code/jb2/v2.1.0/?config=test_data%2Fconfig_demo.json&session=share-J4owOIkT0F&password=orr2h ![](https://user-images.githubusercontent.com/6511937/181639088-9159d60d-a49d-4601-bfb8-6201a26dc185.png) @@ -34,15 +36,15 @@ points showing tumor vs normal coverage ![](https://user-images.githubusercontent.com/6511937/181640836-76257585-bfde-4568-8f44-dbf2590131cb.png) -Dotplot view showing warnings from rendering dotplot, generally due to the -wrong assemblies being compared. Screenshot also shows the dropdown menu to -choose whether mouse click-and-drag pans the view or selects a region +Dotplot view showing warnings from rendering dotplot, generally due to the wrong +assemblies being compared. Screenshot also shows the dropdown menu to choose +whether mouse click-and-drag pans the view or selects a region ![](https://user-images.githubusercontent.com/6511937/181638930-730a522d-b58e-4505-a83a-7eb5ff1fe34d.png) -Undo and redo buttons in the Tools menu, also accessible from keyboard -shortcuts ctrl+z/ctrl+y and cmd+z/cmd+shift+z. The Undo/Redo function is -available in jbrowse-web and jbrowse-desktop currently +Undo and redo buttons in the Tools menu, also accessible from keyboard shortcuts +ctrl+z/ctrl+y and cmd+z/cmd+shift+z. The Undo/Redo function is available in +jbrowse-web and jbrowse-desktop currently ## Downloads @@ -93,26 +95,47 @@ on NPM. #### :rocket: Enhancement - `core` - - [#3111](https://github.com/GMOD/jbrowse-components/pull/3111) Create undo manager in jbrowse-web and jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#3115](https://github.com/GMOD/jbrowse-components/pull/3115) Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view ([@cmdcolin](https://github.com/cmdcolin)) - - [#3102](https://github.com/GMOD/jbrowse-components/pull/3102) Allow creating alternative "add track workflows" from within the "Add track" widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#3043](https://github.com/GMOD/jbrowse-components/pull/3043) Create MultiWiggle track type, adapter, and renderers ([@cmdcolin](https://github.com/cmdcolin)) + - [#3111](https://github.com/GMOD/jbrowse-components/pull/3111) Create undo + manager in jbrowse-web and jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3115](https://github.com/GMOD/jbrowse-components/pull/3115) Add warning + when dotplot renders outside of it's boundaries, and create click-and-drag + panning of dotplot view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3102](https://github.com/GMOD/jbrowse-components/pull/3102) Allow creating + alternative "add track workflows" from within the "Add track" widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3043](https://github.com/GMOD/jbrowse-components/pull/3043) Create + MultiWiggle track type, adapter, and renderers + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3113](https://github.com/GMOD/jbrowse-components/pull/3113) Improve SVG performance by avoiding re-render when feature is clicked ([@cmdcolin](https://github.com/cmdcolin)) - - [#3110](https://github.com/GMOD/jbrowse-components/pull/3110) Remove TSDX from plugin development tools ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3106](https://github.com/GMOD/jbrowse-components/pull/3106) Add "emphasis" mode for no fill/scatterplot mode in XYPlot type renderings ([@cmdcolin](https://github.com/cmdcolin)) + - [#3113](https://github.com/GMOD/jbrowse-components/pull/3113) Improve SVG + performance by avoiding re-render when feature is clicked + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3110](https://github.com/GMOD/jbrowse-components/pull/3110) Remove TSDX + from plugin development tools + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3106](https://github.com/GMOD/jbrowse-components/pull/3106) Add "emphasis" + mode for no fill/scatterplot mode in XYPlot type renderings + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3109](https://github.com/GMOD/jbrowse-components/pull/3109) Better support for developing plugins from within yarn 2+ workspaces (include \_\_virtual folder in build) ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3109](https://github.com/GMOD/jbrowse-components/pull/3109) Better support + for developing plugins from within yarn 2+ workspaces (include \_\_virtual + folder in build) ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3095](https://github.com/GMOD/jbrowse-components/pull/3095) Add MUI exports to re-exports list ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3092](https://github.com/GMOD/jbrowse-components/pull/3092) Fix use of embedded components with vite 3.0 using tsc to compile @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) + - [#3095](https://github.com/GMOD/jbrowse-components/pull/3095) Add MUI + exports to re-exports list + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3092](https://github.com/GMOD/jbrowse-components/pull/3092) Fix use of + embedded components with vite 3.0 using tsc to compile @jbrowse/core + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#3116](https://github.com/GMOD/jbrowse-components/pull/3116) Add docs for multi-wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) +- [#3116](https://github.com/GMOD/jbrowse-components/pull/3116) Add docs for + multi-wiggle tracks ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 diff --git a/website/blog/2022-08-25-v2.1.2-release.md b/website/blog/2022-08-25-v2.1.2-release.md index 4694e5e18c..9d89824327 100644 --- a/website/blog/2022-08-25-v2.1.2-release.md +++ b/website/blog/2022-08-25-v2.1.2-release.md @@ -6,9 +6,9 @@ tags: ['release', 'jbrowse 2'] Hello all, we are pleased to announce v2.1.2! -This release includes a number of small bugfixes to the multi-wiggle track -type, and a new feature for performing small sequence searches/motifs in the -visible region. +This release includes a number of small bugfixes to the multi-wiggle track type, +and a new feature for performing small sequence searches/motifs in the visible +region. ![](https://user-images.githubusercontent.com/6511937/186729490-40cbc638-c64a-4eef-a3f9-b80da4b6fdb6.png) ![](https://user-images.githubusercontent.com/6511937/186729296-2a0dda34-d298-4e7f-8b2b-f938ce89fb76.png) @@ -20,8 +20,8 @@ Also, we just recently published the pre-print for our JBrowse 2 paper on bioRxiv! https://www.biorxiv.org/content/10.1101/2022.07.28.501447v1 This is a tour de force describing the basic ideas behind JBrowse 2 as an app. -We are really pleased with how users and developers have helped to contribute -to JBrowse 2 thus far, and look forward to many more years! +We are really pleased with how users and developers have helped to contribute to +JBrowse 2 thus far, and look forward to many more years! ## Downloads @@ -83,25 +83,50 @@ on NPM. #### :rocket: Enhancement - Other - - [#3152](https://github.com/GMOD/jbrowse-components/pull/3152) Render CSQ and ANN fields in VCF feature details as data grids ([@cmdcolin](https://github.com/cmdcolin)) - - [#3137](https://github.com/GMOD/jbrowse-components/pull/3137) Make ideogram menu item similar to others ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3152](https://github.com/GMOD/jbrowse-components/pull/3152) Render CSQ and + ANN fields in VCF feature details as data grids + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3137](https://github.com/GMOD/jbrowse-components/pull/3137) Make ideogram + menu item similar to others + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3159](https://github.com/GMOD/jbrowse-components/pull/3159) Sequence search track ([@cmdcolin](https://github.com/cmdcolin)) - - [#3132](https://github.com/GMOD/jbrowse-components/pull/3132) Extend theme with module augmentation ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3159](https://github.com/GMOD/jbrowse-components/pull/3159) Sequence + search track ([@cmdcolin](https://github.com/cmdcolin)) + - [#3132](https://github.com/GMOD/jbrowse-components/pull/3132) Extend theme + with module augmentation + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :bug: Bug Fix - Other - - [#3157](https://github.com/GMOD/jbrowse-components/pull/3157) Support the "name" field on multi-wiggle adapter subadapters instead of source ([@cmdcolin](https://github.com/cmdcolin)) - - [#3154](https://github.com/GMOD/jbrowse-components/pull/3154) Use the union of all the subadapter refNames for the MultiWiggleAdapter getRefNames ([@cmdcolin](https://github.com/cmdcolin)) - - [#3156](https://github.com/GMOD/jbrowse-components/pull/3156) Fix for mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode ([@cmdcolin](https://github.com/cmdcolin)) - - [#3151](https://github.com/GMOD/jbrowse-components/pull/3151) Fix ability to click and drag overview scale bar dragging right to left ([@cmdcolin](https://github.com/cmdcolin)) - - [#3133](https://github.com/GMOD/jbrowse-components/pull/3133) Update the ref name box when assembly is changed in LGV import form ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3131](https://github.com/GMOD/jbrowse-components/pull/3131) Use "code" instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3119](https://github.com/GMOD/jbrowse-components/pull/3119) Use es2015 setting for commonjs builds of packages to fix @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) - - [#3142](https://github.com/GMOD/jbrowse-components/pull/3142) Fix unicode arrow icon not rendering with some fonts in configuration editor ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3157](https://github.com/GMOD/jbrowse-components/pull/3157) Support the + "name" field on multi-wiggle adapter subadapters instead of source + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3154](https://github.com/GMOD/jbrowse-components/pull/3154) Use the union + of all the subadapter refNames for the MultiWiggleAdapter getRefNames + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3156](https://github.com/GMOD/jbrowse-components/pull/3156) Fix for + mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3151](https://github.com/GMOD/jbrowse-components/pull/3151) Fix ability to + click and drag overview scale bar dragging right to left + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3133](https://github.com/GMOD/jbrowse-components/pull/3133) Update the ref + name box when assembly is changed in LGV import form + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3131](https://github.com/GMOD/jbrowse-components/pull/3131) Use "code" + instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3119](https://github.com/GMOD/jbrowse-components/pull/3119) Use es2015 + setting for commonjs builds of packages to fix @jbrowse/img + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3142](https://github.com/GMOD/jbrowse-components/pull/3142) Fix unicode + arrow icon not rendering with some fonts in configuration editor + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3120](https://github.com/GMOD/jbrowse-components/pull/3120) Fix menu items for changing display type from track menu ([@cmdcolin](https://github.com/cmdcolin)) + - [#3120](https://github.com/GMOD/jbrowse-components/pull/3120) Fix menu items + for changing display type from track menu + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 2 diff --git a/website/blog/2022-09-15-v2.1.3-release.md b/website/blog/2022-09-15-v2.1.3-release.md index 798c7b7de9..11c4c0986b 100644 --- a/website/blog/2022-09-15-v2.1.3-release.md +++ b/website/blog/2022-09-15-v2.1.3-release.md @@ -6,10 +6,10 @@ tags: ['release', 'jbrowse 2'] This release includes a quality-of-life improvement for users plotting synteny with CIGAR strings. Before this version, the x-axis in the dotplot was assumed -to be target sequence (and similarly, the top row in the linear synteny view -was assumed to be the target sequence). But now, target can be either x- or -y-axis in dotplot, and top or bottom in linear synteny views, removing the need -for the user to care as much about query-vs-target ordering. +to be target sequence (and similarly, the top row in the linear synteny view was +assumed to be the target sequence). But now, target can be either x- or y-axis +in dotplot, and top or bottom in linear synteny views, removing the need for the +user to care as much about query-vs-target ordering. This release also includes several fixes for the the behavior of text searching in the linear genome view, a new button to open a .jbrowse file directly from @@ -18,7 +18,8 @@ inverted alignments on dotplots that affected versions v2.1.0-v2.1.2. ![](https://user-images.githubusercontent.com/6511937/190472800-52cd25f8-a168-4767-afff-b79445dee1a9.png) -Screenshot showing the latest jbrowse desktop start screen, with a button to open .jbrowse sessions +Screenshot showing the latest jbrowse desktop start screen, with a button to +open .jbrowse sessions ![](https://user-images.githubusercontent.com/6511937/190502451-de749592-0023-4030-859b-a7001592736b.png) @@ -73,42 +74,78 @@ on NPM. #### :rocket: Enhancement - Other - - [#3188](https://github.com/GMOD/jbrowse-components/pull/3188) Add 'Open saved session' button to start screen on desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#3187](https://github.com/GMOD/jbrowse-components/pull/3187) Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table ([@cmdcolin](https://github.com/cmdcolin)) - - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target ([@cmdcolin](https://github.com/cmdcolin)) - - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability for CLI to recognize plaintext BED files ([@cmdcolin](https://github.com/cmdcolin)) - - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about dialog with version number for embedded components ([@cmdcolin](https://github.com/cmdcolin)) - - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user to wait before re-launching app on desktop update ([@cmdcolin](https://github.com/cmdcolin)) + - [#3188](https://github.com/GMOD/jbrowse-components/pull/3188) Add 'Open + saved session' button to start screen on desktop + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3187](https://github.com/GMOD/jbrowse-components/pull/3187) Add mouseover + tooltip descriptions to the header of the VariantFeatureDetails + sample/genotype table ([@cmdcolin](https://github.com/cmdcolin)) + - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add + extendSession extension point to web and desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y + assemblies of dotplot or top/bottom selection of synteny views to be either + query or target ([@cmdcolin](https://github.com/cmdcolin)) + - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability + for CLI to recognize plaintext BED files + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about + dialog with version number for embedded components + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user + to wait before re-launching app on desktop update + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3180](https://github.com/GMOD/jbrowse-components/pull/3180) Improve adding assemblies internally, and use the assembly displayName in more places in the UI ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3175](https://github.com/GMOD/jbrowse-components/pull/3175) Add OAuthModel InternetAccount token refresh ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) + - [#3180](https://github.com/GMOD/jbrowse-components/pull/3180) Improve adding + assemblies internally, and use the assembly displayName in more places in + the UI ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make + pluginManager param to getFetcher optional + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3175](https://github.com/GMOD/jbrowse-components/pull/3175) Add OAuthModel + InternetAccount token refresh + ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) #### :bug: Bug Fix - `core` - - [#3168](https://github.com/GMOD/jbrowse-components/pull/3168) Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead state tree node" error by creating snapshots of parent region for block calculations ([@cmdcolin](https://github.com/cmdcolin)) + - [#3168](https://github.com/GMOD/jbrowse-components/pull/3168) Fix search + behavior when there are multiple matches in LGV header and when feature + description matched in import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead + state tree node" error by creating snapshots of parent region for block + calculations ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing inverted CIGAR segments on dotplot ([@cmdcolin](https://github.com/cmdcolin)) + - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing + inverted CIGAR segments on dotplot + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation + overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - Other - - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3165](https://github.com/GMOD/jbrowse-components/pull/3165) Use more defaults in rollup plugins ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add + extendSession extension point to web and desktop + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3165](https://github.com/GMOD/jbrowse-components/pull/3165) Use more + defaults in rollup plugins + ([@garrettjstevens](https://github.com/garrettjstevens)) - `core` - - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) + - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make + pluginManager param to getFetcher optional + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the + QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 4 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) - [@andrzejgrzelak](https://github.com/andrzejgrzelak) diff --git a/website/blog/2022-09-16-v2.1.4-release.md b/website/blog/2022-09-16-v2.1.4-release.md index 500db08bab..904f1deff1 100644 --- a/website/blog/2022-09-16-v2.1.4-release.md +++ b/website/blog/2022-09-16-v2.1.4-release.md @@ -4,7 +4,8 @@ date: 2022-09-16 19:39:53 tags: ['release', 'jbrowse 2'] --- -This release fixes the UMD builds for the react components which failed to upload to npm in 2.1.3 +This release fixes the UMD builds for the react components which failed to +upload to npm in 2.1.3 ## Downloads @@ -34,7 +35,9 @@ on NPM. #### :bug: Bug Fix -- [#3191](https://github.com/GMOD/jbrowse-components/pull/3191) Fix the UMD build of the react embedded components ([@cmdcolin](https://github.com/cmdcolin)) +- [#3191](https://github.com/GMOD/jbrowse-components/pull/3191) Fix the UMD + build of the react embedded components + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 diff --git a/website/blog/2022-10-03-v2.1.5-release.md b/website/blog/2022-10-03-v2.1.5-release.md index 1d327f5642..68b48cd5aa 100644 --- a/website/blog/2022-10-03-v2.1.5-release.md +++ b/website/blog/2022-10-03-v2.1.5-release.md @@ -61,45 +61,88 @@ on NPM. #### :rocket: Enhancement - Other - - [#3200](https://github.com/GMOD/jbrowse-components/pull/3200) Use Alert component for track messages ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3229](https://github.com/GMOD/jbrowse-components/pull/3229) Allow user to select local assembly to add tracks to for trackhub registry ([@cmdcolin](https://github.com/cmdcolin)) - - [#3220](https://github.com/GMOD/jbrowse-components/pull/3220) Improve error reporting on SV inspector/spreadsheet view on import form ([@cmdcolin](https://github.com/cmdcolin)) - - [#3198](https://github.com/GMOD/jbrowse-components/pull/3198) Improve error reporting on jbrowse-web start screen when user attempts to open a broken recent session ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#3200](https://github.com/GMOD/jbrowse-components/pull/3200) Use Alert + component for track messages + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3229](https://github.com/GMOD/jbrowse-components/pull/3229) Allow user to + select local assembly to add tracks to for trackhub registry + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3220](https://github.com/GMOD/jbrowse-components/pull/3220) Improve error + reporting on SV inspector/spreadsheet view on import form + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3198](https://github.com/GMOD/jbrowse-components/pull/3198) Improve error + reporting on jbrowse-web start screen when user attempts to open a broken + recent session + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - `core` - - [#3223](https://github.com/GMOD/jbrowse-components/pull/3223) Allow adding session tracks to embedded react component along with disableAddTracks option if unwanted ([@cmdcolin](https://github.com/cmdcolin)) - - [#3227](https://github.com/GMOD/jbrowse-components/pull/3227) Add infrastructure for creating linear-genome-view sub-classes ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - - [#3215](https://github.com/GMOD/jbrowse-components/pull/3215) Add error boundary on view, track, and drawer widget ([@cmdcolin](https://github.com/cmdcolin)) - - [#3216](https://github.com/GMOD/jbrowse-components/pull/3216) Add ability to set number of bp to fetch up/down stream/inside intron in feature details ([@cmdcolin](https://github.com/cmdcolin)) + - [#3223](https://github.com/GMOD/jbrowse-components/pull/3223) Allow adding + session tracks to embedded react component along with disableAddTracks + option if unwanted ([@cmdcolin](https://github.com/cmdcolin)) + - [#3227](https://github.com/GMOD/jbrowse-components/pull/3227) Add + infrastructure for creating linear-genome-view sub-classes + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) + - [#3215](https://github.com/GMOD/jbrowse-components/pull/3215) Add error + boundary on view, track, and drawer widget + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3216](https://github.com/GMOD/jbrowse-components/pull/3216) Add ability to + set number of bp to fetch up/down stream/inside intron in feature details + ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - Other - - [#3241](https://github.com/GMOD/jbrowse-components/pull/3241) Fix local session failing to load copying between tabs in some cases ([@cmdcolin](https://github.com/cmdcolin)) - - [#3234](https://github.com/GMOD/jbrowse-components/pull/3234) Fix circular embedded view failing to load in v2.1.3 and v2.1.4 ([@cmdcolin](https://github.com/cmdcolin)) - - [#3233](https://github.com/GMOD/jbrowse-components/pull/3233) Fix legend being cutoff on multiwiggle tracks with wide window ([@cmdcolin](https://github.com/cmdcolin)) - - [#3217](https://github.com/GMOD/jbrowse-components/pull/3217) Fix loading tracks from connection using assembly alias ([@cmdcolin](https://github.com/cmdcolin)) - - [#3214](https://github.com/GMOD/jbrowse-components/pull/3214) Fix trackhub registry failing to load in 2.x.y versions of jbrowse ([@cmdcolin](https://github.com/cmdcolin)) - - [#3204](https://github.com/GMOD/jbrowse-components/pull/3204) Fix authentication configuration on jbrowse-desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#3241](https://github.com/GMOD/jbrowse-components/pull/3241) Fix local + session failing to load copying between tabs in some cases + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3234](https://github.com/GMOD/jbrowse-components/pull/3234) Fix circular + embedded view failing to load in v2.1.3 and v2.1.4 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3233](https://github.com/GMOD/jbrowse-components/pull/3233) Fix legend + being cutoff on multiwiggle tracks with wide window + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3217](https://github.com/GMOD/jbrowse-components/pull/3217) Fix loading + tracks from connection using assembly alias + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3214](https://github.com/GMOD/jbrowse-components/pull/3214) Fix trackhub + registry failing to load in 2.x.y versions of jbrowse + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3204](https://github.com/GMOD/jbrowse-components/pull/3204) Fix + authentication configuration on jbrowse-desktop + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3231](https://github.com/GMOD/jbrowse-components/pull/3231) Fix theme coloring for components that use overrides e.g. accordion summary ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3231](https://github.com/GMOD/jbrowse-components/pull/3231) Fix theme + coloring for components that use overrides e.g. accordion summary + ([@garrettjstevens](https://github.com/garrettjstevens)) #### :memo: Documentation -- [#3193](https://github.com/GMOD/jbrowse-components/pull/3193) Add desktop specific plugin tutorial ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- [#3193](https://github.com/GMOD/jbrowse-components/pull/3193) Add desktop + specific plugin tutorial + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) #### :house: Internal - Other - - [#3243](https://github.com/GMOD/jbrowse-components/pull/3243) Add component test for circular genome view ([@cmdcolin](https://github.com/cmdcolin)) - - [#3242](https://github.com/GMOD/jbrowse-components/pull/3242) Fix flaky test in plugins/linear-genome-view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3243](https://github.com/GMOD/jbrowse-components/pull/3243) Add component + test for circular genome view ([@cmdcolin](https://github.com/cmdcolin)) + - [#3242](https://github.com/GMOD/jbrowse-components/pull/3242) Fix flaky test + in plugins/linear-genome-view ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3228](https://github.com/GMOD/jbrowse-components/pull/3228) Improve TypeScript for queueDialog ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3224](https://github.com/GMOD/jbrowse-components/pull/3224) More typescripting of plain js files ([@cmdcolin](https://github.com/cmdcolin)) - - [#3207](https://github.com/GMOD/jbrowse-components/pull/3207) Hardcoded block width of 800px on static blocks ([@cmdcolin](https://github.com/cmdcolin)) - - [#3197](https://github.com/GMOD/jbrowse-components/pull/3197) Use "temporaryAssemblies" to store read vs ref assemblies, and allow selecting "sessionAssemblies" in dropdown ([@cmdcolin](https://github.com/cmdcolin)) + - [#3228](https://github.com/GMOD/jbrowse-components/pull/3228) Improve + TypeScript for queueDialog + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3224](https://github.com/GMOD/jbrowse-components/pull/3224) More + typescripting of plain js files ([@cmdcolin](https://github.com/cmdcolin)) + - [#3207](https://github.com/GMOD/jbrowse-components/pull/3207) Hardcoded + block width of 800px on static blocks + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3197](https://github.com/GMOD/jbrowse-components/pull/3197) Use + "temporaryAssemblies" to store read vs ref assemblies, and allow selecting + "sessionAssemblies" in dropdown ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 -- Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) +- Caroline Bridge + ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) diff --git a/website/blog/2022-10-19-v2.1.6-release.md b/website/blog/2022-10-19-v2.1.6-release.md index d7decdd9b9..7a1e777332 100644 --- a/website/blog/2022-10-19-v2.1.6-release.md +++ b/website/blog/2022-10-19-v2.1.6-release.md @@ -12,22 +12,22 @@ This has several important fixes and improvements browsers, a bug with starting the webworker was fixed - There is now an option to use the WebWorkerRpc on the @jbrowse/react-linear-genome-view. This is a great improvement because the - WebWorkerRpc dramatically reduces the "stalling" of the main thread when - large datasets like BAM/CRAM are being loaded. See + WebWorkerRpc dramatically reduces the "stalling" of the main thread when large + datasets like BAM/CRAM are being loaded. See https://jbrowse.org/storybook/lgv/main/?path=/story/using-webworker-rpc--page for more info! - All feature types, not just gene features, can obtain the underlying feature sequence with upstream/downstream options -- The ability to refer to plugins in a path relative to your data directory - has been fixed, so you can easily refer to plugins in your config file with - e.g. `"plugins":[{"name":"MyPlugin","umdLoc":{"uri":"myplugin.js"}}]` - (`umdLoc` resolves the uri relative to the config.json file that it is in - use). There is also `umdUrl` which can be used in place of `umdLoc` which can - be used like this `"plugins":[{"name":"MyPlugin","umdUrl":"myplugin.js"}]` - and this will resolve relative to the jbrowse root directory e.g. where the - index.html is. We recommend using UMD for now, as ESM modules do not have - full browser support e.g. in firefox yet, but this will likely be changing - soon and we will update tutorials when this occurs! +- The ability to refer to plugins in a path relative to your data directory has + been fixed, so you can easily refer to plugins in your config file with e.g. + `"plugins":[{"name":"MyPlugin","umdLoc":{"uri":"myplugin.js"}}]` (`umdLoc` + resolves the uri relative to the config.json file that it is in use). There is + also `umdUrl` which can be used in place of `umdLoc` which can be used like + this `"plugins":[{"name":"MyPlugin","umdUrl":"myplugin.js"}]` and this will + resolve relative to the jbrowse root directory e.g. where the index.html is. + We recommend using UMD for now, as ESM modules do not have full browser + support e.g. in firefox yet, but this will likely be changing soon and we will + update tutorials when this occurs! See our volvox example for a simple no-build plugin https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/umd_plugin.js @@ -107,34 +107,55 @@ on NPM. #### :rocket: Enhancement - Other - - [#3272](https://github.com/GMOD/jbrowse-components/pull/3272) Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff ([@cmdcolin](https://github.com/cmdcolin)) - - [#3254](https://github.com/GMOD/jbrowse-components/pull/3254) Use tick labels that correspond to the overview's larger zoom level ([@cmdcolin](https://github.com/cmdcolin)) + - [#3272](https://github.com/GMOD/jbrowse-components/pull/3272) Disable + resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3254](https://github.com/GMOD/jbrowse-components/pull/3254) Use tick + labels that correspond to the overview's larger zoom level + ([@cmdcolin](https://github.com/cmdcolin)) - `core` - - [#3230](https://github.com/GMOD/jbrowse-components/pull/3230) Add ability to customize About dialog with callbacks and optionally hide links to data ([@cmdcolin](https://github.com/cmdcolin)) - - [#3275](https://github.com/GMOD/jbrowse-components/pull/3275) Add help dialog for feature sequence panel ([@cmdcolin](https://github.com/cmdcolin)) - - [#3250](https://github.com/GMOD/jbrowse-components/pull/3250) Handle alternate line endings ([@garrettjstevens](https://github.com/garrettjstevens)) - - [#3252](https://github.com/GMOD/jbrowse-components/pull/3252) Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types ([@cmdcolin](https://github.com/cmdcolin)) + - [#3230](https://github.com/GMOD/jbrowse-components/pull/3230) Add ability to + customize About dialog with callbacks and optionally hide links to data + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3275](https://github.com/GMOD/jbrowse-components/pull/3275) Add help + dialog for feature sequence panel ([@cmdcolin](https://github.com/cmdcolin)) + - [#3250](https://github.com/GMOD/jbrowse-components/pull/3250) Handle + alternate line endings + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3252](https://github.com/GMOD/jbrowse-components/pull/3252) Fix gene + sequence fetching in embedded, and allow fetching genomic sequence for other + feature types ([@cmdcolin](https://github.com/cmdcolin)) - `core`, `text-indexing` - - [#3276](https://github.com/GMOD/jbrowse-components/pull/3276) Allow using web worker RPC on embedded LGV ([@cmdcolin](https://github.com/cmdcolin)) + - [#3276](https://github.com/GMOD/jbrowse-components/pull/3276) Allow using + web worker RPC on embedded LGV ([@cmdcolin](https://github.com/cmdcolin)) #### :bug: Bug Fix - `core` - - [#3266](https://github.com/GMOD/jbrowse-components/pull/3266) Fix relative path loading of plugins ([@cmdcolin](https://github.com/cmdcolin)) - - [#3269](https://github.com/GMOD/jbrowse-components/pull/3269) Fix ability to rename session in web/desktop ([@cmdcolin](https://github.com/cmdcolin)) - - [#3256](https://github.com/GMOD/jbrowse-components/pull/3256) Fix tracks hanging in safari and polyfill for bigwig tracks ([@cmdcolin](https://github.com/cmdcolin)) + - [#3266](https://github.com/GMOD/jbrowse-components/pull/3266) Fix relative + path loading of plugins ([@cmdcolin](https://github.com/cmdcolin)) + - [#3269](https://github.com/GMOD/jbrowse-components/pull/3269) Fix ability to + rename session in web/desktop ([@cmdcolin](https://github.com/cmdcolin)) + - [#3256](https://github.com/GMOD/jbrowse-components/pull/3256) Fix tracks + hanging in safari and polyfill for bigwig tracks + ([@cmdcolin](https://github.com/cmdcolin)) - Other - - [#3274](https://github.com/GMOD/jbrowse-components/pull/3274) Update bbi-js for bugfix on webpack 4 ([@cmdcolin](https://github.com/cmdcolin)) - - [#3259](https://github.com/GMOD/jbrowse-components/pull/3259) Fix issue with breakpoint split view using view before initialized ([@cmdcolin](https://github.com/cmdcolin)) + - [#3274](https://github.com/GMOD/jbrowse-components/pull/3274) Update bbi-js + for bugfix on webpack 4 ([@cmdcolin](https://github.com/cmdcolin)) + - [#3259](https://github.com/GMOD/jbrowse-components/pull/3259) Fix issue with + breakpoint split view using view before initialized + ([@cmdcolin](https://github.com/cmdcolin)) #### :memo: Documentation -- [#3255](https://github.com/GMOD/jbrowse-components/pull/3255) Add more docs about color callbacks ([@cmdcolin](https://github.com/cmdcolin)) +- [#3255](https://github.com/GMOD/jbrowse-components/pull/3255) Add more docs + about color callbacks ([@cmdcolin](https://github.com/cmdcolin)) #### :house: Internal - `core` - - [#3261](https://github.com/GMOD/jbrowse-components/pull/3261) Fix for flaky test ([@cmdcolin](https://github.com/cmdcolin)) + - [#3261](https://github.com/GMOD/jbrowse-components/pull/3261) Fix for flaky + test ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 3 diff --git a/website/blog/2022-10-20-v2.1.7-release.md b/website/blog/2022-10-20-v2.1.7-release.md index bdedc50adf..33a1aba941 100644 --- a/website/blog/2022-10-20-v2.1.7-release.md +++ b/website/blog/2022-10-20-v2.1.7-release.md @@ -4,7 +4,8 @@ date: 2022-10-20 06:09:23 tags: ['release', 'jbrowse 2'] --- -This release fixes the build of @jbrowse/react-linear-genome-view under webpack 4, which had trouble due to the web worker support added in v2.1.6 +This release fixes the build of @jbrowse/react-linear-genome-view under webpack +4, which had trouble due to the web worker support added in v2.1.6 ## Downloads @@ -34,7 +35,9 @@ on NPM. #### :bug: Bug Fix -- [#3282](https://github.com/GMOD/jbrowse-components/pull/3282) Fix for embedded build with webpack 4 failing with v2.1.6 ([@cmdcolin](https://github.com/cmdcolin)) +- [#3282](https://github.com/GMOD/jbrowse-components/pull/3282) Fix for embedded + build with webpack 4 failing with v2.1.6 + ([@cmdcolin](https://github.com/cmdcolin)) #### Committers: 1 diff --git a/website/blog/2022-11-04-v2.2.0-release.md b/website/blog/2022-11-04-v2.2.0-release.md new file mode 100644 index 0000000000..9ae4544661 --- /dev/null +++ b/website/blog/2022-11-04-v2.2.0-release.md @@ -0,0 +1,144 @@ +--- +title: v2.2.0 Release +date: 2022-11-04 19:36:44 +tags: ['release', 'jbrowse 2'] +--- + +This release includes several important improvements including + +- Lazily loading assembly refNames: previously when you had multiple assemblies + in your config, it would load all their refNames at browser startup. Now, it + only fetches refNames when you request to use an assembly. +- Simplified "synteny track selector" on the dotplot and synteny import forms +- Improved documentation! The entire jbrowse 2 documentation has been + overhauled, and the monolithic user guide, config guide, and developer guide + pages have been split into smaller pages. We also now auto-generate + documentation on our config and state tree models, and have a search bar +- Improved speed on alignments tracks: a small optimization was made for + alignments tracks that can improve performance on alignments tracks by 30% or + so especially on short reads + +![](https://user-images.githubusercontent.com/6511937/197289612-efc80e3c-6cfd-495b-834e-4c1da1cff0c9.png) +Figure showing improved speed on short read alignments of the refactor (this +release) vs main (which was v2.1.7) + +Note that the changes to allow lazy loading assemblies may have somewhat changed +the "contract", so if your code is using the assemblyManager directly in any +places, please be aware of this change. Proper usage of the assemblyManager API +uses either + +1. use assemblyManager.get(assemblyName) which can return undefined initially, + but then this initiates the lazy load and can be caught by reactivity of + wrapping your components in observers +2. use assemblyManager.waitForAssembly(assemblyName) function, which is + asynchronous but returns a promise. this avoids the initial return undefined + behavior +3. avoid directly accessing e.g. assemblyManager.assemblies + +## Downloads + +- [v2.2.0](https://github.com/GMOD/jbrowse-components/releases/tag/v2.2.0) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +See "Packages in this release" in the changelog for links to packages published +on NPM. + +## 2.2.0 (2022-11-04) + +
    Packages in this release +

    + +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/text-indexing | | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-arc | | +| @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-hic | | +| @jbrowse/plugin-jobs-management | | +| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-menus | | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | +| @jbrowse/plugin-text-indexing | | +| @jbrowse/plugin-trackhub-registry | | +| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

    +
    + +#### :rocket: Enhancement + +- Other + - [#3296](https://github.com/GMOD/jbrowse-components/pull/3296) Add option to + use OAuth "state" param in internet accounts + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3285](https://github.com/GMOD/jbrowse-components/pull/3285) Use typescript + version of @gmod/cram ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3299](https://github.com/GMOD/jbrowse-components/pull/3299) Add ability to + open a synteny track directly from the dotplot/linear synteny view import + forms ([@cmdcolin](https://github.com/cmdcolin)) + - [#3287](https://github.com/GMOD/jbrowse-components/pull/3287) Lazy-load + assemblies on demand instead of all at app startup + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3279](https://github.com/GMOD/jbrowse-components/pull/3279) Remove + unnecessary expanded region query and small refactors + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- `core` + - [#3309](https://github.com/GMOD/jbrowse-components/pull/3309) Fix animated + "Loading..." message keyframes ([@cmdcolin](https://github.com/cmdcolin)) + - [#3306](https://github.com/GMOD/jbrowse-components/pull/3306) Fix the + RefNameAutocomplete displaying a stale value for chromosome names + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3302](https://github.com/GMOD/jbrowse-components/pull/3302) Improve + rubberband zooming across elided regions + ([@cmdcolin](https://github.com/cmdcolin)) +- Other + - [#3293](https://github.com/GMOD/jbrowse-components/pull/3293) Fix CRAM + plotting for data files that encode insertions in uncommon way + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :memo: Documentation + +- `core`, `text-indexing` + - [#3278](https://github.com/GMOD/jbrowse-components/pull/3278) Auto-generate + docs ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- [#3310](https://github.com/GMOD/jbrowse-components/pull/3310) Remove + CacheProvider emotion cache ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 3 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) +- Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) +- Scott Cain ([@scottcain](https://github.com/scottcain)) diff --git a/website/blog/2022-11-21-v2.2.1-release.md b/website/blog/2022-11-21-v2.2.1-release.md new file mode 100644 index 0000000000..3b74b61f22 --- /dev/null +++ b/website/blog/2022-11-21-v2.2.1-release.md @@ -0,0 +1,141 @@ +--- +title: v2.2.1 Release +date: 2022-11-21 19:54:23 +tags: ['release', 'jbrowse 2'] +--- + +Hello, we are happy to release v2.2.1! + +This contains several improvements including + +- Ability to display the reference sequence track as a "GC content" track +- Ability to view SyntenyTracks as a plain track on a regular linear genome + view, and to create synteny views from this + +It also contains two important bug fixes + +- In v2.2.0 CRAM features did not display mismatches correctly on alignments + tracks +- In v2.2.0 the LGV ImportForm froze when changing assemblies that had the same + refnames + +We recommend upgrading to fix these issues! + +Here are some screenshots of the new features in this release as well + +![](https://user-images.githubusercontent.com/6511937/201717083-0e104e42-0455-4b14-a5b2-85b6795f2321.png) + +screenshot showing the GC content display on the reference sequence track + +![](https://user-images.githubusercontent.com/6511937/201717096-394c0f6e-c8f6-418c-84e5-ab1cea717301.png) + +menu items for opening the GC content + +![](https://user-images.githubusercontent.com/6511937/203133899-7449b4fe-048d-46e6-836f-ddff7643646b.png) + +screenshot showing right click on a feature in a SyntenyTrack -> Open synteny +view + +![](https://user-images.githubusercontent.com/6511937/203134007-36d1cefc-6c7a-4029-800c-383fa19f0e94.png) + +screenshot showing large synteny features on a SyntenyTrack in the LGV using a +hg19 vs hg38 chain liftover file + +## Downloads + +- [v2.2.1](https://github.com/GMOD/jbrowse-components/releases/tag/v2.2.1) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +See "Packages in this release" in the changelog for links to packages published +on NPM. + +## 2.2.1 (2022-11-21) + +
    Packages in this release +

    + +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-breakpoint-split-view | | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-rdf | | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

    +
    + +#### :rocket: Enhancement + +- Other + - [#3277](https://github.com/GMOD/jbrowse-components/pull/3277) Create new + "Add track workflow" that allows pasting JSON track configs + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3328](https://github.com/GMOD/jbrowse-components/pull/3328) Add GC content + display type to the reference sequence track + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3316](https://github.com/GMOD/jbrowse-components/pull/3316) Add LGV + typescripting to @jbrowse/react-linear-genome-view + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3298](https://github.com/GMOD/jbrowse-components/pull/3298) Add + authentication plugin to embedded components + ([@garrettjstevens](https://github.com/garrettjstevens)) + - [#3329](https://github.com/GMOD/jbrowse-components/pull/3329) Add ability to + minimize/collapse tracks and views and move views up/down in view stack + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3308](https://github.com/GMOD/jbrowse-components/pull/3308) Add ability to + display synteny track in a normal LGV showing regions of synteny as features + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3317](https://github.com/GMOD/jbrowse-components/pull/3317) Move + ErrorBoundary so that tracks/views that have crashed can be closed more + easily ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- Other + - [#3342](https://github.com/GMOD/jbrowse-components/pull/3342) Fix CRAM + mismatches calculation regression in v2.2.0 + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3319](https://github.com/GMOD/jbrowse-components/pull/3319) Fix pileup + "sort by" setting being lost on zoom level change + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3340](https://github.com/GMOD/jbrowse-components/pull/3340) Fix linear + genome view import form going into infinite loading state changing + assemblies with same refnames ([@cmdcolin](https://github.com/cmdcolin)) + - [#3339](https://github.com/GMOD/jbrowse-components/pull/3339) Fix force flag + for drawing large regions and node-fetch polyfill for node 18 fix in + @jbrowse/img ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 2 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) +- Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) diff --git a/website/blog/2022-12-06-v2.2.2-release.md b/website/blog/2022-12-06-v2.2.2-release.md new file mode 100644 index 0000000000..45ad56a4fc --- /dev/null +++ b/website/blog/2022-12-06-v2.2.2-release.md @@ -0,0 +1,132 @@ +--- +title: v2.2.2 Release +date: 2022-12-06 22:34:44 +tags: ['release', 'jbrowse 2'] +--- + +Hello all, this release contains a bugfix for the circular view and breakpoint +split view with "TRA" type features not being displayed. See release notes below +for a couple other small bugfixes and enhancements. + +## Downloads + +- [v2.2.2](https://github.com/GMOD/jbrowse-components/releases/tag/v2.2.2) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +See "Packages in this release" in the changelog for links to packages published +on NPM. + +## 2.2.2 (2022-12-06) + +
    Packages in this release +

    + +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/text-indexing | | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-arc | | +| @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-breakpoint-split-view | | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-hic | | +| @jbrowse/plugin-jobs-management | | +| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-lollipop | | +| @jbrowse/plugin-menus | | +| @jbrowse/plugin-protein | | +| @jbrowse/plugin-rdf | | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-sv-inspector | | +| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | +| @jbrowse/plugin-text-indexing | | +| @jbrowse/plugin-trackhub-registry | | +| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

    +
    + +#### :rocket: Enhancement + +- Other + - [#3350](https://github.com/GMOD/jbrowse-components/pull/3350) Retain feature + labels in compact display mode for SVG features, and allow keeping feature + description without feature label ([@cmdcolin](https://github.com/cmdcolin)) + - [#3357](https://github.com/GMOD/jbrowse-components/pull/3357) Allow holding + shift key to create rubberband selection on LGV + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3363](https://github.com/GMOD/jbrowse-components/pull/3363) Create + remove-track CLI command ([@cmdcolin](https://github.com/cmdcolin)) + - [#3341](https://github.com/GMOD/jbrowse-components/pull/3341) Add BEDPE + adapter type ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3359](https://github.com/GMOD/jbrowse-components/pull/3359) Fix typos in + codebase using typos-cli ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- Other + - [#3377](https://github.com/GMOD/jbrowse-components/pull/3377) Fix rendering + and clicking synteny features when using MainThreadRpc + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3375](https://github.com/GMOD/jbrowse-components/pull/3375) Fix + `jbrowse upgrade` CLI command overwriting config.json with --branch or + --nightly options ([@cmdcolin](https://github.com/cmdcolin)) + - [#3370](https://github.com/GMOD/jbrowse-components/pull/3370) Fix error with + SNPCoverage not rendering MM tag modifications in some cases + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3366](https://github.com/GMOD/jbrowse-components/pull/3366) Fix ability to + use LGV synteny track on inverted alignments + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3348](https://github.com/GMOD/jbrowse-components/pull/3348) Fix for + breakpoint split view and circular view issues with `` type entries in + v2.2.1 ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3369](https://github.com/GMOD/jbrowse-components/pull/3369) Fix uncaught + promise errors and add lint rule for catching these + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :memo: Documentation + +- [#3347](https://github.com/GMOD/jbrowse-components/pull/3347) Reduce number of + quickstart guides ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- `core` + - [#3368](https://github.com/GMOD/jbrowse-components/pull/3368) Create base + "Dialog" component to standardize dialogs across codebase + ([@cmdcolin](https://github.com/cmdcolin)) +- `text-indexing` + - [#3344](https://github.com/GMOD/jbrowse-components/pull/3344) fix yarn build + error in Windows ([@Lilas-w](https://github.com/Lilas-w)) + +#### Committers: 2 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) +- [@Lilas-w](https://github.com/Lilas-w) diff --git a/website/blog/2022-12-15-v2.3.1-release.md b/website/blog/2022-12-15-v2.3.1-release.md new file mode 100644 index 0000000000..d697b6bbc6 --- /dev/null +++ b/website/blog/2022-12-15-v2.3.1-release.md @@ -0,0 +1,168 @@ +--- +title: v2.3.1 Release +date: 2022-12-15 22:20:37 +tags: ['release', 'jbrowse 2'] +--- + +Hello all! This release adds some great new features! + +- New "arc" and "read cloud" alignments track modes which render long range + connections between read pairs/split reads. These views have a big impact on + being able to visualize structural variants. + +- We now automatically optimize the "prefix size" for our trix indexes created + by `jbrowse text-index` which should help solve issues with slow text + searching. + +- We now refer to many pluggable elements by a "display name" instead of the + coded class name so we have instead of "LinearGCContentDisplay" -> "GC content + display". + +### New alignments track displays + +We created a new display mode that changes the "pileup" of reads into "arcs" +which connects both paired-end reads and split-long read alignments. + +![](https://user-images.githubusercontent.com/6511937/205725535-6b058cc6-7dba-41e9-ac2a-eba4ee881d89.png) + +New track menu showing the ability to replace the "lower panel" with arc display +or read cloud display + +![](https://user-images.githubusercontent.com/6511937/205730944-07347472-a9e6-44b9-8c8c-ca4380a3c75a.png) + +The arc view and read cloud view rendering across discontinuous displayedRegions + +![](https://user-images.githubusercontent.com/6511937/207134568-577cdcb3-4458-4e71-8063-aa493a21593c.png) + +A zoomed in view of long-reads (top) and paired-end reads (bottom) at the +breakpoint of a large deletion + +## Easily toggleable "compact" view of alignments + +![](https://user-images.githubusercontent.com/6511937/207207662-50778dfe-ffa8-4ca1-93fe-febcda3fdcb7.png) + +We now have an easily toggleable compact setting on alignments tracks +(previously had to manually change feature height) + +## Optimized prefix size for text search indexing + +Previously, if indexing long gene IDs with `jbrowse text-index` it would often +be slow because the "trix" format is generally optimized for short gene symbols. +We added the --prefixSize parameter in previous jbrowse versions to allow +optimizing for specific gene ID lengths, but this was sort of a magic number. +Now, `jbrowse text-index` will automatically calculate the --prefixSize if none +is provided, which tries to get an even ~64kb bin size. Let us know how it goes +for your data! + +Re-install the CLI tools with e.g. `npm install -g @jbrowse/cli` to get the +latest version with this feature. + +## Moved "Track Hub Registry" plugin to plugin store + +We removed the "Track Hub Registry" plugin, which was previously a "core +plugin", to the plugin store. This will allow us to update the plugin over time +and respond better to issues when they change their remote API. + +## Downloads + +- [v2.3.1](https://github.com/GMOD/jbrowse-components/releases/tag/v2.3.1) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +See "Packages in this release" in the changelog for links to packages published +on NPM. + +
    Packages in this release +

    + +| Package | Download | +| ----------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | + +

    +
    + +#### :rocket: Enhancement + +- Other + - [#3403](https://github.com/GMOD/jbrowse-components/pull/3403) Reduce + overplotting on dotplot grid lines and other misc improvements + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3381](https://github.com/GMOD/jbrowse-components/pull/3381) Add method for + cache busting requests to the config file in jbrowse-web + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3384](https://github.com/GMOD/jbrowse-components/pull/3384) Add method to + more easily create compact view of alignments + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3391](https://github.com/GMOD/jbrowse-components/pull/3391) Allow arc + display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3387](https://github.com/GMOD/jbrowse-components/pull/3387) Small UI + tweaks for add track workflow ([@cmdcolin](https://github.com/cmdcolin)) + - [#3358](https://github.com/GMOD/jbrowse-components/pull/3358) Create new + "arc" display type to show long range connections between paired-end and + split-reads ([@cmdcolin](https://github.com/cmdcolin)) +- `text-indexing` + - [#3385](https://github.com/GMOD/jbrowse-components/pull/3385) Optimize + prefix size for text indexing automatically + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- Other + - [#3407](https://github.com/GMOD/jbrowse-components/pull/3407) Remove + trackhub registry plugin from core plugins, moved to plugin store + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3406](https://github.com/GMOD/jbrowse-components/pull/3406) Fix loading + connection tracks from connections that don't specify assemblyNames in + config ([@cmdcolin](https://github.com/cmdcolin)) + - [#3390](https://github.com/GMOD/jbrowse-components/pull/3390) Fix + positioning within large alignments for query->target LGV synteny navigation + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3388](https://github.com/GMOD/jbrowse-components/pull/3388) Fix search + result that matches synonyms that matches multiple locations + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3404](https://github.com/GMOD/jbrowse-components/pull/3404) Fix + double-render of some synteny features + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3401](https://github.com/GMOD/jbrowse-components/pull/3401) Remove + y-scalebar rendering placeholder values in blank and loading states + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3389](https://github.com/GMOD/jbrowse-components/pull/3389) Fix issue + where snackbar would not show up when same error message is triggered + multiple times ([@cmdcolin](https://github.com/cmdcolin)) + +#### :memo: Documentation + +- `core` + - [#3396](https://github.com/GMOD/jbrowse-components/pull/3396) Use prettier + to word wrap markdown prose ([@cmdcolin](https://github.com/cmdcolin)) +- Other + - [#3383](https://github.com/GMOD/jbrowse-components/pull/3383) Add note to + user guide about variant callers that can be used for SV inspector + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- `__mocks__`, `core`, `text-indexing` + - [#3400](https://github.com/GMOD/jbrowse-components/pull/3400) Reduce + peerDependency warnings from installing dev environment + ([@cmdcolin](https://github.com/cmdcolin)) +- `core` + - [#3394](https://github.com/GMOD/jbrowse-components/pull/3394) Simplify RPC + watchWorker ([@cmdcolin](https://github.com/cmdcolin)) + - [#3386](https://github.com/GMOD/jbrowse-components/pull/3386) Fix warning + when rendering circular chord displays with web worker RPC + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) diff --git a/website/blog/2022-12-20-v2.3.2-release.md b/website/blog/2022-12-20-v2.3.2-release.md new file mode 100644 index 0000000000..23b21d1cf0 --- /dev/null +++ b/website/blog/2022-12-20-v2.3.2-release.md @@ -0,0 +1,99 @@ +--- +title: v2.3.2 Release +date: 2022-12-20 21:59:19 +tags: ['release', 'jbrowse 2'] +--- + +This release contains important fixes for drawing base-level synteny based on +CIGAR strings, especially in inverted regions. We also fixed refName renaming +(e.g. your BAM file has 'chr1' but the FASTA has '1') on the new arc display +(see v2.3.1). + +Additionally, it offers the ability to reverse/complement the sequence in the +"Get sequence" dialog. + +![](https://user-images.githubusercontent.com/6511937/208767035-90f1fb23-0fa4-468a-8095-14dc597014b2.png) + +Screenshot showing how insertions from relative to one assembly exactly match up +at a "deletion" relative to another, using the LGV synteny display and curved +arcs. Previous versions had bugs but will now match exactly. + +![](https://user-images.githubusercontent.com/6511937/208579806-0b896208-4298-4620-8f7d-5c7d63e73397.png) + +Screenshot showing the reverse and complement checkboxes in the Get sequence +dialog + +## Downloads + +- [v2.3.2](https://github.com/GMOD/jbrowse-components/releases/tag/v2.3.2) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +See "Packages in this release" in the changelog for links to packages published +on NPM. + +## 2.3.2 (2022-12-20) + +
    Packages in this release +

    + +| Package | Download | +| --------------------------------------- | ----------------------------------------------------------------- | +| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | +| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | +| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | +| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | +| @jbrowse/plugin-comparative-adapters | | +| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | +| @jbrowse/plugin-dotplot-view | | +| @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | +| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | +| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | +| @jbrowse/plugin-linear-comparative-view | | +| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | +| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | +| @jbrowse/plugin-spreadsheet-view | | +| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | +| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | +| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | +| @jbrowse/desktop | | +| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | +| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | +| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | +| @jbrowse/web | | + +

    +
    + +#### :rocket: Enhancement + +- `core` + - [#3422](https://github.com/GMOD/jbrowse-components/pull/3422) Auto-adjust + height of reference sequence track to current settings + ([@cmdcolin](https://github.com/cmdcolin)) +- Other + - [#3421](https://github.com/GMOD/jbrowse-components/pull/3421) Add ability to + revcomp sequence in the "Get sequence" dialog + ([@cmdcolin](https://github.com/cmdcolin)) + - [#3413](https://github.com/GMOD/jbrowse-components/pull/3413) Add a "base" + set of tracks and assemblies for the embedded demos + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- [#3419](https://github.com/GMOD/jbrowse-components/pull/3419) Fix rendering + base-level alignments on synteny visualizations, especially in inverted + regions ([@cmdcolin](https://github.com/cmdcolin)) +- [#3416](https://github.com/GMOD/jbrowse-components/pull/3416) Fix rendering + alignment arcs on files that need refname renaming and add jitter setting + ([@cmdcolin](https://github.com/cmdcolin)) +- [#3415](https://github.com/GMOD/jbrowse-components/pull/3415) Fix circular + view being rendered as a blank area if tab is opened in the background + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) diff --git a/website/docs/api_guide.md b/website/docs/api_guide.md index c4324d001a..dab4422ff8 100644 --- a/website/docs/api_guide.md +++ b/website/docs/api_guide.md @@ -6,8 +6,8 @@ toplevel: true import Figure from './figure' -This guide will cover the API level documentation for methods and tools -useful to developers looking to enhance JBrowse or write plugins. +This guide will cover the API level documentation for methods and tools useful +to developers looking to enhance JBrowse or write plugins. ## MenuItems objects diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_01_getting_started.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_01_getting_started.md index ffccdb0bce..e1191e26cd 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_01_getting_started.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_01_getting_started.md @@ -3,9 +3,11 @@ id: bcc2020_embedding_jbrowse_01_getting_started title: Getting started --- -:::danger Out of date -Please see the +:::danger + +Out of date Please see the [updated version of this tutorial](/docs/tutorials/embed_linear_genome_view/01_introduction) + ::: ## Welcome! @@ -41,32 +43,36 @@ like, you can follow along with the tutorial using the recording below. ## What you need If you use our provided virtual machine (VM) (download -[here](https://jbrowse-tutorials.s3.amazonaws.com/JBrowse%202%20BOSC.ova)), -then you'll have everything you need ready to go. To run the VM, you'll need to +[here](https://jbrowse-tutorials.s3.amazonaws.com/JBrowse%202%20BOSC.ova)), then +you'll have everything you need ready to go. To run the VM, you'll need to download the Oracle VirtualBox software (download [here](https://www.virtualbox.org/wiki/Downloads)). Also download the extension -pack on that page. Once VirtualBox is installed, go to `Tools -> Preferences -> Extensions -> Add` and select the downloaded extension pack to add it. +pack on that page. Once VirtualBox is installed, go to +`Tools -> Preferences -> Extensions -> Add` and select the downloaded extension +pack to add it. -Once VirtualBox and the extension pack are installed, open the VM we -provided and it will import itself into VirtualBox (the name of the VM will be -"JBrowse 2 BOSC"). Then just click `Start` and it will start an Ubuntu Linux -machine with everything you need pre-installed. Note that the user name is -'jbrowse' and the password is 'gmod', which you will need if you ever need to -use `sudo` to run any commands. +Once VirtualBox and the extension pack are installed, open the VM we provided +and it will import itself into VirtualBox (the name of the VM will be "JBrowse 2 +BOSC"). Then just click `Start` and it will start an Ubuntu Linux machine with +everything you need pre-installed. Note that the user name is 'jbrowse' and the +password is 'gmod', which you will need if you ever need to use `sudo` to run +any commands. -A second option is to use an AWS AMI Ubuntu 2020 server set up to work with -this course. The AMI ID for the course machine is ami-06d3d077f91ea603e and -is located in us-east-1 (Northern Virginia). If you choose to run this machine, -be sure to open incoming access on port 80 and 3000 in the security groups. The +A second option is to use an AWS AMI Ubuntu 2020 server set up to work with this +course. The AMI ID for the course machine is ami-06d3d077f91ea603e and is +located in us-east-1 (Northern Virginia). If you choose to run this machine, be +sure to open incoming access on port 80 and 3000 in the security groups. The user name is 'ubuntu' and there is no password, so `sudo` will just work. If you're not using the provided virtual machine, you can do most of the -tutorial with a simple text editor and some way to serve files (just opening -the HTML files we create in a browser won't work, you'll need a server). If you -have node installed, you can run a simple server by running `npx serve` (or you -can install it globally with `npm install -g serve` or `yarn global add serve` -and then run `serve`). +tutorial with a simple text editor and some way to serve files (just opening the +HTML files we create in a browser won't work, you'll need a server). If you have +node installed, you can run a simple server by running `npx serve` (or you can +install it globally with `npm install -g serve` or `yarn global add serve` and +then run `serve`). We'll also be using the JBrowse CLI, although you can technically complete the tutorial without it. You can install it by making sure you have node installed -and then running `[sudo] npm install -g @jbrowse/cli` (or `yarn global add @jbrowse/cli`). Check that it installed properly by running `jbrowse --help`. +and then running `[sudo] npm install -g @jbrowse/cli` (or +`yarn global add @jbrowse/cli`). Check that it installed properly by running +`jbrowse --help`. diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_02_introduction.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_02_introduction.md index 7289f30a36..c759a3c07b 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_02_introduction.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_02_introduction.md @@ -3,9 +3,11 @@ id: bcc2020_embedding_jbrowse_02_introduction title: Introduction --- -:::danger Out of date -Please see the +:::danger + +Out of date Please see the [updated version of this tutorial](/docs/tutorials/embed_linear_genome_view/01_introduction) + ::: ## What is JBrowse 2 @@ -35,6 +37,6 @@ simultaneously. Today we'll be using JBrowse Linear View, which has a subset of features of the full app. It can display a single linear view, which is the most common mode of genome visualization. Where JBrowse Web is a full-page web app, though, JBrowse -Linear View is designed to work within an existing web page. You can easily -add one or several of them to a page without the use of iframes, and control and +Linear View is designed to work within an existing web page. You can easily add +one or several of them to a page without the use of iframes, and control and react to each instance. diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_03_simple_site.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_03_simple_site.md index 1724fe6f31..c78c0b0c8c 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_03_simple_site.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_03_simple_site.md @@ -3,19 +3,21 @@ id: bcc2020_embedding_jbrowse_03_simple_site title: Beginnings of a simple site --- -:::danger Out of date -Please see the +:::danger + +Out of date Please see the [updated version of this tutorial](/docs/tutorials/embed_linear_genome_view/01_introduction) + ::: ## Create a simple web page Let's get started! The first thing we're going to do is create a simple web page -into which we can embed JBrowse Linear View. If you're using the VM, the -easiest way to get started is to open the terminal (second icon from the top on -the left side), and run `code ~/html/`. This opens the Visual Studio Code -(VS Code) editor in the `~/html/` directory. There is a server already -set up that will serve any files we put in this folder. +into which we can embed JBrowse Linear View. If you're using the VM, the easiest +way to get started is to open the terminal (second icon from the top on the left +side), and run `code ~/html/`. This opens the Visual Studio Code (VS Code) +editor in the `~/html/` directory. There is a server already set up that will +serve any files we put in this folder. In VS Code, in the left sidebar you will see the `HTML` folder, which has a file pre-populated called "index.ngingx-debian.html". Delete that file. Next, hover @@ -31,13 +33,17 @@ Then paste the following into the file and save it: ``` :::tip + Open this page in the web browser in the VM so that you can easily copy and paste code. + ::: -:::note If you're not using the VM -You can put the index.html file wherever you'd like, but it would probably be -best to create a new directory somewhere to put it in. +:::note + +If you're not using the VM You can put the index.html file wherever you'd like, +but it would probably be best to create a new directory somewhere to put it in. + ::: ## Check that the server is working @@ -46,10 +52,13 @@ Open a new tab in the Chrome browser and enter `localhost` into the address bar. You should see a web page that says "We're using JBrowse Linear View!". If you, congrats, you're on your way to adding JBrowse Linear View to a web site! -:::note If you're not using the VM -Go to the directory where you put your "index.html" and start your server (e.g. -run `npx serve`). Open your browser to the page indicated by your server (e.g. -for `serve` the default is "http://localhost:5000"). +:::note + +If you're not using the VM Go to the directory where you put your "index.html" +and start your server (e.g. run `npx serve`). Open your browser to the page +indicated by your server (e.g. for `serve` the default is +"http://localhost:5000"). + ::: ## Add JBrowse diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_04_assemblies.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_04_assemblies.md index 1712c19089..03111000b8 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_04_assemblies.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_04_assemblies.md @@ -3,9 +3,11 @@ id: bcc2020_embedding_jbrowse_04_assemblies title: About assemblies --- -:::danger Out of date -Please see the +:::danger + +Out of date Please see the [updated version of this tutorial](/docs/tutorials/embed_linear_genome_view/01_introduction) + ::: ## What is an assembly? @@ -24,16 +26,16 @@ These are the options you can specify for an assembly: - **Aliases** - Potential aliases for your assembly, such as "hg38" being an alias for "GRCh38". - **Reference Sequence** - The file that has the genome sequence for your - organism. JBrowse natively supports indexed FASTA (compressed or not), 2BIT, and - chrom.sizes sequence files. + organism. JBrowse natively supports indexed FASTA (compressed or not), 2BIT, + and chrom.sizes sequence files. - **Reference Sequence Name Aliases** - You can define aliases for the names in your reference sequence file, so if for example your reference sequence uses - "chr1", you can add an alias for it so that data file that use "1" instead will - still display correctly. + "chr1", you can add an alias for it so that data file that use "1" instead + will still display correctly. - **Colors** - You can define a list of colors that will be used to color the reference sequences. If you supply fewer colors than reference sequences, - JBrowse will cycle through them. By default JBrowse will use its built-in color - scheme of 26 colors based on the UCSC Genome Browser color scheme. + JBrowse will cycle through them. By default JBrowse will use its built-in + color scheme of 26 colors based on the UCSC Genome Browser color scheme. ## Adding an assembly @@ -63,15 +65,16 @@ something like this: ![The output of `jbrowse --help` in a terminal](../../../img/bcc2020_jbrowse_help.png) -:::note If you're not using the VM -You may already have `yarn` or `npm` set up to do global installations, so you -might be able to skip the part about adding the `yarn global bin` location to -your `PATH`. +:::note + +If you're not using the VM You may already have `yarn` or `npm` set up to do +global installations, so you might be able to skip the part about adding the +`yarn global bin` location to your `PATH`. If you don't want to install the CLI and you have NPM installed, you can also do all of the things we will do in this tutorial by replacing `jbrowse` in any -commands with `npx @jbrowse/cli`. For example, to get the help output you -would run +commands with `npx @jbrowse/cli`. For example, to get the help output you would +run ```sh npx @jbrowse/cli --help diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_05_tracks.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_05_tracks.md index 3e08d16db7..88d6f74a87 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_05_tracks.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_05_tracks.md @@ -3,17 +3,19 @@ id: bcc2020_embedding_jbrowse_05_tracks title: About tracks --- -:::danger Out of date -Please see the +:::danger + +Out of date Please see the [updated version of this tutorial](/docs/tutorials/embed_linear_genome_view/01_introduction) + ::: ## What is a track? -A track is the place to display your data files in JBrowse Linear View. For -this tutorial we're going to add a gene track, an [alignments -track](/docs/user_guides/alignments_track), and a [variants -track](/docs/user_guides/variant_track). We're just going to use basic +A track is the place to display your data files in JBrowse Linear View. For this +tutorial we're going to add a gene track, an +[alignments track](/docs/user_guides/alignments_track), and a +[variants track](/docs/user_guides/variant_track). We're just going to use basic configuration, but check the links for the track types to see what kinds of things you can configure in them. @@ -23,13 +25,13 @@ things you can configure in them. For genes, we'll use a [GFF3](https://github.com/The-Sequence-Ontology/Specifications/blob/5c119af6316ccfbc6975af86d0e34157226d208d/gff3.md) -file of the [NCBI RefSeq](https://www.ncbi.nlm.nih.gov/refseq/) human genes. -The link is +file of the [NCBI RefSeq](https://www.ncbi.nlm.nih.gov/refseq/) human genes. The +link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz For alignments, we're going to use on the 1000 Genomes sample -[NA12878](https://www.internationalgenome.org/data-portal/sample/NA12878). -We'll use a [CRAM](https://samtools.github.io/hts-specs/CRAMv3.pdf) file +[NA12878](https://www.internationalgenome.org/data-portal/sample/NA12878). We'll +use a [CRAM](https://samtools.github.io/hts-specs/CRAMv3.pdf) file ([BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) is also supported), and the link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_07_creating_the_view.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_07_creating_the_view.md index 7ec0fdddd7..16817118ce 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_07_creating_the_view.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_07_creating_the_view.md @@ -48,10 +48,10 @@ has other display options. ## Controlling the view -Any action taken in the UI can also be performed programmatically. An -instance of JBrowseLinearView has an attribute called "view" that can be used -to control the state of the view. As an example, we will add some buttons on the -page that navigate to the locations of a couple of genes. +Any action taken in the UI can also be performed programmatically. An instance +of JBrowseLinearView has an attribute called "view" that can be used to control +the state of the view. As an example, we will add some buttons on the page that +navigate to the locations of a couple of genes. Modify "index.html" so that it looks like the following: diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_08_default_session.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_08_default_session.md index fe0aac89ad..c891e967cd 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_08_default_session.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_08_default_session.md @@ -13,12 +13,14 @@ Please see the ## What is a session? A session is a way to define what the state of the view is. By providing a -default session, you can have tracks already open when the view loads, have -the overview hidden, or set any other aspect of the state. +default session, you can have tracks already open when the view loads, have the +overview hidden, or set any other aspect of the state. :::tip + If you provide "location" when constructing the view, it will override the location defined in the defaultSession. + ::: ## What does a session look like? @@ -94,8 +96,8 @@ with the view and see what in the view state changes when you do certain things. Some of the view state entries are: - `bpPerPx` - This is a zoom level. A smaller number is more zoomed in. -- `displayedRegions` - The extent of the areas currently in view. By default - it will be the full extent of a single chromosome, but you can add multiple - regions, have the regions cover only part of a chromosome, reverse the regions, - etc. +- `displayedRegions` - The extent of the areas currently in view. By default it + will be the full extent of a single chromosome, but you can add multiple + regions, have the regions cover only part of a chromosome, reverse the + regions, etc. - `hideHeader` - Whether or not the header is hidden. diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_09_reacting.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_09_reacting.md index dc9e523272..7c5d5980c1 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_09_reacting.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_09_reacting.md @@ -4,8 +4,10 @@ title: Reacting to the view --- :::danger Out of date + Please see the [updated version of this tutorial](/docs/tutorials/embed_linear_genome_view/01_introduction). + ::: You can not only control the view, you can react to it as well. By providing an diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_10_conclusion.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_10_conclusion.md index 4036dbd301..c2b199bdcb 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_10_conclusion.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_10_conclusion.md @@ -17,8 +17,8 @@ experiment and explore. Some things to try might be: - Add two views to the same web page - Find your own files to add as tracks -- Explore the [configuration guide](../../../config_guide) and learn how to do things - like customize the colors of features in your tracks +- Explore the [configuration guide](/docs/config_guide) and learn how to do + things like customize the colors of features in your tracks Let us know how things go. We'd love to hear your feedback or help you in any way we can. Our contact information can be found [here](/contact). diff --git a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_aliases.md b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_aliases.md index 92d1a47395..4c2f1b8216 100644 --- a/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_aliases.md +++ b/website/docs/archive/bcc2020_embedding/bcc2020_embedding_jbrowse_aliases.md @@ -4,8 +4,10 @@ title: GRCh38 Reference Name Aliases --- :::danger Out of date + Please see the [updated version of this tutorial](/docs/tutorials/embed_linear_genome_view/01_introduction). + ::: This should be the content of your "GRCh38.aliases.txt" file. diff --git a/website/docs/archive/bcc2020_plugin_development.md b/website/docs/archive/bcc2020_plugin_development.md index 7fb63a369a..6c6f515bae 100644 --- a/website/docs/archive/bcc2020_plugin_development.md +++ b/website/docs/archive/bcc2020_plugin_development.md @@ -28,12 +28,14 @@ Here is a video recording of the presentation that we made You can also follow along with the text presented below -### Pre-requsites +### Pre-requisites Please have the following -- yarn, installed via https://classic.yarnpkg.com/en/docs/install/#debian-stable or `npm install -g yarn` -- node v10 or greater, installed via https://github.com/nodesource/distributions#installation-instructions +- yarn, installed via https://classic.yarnpkg.com/en/docs/install/#debian-stable + or `npm install -g yarn` +- node v10 or greater, installed via + https://github.com/nodesource/distributions#installation-instructions These links above provide more reliable installation than the apt repositories version, but you can try to install these however you feel comfortable @@ -46,8 +48,8 @@ To start, we will install the jbrowse-cli sudo npm install -g @jbrowse/cli ``` -Depending on your setup you might need to use sudo for this. We will use the -CLI to download the latest release from github, this is a convenience tool that +Depending on your setup you might need to use sudo for this. We will use the CLI +to download the latest release from github, this is a convenience tool that saves us some steps from manually downloading it ### Create a jbrowse 2 production instance @@ -73,14 +75,17 @@ We are going to create several plugins for this tutorial ### UCSC API data adapter -Let's start with creating a plugin that accesses the UCSC REST API. See https://genome.ucsc.edu/goldenPath/help/api.html for docs +Let's start with creating a plugin that accesses the UCSC REST API. See +https://genome.ucsc.edu/goldenPath/help/api.html for docs We will clone a working version of this plugin for brevity and analyze it :::caution + The development and build process for plugins has changed since this tutorial was created. See https://github.com/GMOD/jbrowse-plugin-template#readme for current instructions. + ::: ```sh @@ -99,8 +104,7 @@ http://localhost/myfolder/?config=http://localhost:9001/config_ucsc_api.json If you had a github clone of jbrowse-components, with the products/jbrowse-web started, you could do this with -http://localhost:3000/?config=http://localhost:9001/config_ucsc_api.json -instead +http://localhost:3000/?config=http://localhost:9001/config_ucsc_api.json instead ### Analysis of the UCSC REST API plugin @@ -121,8 +125,8 @@ Interaction data is often displayed using arcs to connect enhancer to gene. We will create a custom renderer to illustrate this But what is a renderer? It is code that performs drawing. See the renderer docs -here for more details [on creating -renderers](/docs/developer_guides/pluggable_elements/#creating-custom-renderers) +here for more details +[on creating renderers](/docs/developer_guides/pluggable_elements/#creating-custom-renderers) Let's clone a working arc renderer plugin @@ -148,8 +152,7 @@ renders the UCSC GeneHancer interactions as arcs ### Making custom view types with plugins -Many new things are possible by making completely custom view types in JBrowse -2 +Many new things are possible by making completely custom view types in JBrowse 2 Plugins can basically register a new view type that is a ReactComponent without much else, allowing integration of diverse other view types that are not really @@ -159,14 +162,14 @@ Here is a template we can work from https://github.com/cmdcolin/jbrowse-plugin-barchart-view -Here is a silly example with a custom Hello world view type. I started this as -a "bar chart" concept but only got as far as making it say hello world. +Here is a silly example with a custom Hello world view type. I started this as a +"bar chart" concept but only got as far as making it say hello world. Looking at the code, it is fairly simple and demonstrates that we can basically -have any sort of ReactComponent rendered into our view. That means we could -have a gene expression heatmap, barchart, get charts dynamically from an R -server side component, make a graph genome, etc. The ideas are endless! And we -can make it interact with other views! +have any sort of ReactComponent rendered into our view. That means we could have +a gene expression heatmap, barchart, get charts dynamically from an R server +side component, make a graph genome, etc. The ideas are endless! And we can make +it interact with other views!
    @@ -174,8 +177,8 @@ can make it interact with other views! The examples allowed us to get us quickly setup -In your daily work we encourage you to clone the jbrowse-components repo and -run off a dev version of jbrowse 2 e.g. follow the steps below +In your daily work we encourage you to clone the jbrowse-components repo and run +off a dev version of jbrowse 2 e.g. follow the steps below ``` git clone https://github.com/gmod/jbrowse-components diff --git a/website/docs/archive/pag2022_synteny_tutorial.md b/website/docs/archive/pag2022_synteny_tutorial.md index a033f55c8f..f39c44b918 100644 --- a/website/docs/archive/pag2022_synteny_tutorial.md +++ b/website/docs/archive/pag2022_synteny_tutorial.md @@ -5,7 +5,8 @@ title: PAG2022 - Synteny visualization using JBrowse Desktop We presented a tutorial of visualizing synteny with JBrowse Desktop at PAG 2022 -A guide to follow along is written here: http://gmod.org/wiki/JBrowse_2_Tutorial_PAG_2022 +A guide to follow along is written here: +http://gmod.org/wiki/JBrowse_2_Tutorial_PAG_2022 The video recording of the presentation that we made is below diff --git a/website/docs/config/AlignmentsTrack.md b/website/docs/config/AlignmentsTrack.md index cf247f62ea..9d7d6039fe 100644 --- a/website/docs/config/AlignmentsTrack.md +++ b/website/docs/config/AlignmentsTrack.md @@ -4,8 +4,8 @@ title: AlignmentsTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/ArcRenderer.md b/website/docs/config/ArcRenderer.md index 8225cd0219..9974a4b920 100644 --- a/website/docs/config/ArcRenderer.md +++ b/website/docs/config/ArcRenderer.md @@ -4,8 +4,8 @@ title: ArcRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BamAdapter.md b/website/docs/config/BamAdapter.md index a9fc6165e7..986a3fddc7 100644 --- a/website/docs/config/BamAdapter.md +++ b/website/docs/config/BamAdapter.md @@ -4,8 +4,8 @@ title: BamAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -50,15 +50,15 @@ location: { fetchSizeLimit: { type: 'number', description: - 'used to determine when to display a warning to the user that too much data will be fetched', + 'size to fetch in bytes over which to display a warning to the user that too much data will be fetched', defaultValue: 5_000_000, } ``` #### slot: sequenceAdapter -generally refers to the reference genome assembly's sequence adapter -currently needs to be manually added +generally refers to the reference genome assembly's sequence adapter currently +needs to be manually added ```js sequenceAdapter: { diff --git a/website/docs/config/BaseAssembly.md b/website/docs/config/BaseAssembly.md index 8c909fe082..c1d28f29db 100644 --- a/website/docs/config/BaseAssembly.md +++ b/website/docs/config/BaseAssembly.md @@ -4,8 +4,8 @@ title: BaseAssembly toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -51,9 +51,9 @@ refNameColors: { #### slot: refNameAliases.adapter -refNameAliases help resolve e.g. chr1 and 1 as the same entity -the data for refNameAliases are fetched from an adapter, that is -commonly a tsv like chromAliases.txt from UCSC or similar +refNameAliases help resolve e.g. chr1 and 1 as the same entity the data for +refNameAliases are fetched from an adapter, that is commonly a tsv like +chromAliases.txt from UCSC or similar ```js adapter: pluginManager.pluggableConfigSchemaType('adapter') @@ -61,8 +61,8 @@ adapter: pluginManager.pluggableConfigSchemaType('adapter') #### slot: cytobands.adapter -cytoband data is fetched from an adapter, and can be displayed by a -view type as ideograms +cytoband data is fetched from an adapter, and can be displayed by a view type as +ideograms ```js adapter: pluginManager.pluggableConfigSchemaType('adapter') diff --git a/website/docs/config/BaseChordDisplay.md b/website/docs/config/BaseChordDisplay.md index 794cfb5140..84a1a074d6 100644 --- a/website/docs/config/BaseChordDisplay.md +++ b/website/docs/config/BaseChordDisplay.md @@ -4,8 +4,8 @@ title: BaseChordDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BaseConnection.md b/website/docs/config/BaseConnection.md index 4b0649c8bb..e01b843c25 100644 --- a/website/docs/config/BaseConnection.md +++ b/website/docs/config/BaseConnection.md @@ -4,8 +4,8 @@ title: BaseConnection toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BaseLinearDisplay.md b/website/docs/config/BaseLinearDisplay.md index 72cd2246f7..1cd406f04a 100644 --- a/website/docs/config/BaseLinearDisplay.md +++ b/website/docs/config/BaseLinearDisplay.md @@ -4,13 +4,13 @@ title: BaseLinearDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs -BaseLinearDisplay is a "base" config that is extended by classes like -"LinearBasicDisplay" (used for feature tracks, etc) and "LinearBareDisplay" +`BaseLinearDisplay` is a "base" config that is extended by classes like +`LinearBasicDisplay` (used for feature tracks, etc) and `LinearBareDisplay` (more stripped down than even the basic display, not commonly used) ### BaseLinearDisplay - Identifier diff --git a/website/docs/config/BaseRpcDriver.md b/website/docs/config/BaseRpcDriver.md index cd0967f73c..c050ef8f25 100644 --- a/website/docs/config/BaseRpcDriver.md +++ b/website/docs/config/BaseRpcDriver.md @@ -4,8 +4,8 @@ title: BaseRpcDriver toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BaseTrack.md b/website/docs/config/BaseTrack.md index f324e3d7c0..f20b7e2024 100644 --- a/website/docs/config/BaseTrack.md +++ b/website/docs/config/BaseTrack.md @@ -4,11 +4,15 @@ title: BaseTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs +### BaseTrack - Identifier + +#### slot: explicitIdentifier + ### BaseTrack - Slots #### slot: name @@ -134,3 +138,23 @@ depth: { 'depth of subfeatures to iterate the formatter on formatDetails.subfeatures (e.g. you may not want to format the exon/cds subfeatures, so limited to 2', } ``` + +#### slot: formatAbout.config + +```js +config: { + type: 'frozen', + description: 'formats configuration object in about dialog', + defaultValue: {}, + contextVariable: ['config'], + } +``` + +#### slot: formatAbout.hideUris + +```js +hideUris: { + type: 'boolean', + defaultValue: false, + } +``` diff --git a/website/docs/config/BasicTrack.md b/website/docs/config/BasicTrack.md index 2681f12cd3..e41334fb51 100644 --- a/website/docs/config/BasicTrack.md +++ b/website/docs/config/BasicTrack.md @@ -4,8 +4,8 @@ title: BasicTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BedAdapter.md b/website/docs/config/BedAdapter.md index 15d96c17a9..c9bd6185c8 100644 --- a/website/docs/config/BedAdapter.md +++ b/website/docs/config/BedAdapter.md @@ -4,8 +4,8 @@ title: BedAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BedTabixAdapter.md b/website/docs/config/BedTabixAdapter.md index eda0c8968c..9dfc9ea947 100644 --- a/website/docs/config/BedTabixAdapter.md +++ b/website/docs/config/BedTabixAdapter.md @@ -4,8 +4,8 @@ title: BedTabixAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BedpeAdapter.md b/website/docs/config/BedpeAdapter.md new file mode 100644 index 0000000000..0a65a23892 --- /dev/null +++ b/website/docs/config/BedpeAdapter.md @@ -0,0 +1,38 @@ +--- +id: bedpeadapter +title: BedpeAdapter +toplevel: true +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +## Docs + +intended for SVs in a single assembly + +### BedpeAdapter - Slots + +#### slot: bedpeLocation + +can be plaintext or gzipped, not indexed so loaded into memory on startup + +```js +bedpeLocation: { + type: 'fileLocation', + defaultValue: { + uri: '/path/to/my.bedpe.gz', + locationType: 'UriLocation', + }, + } +``` + +#### slot: columnNames + +```js +columnNames: { + type: 'stringArray', + description: 'List of column names', + defaultValue: [], + } +``` diff --git a/website/docs/config/BgzipFastaAdapter.md b/website/docs/config/BgzipFastaAdapter.md index 2f5fbaf6e3..4401225786 100644 --- a/website/docs/config/BgzipFastaAdapter.md +++ b/website/docs/config/BgzipFastaAdapter.md @@ -4,8 +4,8 @@ title: BgzipFastaAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BigBedAdapter.md b/website/docs/config/BigBedAdapter.md index 9d64a035b1..6f4771fed2 100644 --- a/website/docs/config/BigBedAdapter.md +++ b/website/docs/config/BigBedAdapter.md @@ -4,8 +4,8 @@ title: BigBedAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/BigWigAdapter.md b/website/docs/config/BigWigAdapter.md index a24ef0ae80..1dd5355036 100644 --- a/website/docs/config/BigWigAdapter.md +++ b/website/docs/config/BigWigAdapter.md @@ -4,8 +4,8 @@ title: BigWigAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/ChainAdapter.md b/website/docs/config/ChainAdapter.md index 2389151401..0df508eed2 100644 --- a/website/docs/config/ChainAdapter.md +++ b/website/docs/config/ChainAdapter.md @@ -4,8 +4,8 @@ title: ChainAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/ChordVariantDisplay.md b/website/docs/config/ChordVariantDisplay.md index 4fd9b17f45..0ecc1a6313 100644 --- a/website/docs/config/ChordVariantDisplay.md +++ b/website/docs/config/ChordVariantDisplay.md @@ -4,8 +4,8 @@ title: ChordVariantDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/ChromSizesAdapter.md b/website/docs/config/ChromSizesAdapter.md index 5a74911b42..a752018d1a 100644 --- a/website/docs/config/ChromSizesAdapter.md +++ b/website/docs/config/ChromSizesAdapter.md @@ -4,8 +4,8 @@ title: ChromSizesAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/CramAdapter.md b/website/docs/config/CramAdapter.md index 52b7860bdd..33c7d0df92 100644 --- a/website/docs/config/CramAdapter.md +++ b/website/docs/config/CramAdapter.md @@ -4,8 +4,8 @@ title: CramAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -19,7 +19,7 @@ used to configure CRAM adapter fetchSizeLimit: { type: 'number', description: - 'used to determine when to display a warning to the user that too much data will be fetched', + 'size in bytes over which to display a warning to the user that too much data will be fetched', defaultValue: 3_000_000, } ``` @@ -50,14 +50,13 @@ craiLocation: { #### slot: sequenceAdapter -generally refers to the reference genome assembly's sequence adapter -currently needs to be manually added +generally refers to the reference genome assembly's sequence adapter currently +needs to be manually added ```js sequenceAdapter: { type: 'frozen', - description: - 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags', + description: 'sequence data adapter', defaultValue: null, } ``` diff --git a/website/docs/config/CytobandAdapter.md b/website/docs/config/CytobandAdapter.md index a841fc8282..e45a858b5f 100644 --- a/website/docs/config/CytobandAdapter.md +++ b/website/docs/config/CytobandAdapter.md @@ -4,8 +4,8 @@ title: CytobandAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/DeltaAdapter.md b/website/docs/config/DeltaAdapter.md index b0af3aad72..65a94e9f9e 100644 --- a/website/docs/config/DeltaAdapter.md +++ b/website/docs/config/DeltaAdapter.md @@ -4,8 +4,8 @@ title: DeltaAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/DensityRenderer.md b/website/docs/config/DensityRenderer.md index 05ddf14a7e..0ecf6b6fe6 100644 --- a/website/docs/config/DensityRenderer.md +++ b/website/docs/config/DensityRenderer.md @@ -4,8 +4,8 @@ title: DensityRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/DivSequenceRenderer.md b/website/docs/config/DivSequenceRenderer.md index 5d9a2d03af..3519129275 100644 --- a/website/docs/config/DivSequenceRenderer.md +++ b/website/docs/config/DivSequenceRenderer.md @@ -4,8 +4,8 @@ title: DivSequenceRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/DotplotDisplay.md b/website/docs/config/DotplotDisplay.md index 541132ab95..bd2f927024 100644 --- a/website/docs/config/DotplotDisplay.md +++ b/website/docs/config/DotplotDisplay.md @@ -4,8 +4,8 @@ title: DotplotDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/DotplotRenderer.md b/website/docs/config/DotplotRenderer.md index d8b1d7591f..ad393c3db6 100644 --- a/website/docs/config/DotplotRenderer.md +++ b/website/docs/config/DotplotRenderer.md @@ -4,8 +4,8 @@ title: DotplotRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/DropboxOAuthInternetAccount.md b/website/docs/config/DropboxOAuthInternetAccount.md index 5f7e2c6873..255bcd92ef 100644 --- a/website/docs/config/DropboxOAuthInternetAccount.md +++ b/website/docs/config/DropboxOAuthInternetAccount.md @@ -4,8 +4,8 @@ title: DropboxOAuthInternetAccount toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/ExternalTokenInternetAccount.md b/website/docs/config/ExternalTokenInternetAccount.md index 77e4081403..43aed9d6d9 100644 --- a/website/docs/config/ExternalTokenInternetAccount.md +++ b/website/docs/config/ExternalTokenInternetAccount.md @@ -4,8 +4,8 @@ title: ExternalTokenInternetAccount toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/FeatureTrack.md b/website/docs/config/FeatureTrack.md index 46cbca9853..8666257d6e 100644 --- a/website/docs/config/FeatureTrack.md +++ b/website/docs/config/FeatureTrack.md @@ -4,8 +4,8 @@ title: FeatureTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/FromConfigAdapter.md b/website/docs/config/FromConfigAdapter.md index afa1fa5292..178c5e2811 100644 --- a/website/docs/config/FromConfigAdapter.md +++ b/website/docs/config/FromConfigAdapter.md @@ -4,8 +4,8 @@ title: FromConfigAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -19,12 +19,3 @@ features: { defaultValue: [], } ``` - -#### slot: featureClass - -```js -featureClass: { - type: 'string', - defaultValue: 'SimpleFeature', - } -``` diff --git a/website/docs/config/FromConfigRegionsAdapter.md b/website/docs/config/FromConfigRegionsAdapter.md index fdc70d562f..b8df4d6a9e 100644 --- a/website/docs/config/FromConfigRegionsAdapter.md +++ b/website/docs/config/FromConfigRegionsAdapter.md @@ -4,8 +4,8 @@ title: FromConfigRegionsAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -21,12 +21,3 @@ features: { defaultValue: [], } ``` - -#### slot: featureClass - -```js -featureClass: { - type: 'string', - defaultValue: 'SimpleFeature', - } -``` diff --git a/website/docs/config/FromConfigSequenceAdapter.md b/website/docs/config/FromConfigSequenceAdapter.md index eca998c42c..7de454badc 100644 --- a/website/docs/config/FromConfigSequenceAdapter.md +++ b/website/docs/config/FromConfigSequenceAdapter.md @@ -4,8 +4,8 @@ title: FromConfigSequenceAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -19,12 +19,3 @@ features: { defaultValue: [], } ``` - -#### slot: featureClass - -```js -featureClass: { - type: 'string', - defaultValue: 'SimpleFeature', - } -``` diff --git a/website/docs/config/GCContentAdapter.md b/website/docs/config/GCContentAdapter.md index 25a200212e..495c808935 100644 --- a/website/docs/config/GCContentAdapter.md +++ b/website/docs/config/GCContentAdapter.md @@ -4,8 +4,8 @@ title: GCContentAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -14,5 +14,8 @@ our source code. See [Config guide](/docs/config_guide) for more info #### slot: sequenceAdapter ```js -sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter') +sequenceAdapter: { + type: 'frozen', + defaultValue: null, + } ``` diff --git a/website/docs/config/Gff3Adapter.md b/website/docs/config/Gff3Adapter.md index 7048d9c8d1..3b5c9087d9 100644 --- a/website/docs/config/Gff3Adapter.md +++ b/website/docs/config/Gff3Adapter.md @@ -4,8 +4,8 @@ title: Gff3Adapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/Gff3TabixAdapter.md b/website/docs/config/Gff3TabixAdapter.md index 9f77048ffd..c5417e7851 100644 --- a/website/docs/config/Gff3TabixAdapter.md +++ b/website/docs/config/Gff3TabixAdapter.md @@ -4,8 +4,8 @@ title: Gff3TabixAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -44,10 +44,9 @@ location: { #### slot: dontRedispatch -the Gff3TabixAdapter has to "redispatch" if it fetches a region and -features it finds inside that region extend outside the region we requested. -you can disable this for certain feature types to avoid fetching e.g. the -entire chromosome +the Gff3TabixAdapter has to "redispatch" if it fetches a region and features it +finds inside that region extend outside the region we requested. you can disable +this for certain feature types to avoid fetching e.g. the entire chromosome ```js dontRedispatch: { diff --git a/website/docs/config/GoogleDriveOAuthInternetAccount.md b/website/docs/config/GoogleDriveOAuthInternetAccount.md index 4e0c395706..03dcc6ddd2 100644 --- a/website/docs/config/GoogleDriveOAuthInternetAccount.md +++ b/website/docs/config/GoogleDriveOAuthInternetAccount.md @@ -4,8 +4,8 @@ title: GoogleDriveOAuthInternetAccount toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/GtfAdapter.md b/website/docs/config/GtfAdapter.md index e30bc84d40..7acedccddf 100644 --- a/website/docs/config/GtfAdapter.md +++ b/website/docs/config/GtfAdapter.md @@ -4,8 +4,8 @@ title: GtfAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/HTTPBasicInternetAccount.md b/website/docs/config/HTTPBasicInternetAccount.md index 5d75a129f9..edf9eac94c 100644 --- a/website/docs/config/HTTPBasicInternetAccount.md +++ b/website/docs/config/HTTPBasicInternetAccount.md @@ -4,8 +4,8 @@ title: HTTPBasicInternetAccount toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/HicAdapter.md b/website/docs/config/HicAdapter.md index 6c76d952e9..f13a2ef62b 100644 --- a/website/docs/config/HicAdapter.md +++ b/website/docs/config/HicAdapter.md @@ -4,8 +4,8 @@ title: HicAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/HicRenderer.md b/website/docs/config/HicRenderer.md index 93da322415..035e8f76cf 100644 --- a/website/docs/config/HicRenderer.md +++ b/website/docs/config/HicRenderer.md @@ -4,8 +4,8 @@ title: HicRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/HicTrack.md b/website/docs/config/HicTrack.md index 5b9f0d36ad..eefe8f081c 100644 --- a/website/docs/config/HicTrack.md +++ b/website/docs/config/HicTrack.md @@ -4,8 +4,8 @@ title: HicTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/HtsgetBamAdapter.md b/website/docs/config/HtsgetBamAdapter.md index 0fa95e26e7..567ba94459 100644 --- a/website/docs/config/HtsgetBamAdapter.md +++ b/website/docs/config/HtsgetBamAdapter.md @@ -4,12 +4,13 @@ title: HtsgetBamAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs -Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library +Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam +library ### HtsgetBamAdapter - Slots diff --git a/website/docs/config/IndexedFastaAdapter.md b/website/docs/config/IndexedFastaAdapter.md index 07beae276e..bee9322db5 100644 --- a/website/docs/config/IndexedFastaAdapter.md +++ b/website/docs/config/IndexedFastaAdapter.md @@ -4,8 +4,8 @@ title: IndexedFastaAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/InternetAccount.md b/website/docs/config/InternetAccount.md index 94650a98d1..8ddf677c42 100644 --- a/website/docs/config/InternetAccount.md +++ b/website/docs/config/InternetAccount.md @@ -4,8 +4,8 @@ title: InternetAccount toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/JBrowse1Connection.md b/website/docs/config/JBrowse1Connection.md index 95d6602f85..37cdf79fb1 100644 --- a/website/docs/config/JBrowse1Connection.md +++ b/website/docs/config/JBrowse1Connection.md @@ -4,8 +4,8 @@ title: JBrowse1Connection toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/JBrowse1TextSearchAdapter.md b/website/docs/config/JBrowse1TextSearchAdapter.md index a5cfc9149e..d61a3b6735 100644 --- a/website/docs/config/JBrowse1TextSearchAdapter.md +++ b/website/docs/config/JBrowse1TextSearchAdapter.md @@ -4,8 +4,8 @@ title: JBrowse1TextSearchAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/JBrowseWebConfiguration.md b/website/docs/config/JBrowseWebConfiguration.md index f3d395cc95..acf7dc2360 100644 --- a/website/docs/config/JBrowseWebConfiguration.md +++ b/website/docs/config/JBrowseWebConfiguration.md @@ -4,12 +4,13 @@ title: JBrowseWebConfiguration toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs -configuration here appears as a "configuration" object on the root of config.json +configuration here appears as a "configuration" object on the root of +config.json ### JBrowseWebConfiguration - Slots diff --git a/website/docs/config/LGVSyntenyDisplay.md b/website/docs/config/LGVSyntenyDisplay.md new file mode 100644 index 0000000000..8c55ed7b7a --- /dev/null +++ b/website/docs/config/LGVSyntenyDisplay.md @@ -0,0 +1,16 @@ +--- +id: lgvsyntenydisplay +title: LGVSyntenyDisplay +toplevel: true +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +## Docs + +## LGVSyntenyDisplay - Derives from + +```js +baseConfiguration: linearPileupDisplayConfigSchemaFactory(pluginManager) +``` diff --git a/website/docs/config/LinePlotRenderer.md b/website/docs/config/LinePlotRenderer.md index a9a7e03bf1..139d1dd6df 100644 --- a/website/docs/config/LinePlotRenderer.md +++ b/website/docs/config/LinePlotRenderer.md @@ -4,8 +4,8 @@ title: LinePlotRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearAlignmentsDisplay.md b/website/docs/config/LinearAlignmentsDisplay.md index dd16fee322..0c460b1889 100644 --- a/website/docs/config/LinearAlignmentsDisplay.md +++ b/website/docs/config/LinearAlignmentsDisplay.md @@ -4,8 +4,8 @@ title: LinearAlignmentsDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearArcDisplay.md b/website/docs/config/LinearArcDisplay.md index eab0388d97..8702fbe55e 100644 --- a/website/docs/config/LinearArcDisplay.md +++ b/website/docs/config/LinearArcDisplay.md @@ -4,8 +4,8 @@ title: LinearArcDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearBareDisplay.md b/website/docs/config/LinearBareDisplay.md index f3efb3ac6f..9ec2f45aec 100644 --- a/website/docs/config/LinearBareDisplay.md +++ b/website/docs/config/LinearBareDisplay.md @@ -4,8 +4,8 @@ title: LinearBareDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearBasicDisplay.md b/website/docs/config/LinearBasicDisplay.md index e940501b1f..27231d9b45 100644 --- a/website/docs/config/LinearBasicDisplay.md +++ b/website/docs/config/LinearBasicDisplay.md @@ -4,8 +4,8 @@ title: LinearBasicDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearComparativeDisplay.md b/website/docs/config/LinearComparativeDisplay.md index a45954d39a..c0efb74006 100644 --- a/website/docs/config/LinearComparativeDisplay.md +++ b/website/docs/config/LinearComparativeDisplay.md @@ -4,8 +4,8 @@ title: LinearComparativeDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearGCContentDisplay.md b/website/docs/config/LinearGCContentDisplay.md new file mode 100644 index 0000000000..4c2c510ef6 --- /dev/null +++ b/website/docs/config/LinearGCContentDisplay.md @@ -0,0 +1,17 @@ +--- +id: lineargccontentdisplay +title: LinearGCContentDisplay +toplevel: true +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +## Docs + +## LinearGCContentDisplay - Derives from + +```js +baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay') + .configSchema +``` diff --git a/website/docs/config/LinearHicDisplay.md b/website/docs/config/LinearHicDisplay.md index 33aa74c50b..35a67d9def 100644 --- a/website/docs/config/LinearHicDisplay.md +++ b/website/docs/config/LinearHicDisplay.md @@ -4,8 +4,8 @@ title: LinearHicDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearPileupDisplay.md b/website/docs/config/LinearPileupDisplay.md index 65ef0c47bd..78da2fbce8 100644 --- a/website/docs/config/LinearPileupDisplay.md +++ b/website/docs/config/LinearPileupDisplay.md @@ -4,8 +4,8 @@ title: LinearPileupDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearReadArcsDisplay.md b/website/docs/config/LinearReadArcsDisplay.md new file mode 100644 index 0000000000..b9d11827cf --- /dev/null +++ b/website/docs/config/LinearReadArcsDisplay.md @@ -0,0 +1,67 @@ +--- +id: linearreadarcsdisplay +title: LinearReadArcsDisplay +toplevel: true +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +## Docs + +### LinearReadArcsDisplay - Slots + +#### slot: maxFeatureScreenDensity + +```js +maxFeatureScreenDensity: { + type: 'number', + description: 'maximum features per pixel that is displayed in the view', + defaultValue: 5, + } +``` + +#### slot: lineWidth + +```js +lineWidth: { + type: 'number', + description: 'set arc line width', + defaultValue: 1, + } +``` + +#### slot: jitter + +```js +jitter: { + type: 'number', + description: + 'jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them', + defaultValue: 0, + } +``` + +#### slot: colorScheme + +```js +colorScheme: { + type: 'stringEnum', + model: types.enumeration('colorScheme', [ + 'strand', + 'normal', + 'insertSize', + 'insertSizeAndOrientation', + 'mappingQuality', + 'tag', + ]), + description: 'color scheme to use', + defaultValue: 'normal', + } +``` + +## LinearReadArcsDisplay - Derives from + +```js +baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager) +``` diff --git a/website/docs/config/LinearReadCloudDisplay.md b/website/docs/config/LinearReadCloudDisplay.md new file mode 100644 index 0000000000..5ab83503a9 --- /dev/null +++ b/website/docs/config/LinearReadCloudDisplay.md @@ -0,0 +1,55 @@ +--- +id: linearreadclouddisplay +title: LinearReadCloudDisplay +toplevel: true +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +## Docs + +### LinearReadCloudDisplay - Slots + +#### slot: maxFeatureScreenDensity + +```js +maxFeatureScreenDensity: { + type: 'number', + description: 'maximum features per pixel that is displayed in the view', + defaultValue: 5, + } +``` + +#### slot: featureHeight + +```js +featureHeight: { + type: 'number', + defaultValue: 7, + } +``` + +#### slot: colorScheme + +```js +colorScheme: { + type: 'stringEnum', + model: types.enumeration('colorScheme', [ + 'strand', + 'normal', + 'insertSize', + 'insertSizeAndOrientation', + 'mappingQuality', + 'tag', + ]), + description: 'color scheme to use', + defaultValue: 'normal', + } +``` + +## LinearReadCloudDisplay - Derives from + +```js +baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager) +``` diff --git a/website/docs/config/LinearReferenceSequenceDisplay.md b/website/docs/config/LinearReferenceSequenceDisplay.md index e1c5c18daf..af9c10ed70 100644 --- a/website/docs/config/LinearReferenceSequenceDisplay.md +++ b/website/docs/config/LinearReferenceSequenceDisplay.md @@ -4,8 +4,8 @@ title: LinearReferenceSequenceDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearSNPCoverageDisplay.md b/website/docs/config/LinearSNPCoverageDisplay.md index 883672a7e8..ceee2f64c9 100644 --- a/website/docs/config/LinearSNPCoverageDisplay.md +++ b/website/docs/config/LinearSNPCoverageDisplay.md @@ -4,8 +4,8 @@ title: LinearSNPCoverageDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearSyntenyDisplay.md b/website/docs/config/LinearSyntenyDisplay.md index ada05bb842..accf8e525e 100644 --- a/website/docs/config/LinearSyntenyDisplay.md +++ b/website/docs/config/LinearSyntenyDisplay.md @@ -4,8 +4,8 @@ title: LinearSyntenyDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearSyntenyRenderer.md b/website/docs/config/LinearSyntenyRenderer.md index 4635868cbf..cb50fe5202 100644 --- a/website/docs/config/LinearSyntenyRenderer.md +++ b/website/docs/config/LinearSyntenyRenderer.md @@ -4,8 +4,8 @@ title: LinearSyntenyRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/LinearVariantDisplay.md b/website/docs/config/LinearVariantDisplay.md index 2f15d05886..39a298e981 100644 --- a/website/docs/config/LinearVariantDisplay.md +++ b/website/docs/config/LinearVariantDisplay.md @@ -4,14 +4,13 @@ title: LinearVariantDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs -mostly empty, this display type is very much -like a `FeatureTrack` with a `LinearBasicDisplay` except it has a custom -feature details widget +mostly empty, this display type is very much like a `FeatureTrack` with a +`LinearBasicDisplay` except it has a custom feature details widget ## LinearVariantDisplay - Derives from diff --git a/website/docs/config/LinearWiggleDisplay.md b/website/docs/config/LinearWiggleDisplay.md index 1b88e85020..27e25a2b72 100644 --- a/website/docs/config/LinearWiggleDisplay.md +++ b/website/docs/config/LinearWiggleDisplay.md @@ -4,8 +4,8 @@ title: LinearWiggleDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MCScanAnchorsAdapter.md b/website/docs/config/MCScanAnchorsAdapter.md index 9dedb69248..898b1b49fc 100644 --- a/website/docs/config/MCScanAnchorsAdapter.md +++ b/website/docs/config/MCScanAnchorsAdapter.md @@ -4,8 +4,8 @@ title: MCScanAnchorsAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MCScanSimpleAnchorsAdapter.md b/website/docs/config/MCScanSimpleAnchorsAdapter.md index 85bbb2cc0d..f9f350b164 100644 --- a/website/docs/config/MCScanSimpleAnchorsAdapter.md +++ b/website/docs/config/MCScanSimpleAnchorsAdapter.md @@ -4,8 +4,8 @@ title: MCScanSimpleAnchorsAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MainThreadRpcDriver.md b/website/docs/config/MainThreadRpcDriver.md index 5be9a92803..8b2d4a8b43 100644 --- a/website/docs/config/MainThreadRpcDriver.md +++ b/website/docs/config/MainThreadRpcDriver.md @@ -4,8 +4,8 @@ title: MainThreadRpcDriver toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MashMapAdapter.md b/website/docs/config/MashMapAdapter.md index 1274f3d30f..d81d95b2df 100644 --- a/website/docs/config/MashMapAdapter.md +++ b/website/docs/config/MashMapAdapter.md @@ -4,8 +4,8 @@ title: MashMapAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiDensityRenderer.md b/website/docs/config/MultiDensityRenderer.md index 9db8c77ff4..1598a14b01 100644 --- a/website/docs/config/MultiDensityRenderer.md +++ b/website/docs/config/MultiDensityRenderer.md @@ -4,8 +4,8 @@ title: MultiDensityRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiLineRenderer.md b/website/docs/config/MultiLineRenderer.md index 87cda06336..3b646f91a2 100644 --- a/website/docs/config/MultiLineRenderer.md +++ b/website/docs/config/MultiLineRenderer.md @@ -4,8 +4,8 @@ title: MultiLineRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiLinearWiggleDisplay.md b/website/docs/config/MultiLinearWiggleDisplay.md index dad3512b00..bdd7995c14 100644 --- a/website/docs/config/MultiLinearWiggleDisplay.md +++ b/website/docs/config/MultiLinearWiggleDisplay.md @@ -4,8 +4,8 @@ title: MultiLinearWiggleDisplay toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiQuantitativeTrack.md b/website/docs/config/MultiQuantitativeTrack.md index c088bb87f4..abae1e207f 100644 --- a/website/docs/config/MultiQuantitativeTrack.md +++ b/website/docs/config/MultiQuantitativeTrack.md @@ -4,8 +4,8 @@ title: MultiQuantitativeTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiRowLineRenderer.md b/website/docs/config/MultiRowLineRenderer.md index 4d86c70637..2d7ac8c885 100644 --- a/website/docs/config/MultiRowLineRenderer.md +++ b/website/docs/config/MultiRowLineRenderer.md @@ -4,8 +4,8 @@ title: MultiRowLineRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiRowXYPlotRenderer.md b/website/docs/config/MultiRowXYPlotRenderer.md index 2e5ad46810..95aa92a7f6 100644 --- a/website/docs/config/MultiRowXYPlotRenderer.md +++ b/website/docs/config/MultiRowXYPlotRenderer.md @@ -4,8 +4,8 @@ title: MultiRowXYPlotRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiWiggleAdapter.md b/website/docs/config/MultiWiggleAdapter.md index 10217085d9..581d42bd9a 100644 --- a/website/docs/config/MultiWiggleAdapter.md +++ b/website/docs/config/MultiWiggleAdapter.md @@ -4,8 +4,8 @@ title: MultiWiggleAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/MultiXYPlotRenderer.md b/website/docs/config/MultiXYPlotRenderer.md index bb1c98ce68..2fc0b6be2f 100644 --- a/website/docs/config/MultiXYPlotRenderer.md +++ b/website/docs/config/MultiXYPlotRenderer.md @@ -4,8 +4,8 @@ title: MultiXYPlotRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/NCListAdapter.md b/website/docs/config/NCListAdapter.md index c11a9039d9..5fc5148e1b 100644 --- a/website/docs/config/NCListAdapter.md +++ b/website/docs/config/NCListAdapter.md @@ -4,8 +4,8 @@ title: NCListAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/OAuthInternetAccount.md b/website/docs/config/OAuthInternetAccount.md index 30e33aa27d..d22f11216c 100644 --- a/website/docs/config/OAuthInternetAccount.md +++ b/website/docs/config/OAuthInternetAccount.md @@ -4,8 +4,8 @@ title: OAuthInternetAccount toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -71,6 +71,16 @@ scopes: { } ``` +#### slot: state + +```js +state: { + description: 'optional state for the authorization call', + type: 'string', + defaultValue: '', + } +``` + #### slot: responseType ```js diff --git a/website/docs/config/PAFAdapter.md b/website/docs/config/PAFAdapter.md index 32a9f9cbcc..5c328ca98d 100644 --- a/website/docs/config/PAFAdapter.md +++ b/website/docs/config/PAFAdapter.md @@ -4,8 +4,8 @@ title: PAFAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/PileupRenderer.md b/website/docs/config/PileupRenderer.md index d74dfe55ec..f526b2385e 100644 --- a/website/docs/config/PileupRenderer.md +++ b/website/docs/config/PileupRenderer.md @@ -4,8 +4,8 @@ title: PileupRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -32,7 +32,7 @@ orientationType: { model: types.enumeration('orientationType', ['fr', 'rf', 'ff']), defaultValue: 'fr', description: - 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options', + 'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options', } ``` diff --git a/website/docs/config/QuantitativeTrack.md b/website/docs/config/QuantitativeTrack.md index d93aa93dd3..7cf63b4540 100644 --- a/website/docs/config/QuantitativeTrack.md +++ b/website/docs/config/QuantitativeTrack.md @@ -4,8 +4,8 @@ title: QuantitativeTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/RefNameAliasAdapter.md b/website/docs/config/RefNameAliasAdapter.md index e4ecb4f737..f555d74e2a 100644 --- a/website/docs/config/RefNameAliasAdapter.md +++ b/website/docs/config/RefNameAliasAdapter.md @@ -4,11 +4,14 @@ title: RefNameAliasAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs +can read "chromAliases" type files from UCSC or any tab separated file of +refName aliases + ### RefNameAliasAdapter - Slots #### slot: location @@ -25,6 +28,9 @@ location: { #### slot: refNameColumn +by default, the "ref names that match the fasta" are assumed to be in the first +column (0), change this variable if needed + ```js refNameColumn: { type: 'number', diff --git a/website/docs/config/ReferenceSequenceTrack.md b/website/docs/config/ReferenceSequenceTrack.md index bf1ddd1a3a..9186744152 100644 --- a/website/docs/config/ReferenceSequenceTrack.md +++ b/website/docs/config/ReferenceSequenceTrack.md @@ -4,8 +4,8 @@ title: ReferenceSequenceTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/RpcOptions.md b/website/docs/config/RpcOptions.md index 21c8badb02..e152cb5429 100644 --- a/website/docs/config/RpcOptions.md +++ b/website/docs/config/RpcOptions.md @@ -4,8 +4,8 @@ title: RpcOptions toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/SNPCoverageAdapter.md b/website/docs/config/SNPCoverageAdapter.md index 7b82f8bf8e..779389149d 100644 --- a/website/docs/config/SNPCoverageAdapter.md +++ b/website/docs/config/SNPCoverageAdapter.md @@ -4,8 +4,8 @@ title: SNPCoverageAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs @@ -16,5 +16,8 @@ our source code. See [Config guide](/docs/config_guide) for more info normally refers to a BAM or CRAM adapter ```js -subadapter: pluginManager.pluggableConfigSchemaType('adapter') +subadapter: { + type: 'frozen', + defaultValue: null, + } ``` diff --git a/website/docs/config/SNPCoverageRenderer.md b/website/docs/config/SNPCoverageRenderer.md index 1fdb794936..47005fb597 100644 --- a/website/docs/config/SNPCoverageRenderer.md +++ b/website/docs/config/SNPCoverageRenderer.md @@ -4,8 +4,8 @@ title: SNPCoverageRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/SequenceSearchAdapter.md b/website/docs/config/SequenceSearchAdapter.md index be9563c418..ad21f158b7 100644 --- a/website/docs/config/SequenceSearchAdapter.md +++ b/website/docs/config/SequenceSearchAdapter.md @@ -4,8 +4,8 @@ title: SequenceSearchAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/StructuralVariantChordRenderer.md b/website/docs/config/StructuralVariantChordRenderer.md index 698637094b..eb38b2395c 100644 --- a/website/docs/config/StructuralVariantChordRenderer.md +++ b/website/docs/config/StructuralVariantChordRenderer.md @@ -4,8 +4,8 @@ title: StructuralVariantChordRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/SvgFeatureRenderer.md b/website/docs/config/SvgFeatureRenderer.md index 3e2944df7c..cb6683a783 100644 --- a/website/docs/config/SvgFeatureRenderer.md +++ b/website/docs/config/SvgFeatureRenderer.md @@ -4,8 +4,8 @@ title: SvgFeatureRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/SyntenyTrack.md b/website/docs/config/SyntenyTrack.md index 7a6c6e2255..8a50aafbd0 100644 --- a/website/docs/config/SyntenyTrack.md +++ b/website/docs/config/SyntenyTrack.md @@ -4,8 +4,8 @@ title: SyntenyTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/TheTrackHubRegistryConnection.md b/website/docs/config/TheTrackHubRegistryConnection.md deleted file mode 100644 index 55e8dc25d0..0000000000 --- a/website/docs/config/TheTrackHubRegistryConnection.md +++ /dev/null @@ -1,28 +0,0 @@ ---- -id: thetrackhubregistryconnection -title: TheTrackHubRegistryConnection -toplevel: true ---- - -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info - -## Docs - -### TheTrackHubRegistryConnection - Slots - -#### slot: trackDbId - -```js -trackDbId: { - type: 'string', - defaultValue: '', - description: 'id of the trackDb in The Track Hub Registry', - } -``` - -## TheTrackHubRegistryConnection - Derives from - -```js -baseConfiguration: baseConnectionConfig -``` diff --git a/website/docs/config/TrixTextSearchAdapter.md b/website/docs/config/TrixTextSearchAdapter.md index 9bf5fbbdee..94d9e90344 100644 --- a/website/docs/config/TrixTextSearchAdapter.md +++ b/website/docs/config/TrixTextSearchAdapter.md @@ -4,8 +4,8 @@ title: TrixTextSearchAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/TwoBitAdapter.md b/website/docs/config/TwoBitAdapter.md index f09d536ea2..ef7796973b 100644 --- a/website/docs/config/TwoBitAdapter.md +++ b/website/docs/config/TwoBitAdapter.md @@ -4,8 +4,8 @@ title: TwoBitAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/UCSCTrackHubConnection.md b/website/docs/config/UCSCTrackHubConnection.md index 2f58421c35..6f5c0b29db 100644 --- a/website/docs/config/UCSCTrackHubConnection.md +++ b/website/docs/config/UCSCTrackHubConnection.md @@ -4,8 +4,8 @@ title: UCSCTrackHubConnection toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/VariantTrack.md b/website/docs/config/VariantTrack.md index fe9df1b3b4..60e49546c6 100644 --- a/website/docs/config/VariantTrack.md +++ b/website/docs/config/VariantTrack.md @@ -4,8 +4,8 @@ title: VariantTrack toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/VcfAdapter.md b/website/docs/config/VcfAdapter.md index a8c8e3cb85..a0f8ac0efd 100644 --- a/website/docs/config/VcfAdapter.md +++ b/website/docs/config/VcfAdapter.md @@ -4,8 +4,8 @@ title: VcfAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/VcfTabixAdapter.md b/website/docs/config/VcfTabixAdapter.md index 85930894f5..0abf977598 100644 --- a/website/docs/config/VcfTabixAdapter.md +++ b/website/docs/config/VcfTabixAdapter.md @@ -4,8 +4,8 @@ title: VcfTabixAdapter toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/WebWorkerRpcDriver.md b/website/docs/config/WebWorkerRpcDriver.md index a80d7eb5bb..4fc7dd3309 100644 --- a/website/docs/config/WebWorkerRpcDriver.md +++ b/website/docs/config/WebWorkerRpcDriver.md @@ -4,8 +4,8 @@ title: WebWorkerRpcDriver toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/WiggleRenderer.md b/website/docs/config/WiggleRenderer.md index 8f1fb7e186..802b6f6505 100644 --- a/website/docs/config/WiggleRenderer.md +++ b/website/docs/config/WiggleRenderer.md @@ -4,8 +4,8 @@ title: WiggleRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config/XYPlotRenderer.md b/website/docs/config/XYPlotRenderer.md index 394ae6e32b..f62065b486 100644 --- a/website/docs/config/XYPlotRenderer.md +++ b/website/docs/config/XYPlotRenderer.md @@ -4,8 +4,8 @@ title: XYPlotRenderer toplevel: true --- -Note: this document is automatically generated from configuration objects in -our source code. See [Config guide](/docs/config_guide) for more info +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info ## Docs diff --git a/website/docs/config_guide.md b/website/docs/config_guide.md index 6fd0306c75..aa96655f58 100644 --- a/website/docs/config_guide.md +++ b/website/docs/config_guide.md @@ -6,8 +6,8 @@ toplevel: true import Figure from './figure' -The following guide provides comprehensive information regarding the anatomy -and usage of the `config.json` file that is critical for running a JBrowse 2 +The following guide provides comprehensive information regarding the anatomy and +usage of the `config.json` file that is critical for running a JBrowse 2 session. Also see our quick-start tutorials for configuring assemblies and tracks diff --git a/website/docs/config_guides/alignments_track.md b/website/docs/config_guides/alignments_track.md index 427072c705..f5aa67b5b0 100644 --- a/website/docs/config_guides/alignments_track.md +++ b/website/docs/config_guides/alignments_track.md @@ -53,6 +53,9 @@ Example `BamAdapter` config: - `cramLocation` - a 'file location' for the CRAM - `craiLocation` - a 'file location' for the CRAI +- `sequenceAdapter` - a subadapter describing the location of the reference + assembly (_e.g._ an + [IndexedFastaAdapter](/docs/config_guides/assemblies/#IndexedFastaAdapter)) Example `CramAdapter` config: @@ -64,6 +67,17 @@ Example `CramAdapter` config: }, "craiLocation": { "uri": "http://yourhost/file.cram.crai" + }, + "sequenceAdapter": { + "type": "IndexedFastaAdapter", + "fastaLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa", + "locationType": "UriLocation" + }, + "faiLocation": { + "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.fai", + "locationType": "UriLocation" + } } } ``` diff --git a/website/docs/config_guides/assemblies.md b/website/docs/config_guides/assemblies.md index 2510f6629a..ce45ebbe81 100644 --- a/website/docs/config_guides/assemblies.md +++ b/website/docs/config_guides/assemblies.md @@ -73,8 +73,9 @@ The refNameAliases in the above config provides this functionality: } ``` -The hg19_aliases then is a tab delimited file that looks like the following; the first column should be the names that are in your FASTA sequence, and the -rest of the columns are aliases: +The hg19_aliases then is a tab delimited file that looks like the following; the +first column should be the names that are in your FASTA sequence, and the rest +of the columns are aliases: ``` 1 chr1 @@ -105,9 +106,11 @@ M chrM MT ``` :::note -"chromAliases" files [from -UCSC](https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chromAlias.txt) + +"chromAliases" files +[from UCSC](https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chromAlias.txt) match this format. + ::: ## Adding an assembly with the CLI @@ -126,15 +129,19 @@ myfile.fa and myfile.fa.fai to your data folder at /var/www/html/jbrowse2 jbrowse add-assembly myfile.fa --load copy --out /var/www/html/jbrowse2 ``` -See our [configure JBrowse using the -cli](/docs/tutorials/config_cli/#adding-a-genome-assembly) tutorial for more -in-depth instructions, or more information on the `add-assembly` command -through our [CLI tools guide](/docs/cli/#jbrowse-add-assembly-sequence). +See our +[configure JBrowse using the cli](/docs/tutorials/config_cli/#adding-a-genome-assembly) +tutorial for more in-depth instructions, or more information on the +`add-assembly` command through our +[CLI tools guide](/docs/cli/#jbrowse-add-assembly-sequence). :::note -Assemblies can also be added graphically using the assembly manager when you -are using the `admin-server`. See how to [configure JBrowse using the -GUI](/docs/tutorials/config_gui/#adding-a-genome-assembly) for more details. + +Assemblies can also be added graphically using the assembly manager when you are +using the `admin-server`. See how to +[configure JBrowse using the GUI](/docs/tutorials/config_gui/#adding-a-genome-assembly) +for more details. + ::: ## Assembly config @@ -195,24 +202,24 @@ The top level config is an array of assemblies; each assembly contains: - `name` - a name to refer to the assembly by. each track that is related to this assembly references this name -- `aliases` - sometimes genome assemblies have aliases like hg19, GRCh37, - b37p5, etc. while there may be small differences between these different - sequences, they often largely have the same coordinates, so you might want to - be able to associate tracks from these different assemblies together. The - assembly aliases are most helpful when loading from a UCSC trackHub which - specifies the genome assembly names it uses, so you can connect to a UCSC - trackHub if your assembly name or aliases match. +- `aliases` - sometimes genome assemblies have aliases like hg19, GRCh37, b37p5, + etc. while there may be small differences between these different sequences, + they often largely have the same coordinates, so you might want to be able to + associate tracks from these different assemblies together. The assembly + aliases are most helpful when loading from a UCSC trackHub which specifies the + genome assembly names it uses, so you can connect to a UCSC trackHub if your + assembly name or aliases match. - `sequence` - this is a complete "track" definition for your genome assembly. we specify that it is a track of type ReferenceSequenceTrack, give it a trackId, and an adapter configuration. an adapter configuration can specify IndexedFastaAdapter (fasta.fa and fasta.fai), BgzipFastaAdapter (fasta.fa.gz, - fasta.fa.gz.fai, fasta.gz.gzi), ChromSizesAdapter (which fetches no - sequences, just chromosome names) + fasta.fa.gz.fai, fasta.gz.gzi), ChromSizesAdapter (which fetches no sequences, + just chromosome names) ### ReferenceSequenceTrack -Example ReferenceSequenceTrack config, which as above, is specified as the -child of the assembly section of the config: +Example ReferenceSequenceTrack config, which as above, is specified as the child +of the assembly section of the config: ```json { @@ -275,7 +282,8 @@ These are loaded into a BgzipFastaAdapter as follows ### IndexedFastaAdapter -An indexed FASTA file is similar to the above, but the sequence is not compressed +An indexed FASTA file is similar to the above, but the sequence is not +compressed ```bash samtools faidx sequence.fa @@ -319,8 +327,8 @@ plaintext is displayed for this file so the format is not strict. ### TwoBitAdapter -The UCSC twoBit adapter is also supported. Note however that the 2bit format -has a longer startup time than other adapters because there is a larger upfront +The UCSC twoBit adapter is also supported. Note however that the 2bit format has +a longer startup time than other adapters because there is a larger upfront parsing time. ```json diff --git a/website/docs/config_guides/avoiding_stale_config.md b/website/docs/config_guides/avoiding_stale_config.md new file mode 100644 index 0000000000..2a26c551c9 --- /dev/null +++ b/website/docs/config_guides/avoiding_stale_config.md @@ -0,0 +1,23 @@ +--- +id: avoiding_stale_config +title: Avoiding stale config +toplevel: true +--- + +Some servers strongly cache the "config.json" file. If you want to avoid this, +you can edit the index.html of JBrowse to include the following + +``` + + + + + + +``` + +This will request the config.json file with a random query string appended to +force the data to be fetched from the server instead of being loaded from the +local browser cache diff --git a/website/docs/config_guides/customizing_feature_details.md b/website/docs/config_guides/customizing_feature_details.md index f180263a9e..2d773ecdbd 100644 --- a/website/docs/config_guides/customizing_feature_details.md +++ b/website/docs/config_guides/customizing_feature_details.md @@ -35,9 +35,9 @@ Here is an example track with a formatter:
    -This feature formatter changes the `"name"` field in the feature detail panel -to have a link to a google search for that feature's name. This can be used to -link to gene pages for example as well. +This feature formatter changes the `"name"` field in the feature detail panel to +have a link to a google search for that feature's name. This can be used to link +to gene pages for example as well. In addition, this example also adds a custom field called `"newfield"` and removes e.g. `"type"` from being displayed. @@ -49,9 +49,11 @@ The schema for `formatDetails` is: - `depth` - depth to customize the subfeatures to, default 1 The general way this is done is by making a jexl callback either or both of -`feature` and `subfeatures` (if you want both feature and subfeatures, you can copy the same thing to both config slots). +`feature` and `subfeatures` (if you want both feature and subfeatures, you can +copy the same thing to both config slots). -The callback returns an object where the keys of the object are what you want to replace. +The callback returns an object where the keys of the object are what you want to +replace. In the example above we return an object with: @@ -111,8 +113,8 @@ use the custom `jexl` function in your config callbacks as follows: } ``` -See [our no-build plugin tutorial](/docs/tutorials/no_build_plugin_tutorial/) for -more info on setting up a simple plugin for doing these customizations. +See [our no-build plugin tutorial](/docs/tutorials/no_build_plugin_tutorial/) +for more info on setting up a simple plugin for doing these customizations. #### Footnote 1 @@ -126,6 +128,6 @@ You might also ask why aren't all features serialized or plain JSON objects normally? Well, some feature types like alignments features benefit from only being partially serialized e.g. getting only a couple attributes via `feature.get('attribute')` (completely converting them to a raw JSON expression -is expensive). It is a little confusing, but that is why in the feature -details, you can access the plain JS object e.g. `feature.start` while in color -callbacks you use e.g. `feature.get('start')`. +is expensive). It is a little confusing, but that is why in the feature details, +you can access the plain JS object e.g. `feature.start` while in color callbacks +you use e.g. `feature.get('start')`. diff --git a/website/docs/config_guides/disable_analytics.md b/website/docs/config_guides/disable_analytics.md index 672968c3b5..c8bebd7f4a 100644 --- a/website/docs/config_guides/disable_analytics.md +++ b/website/docs/config_guides/disable_analytics.md @@ -7,7 +7,8 @@ toplevel: true Currently, jbrowse-web and jbrowse-desktop use Google Analytics for collecting usage data. -You can disable this behavior by adding a field in your config.json. For example: +You can disable this behavior by adding a field in your config.json. For +example: ```json { diff --git a/website/docs/config_guides/from_config.md b/website/docs/config_guides/from_config.md index 7574923ec9..83bac3c334 100644 --- a/website/docs/config_guides/from_config.md +++ b/website/docs/config_guides/from_config.md @@ -4,15 +4,15 @@ title: FromConfig adapters toplevel: true --- -There are two useful adapter types that can be used for more advanced use -cases, such as generating configuration for data returned by an API. These are -the `FromConfigAdapter` and `FromConfigSequenceAdapter`. They can be used as -the `adapter` value for any track type. +There are two useful adapter types that can be used for more advanced use cases, +such as generating configuration for data returned by an API. These are the +`FromConfigAdapter` and `FromConfigSequenceAdapter`. They can be used as the +`adapter` value for any track type. #### FromConfigAdapter -This adapter can be used to generate features directly from values stored in -the configuration. +This adapter can be used to generate features directly from values stored in the +configuration. Example `FromConfigAdapter`: diff --git a/website/docs/config_guides/intro.md b/website/docs/config_guides/intro.md index 078adecc28..da12e1acc3 100644 --- a/website/docs/config_guides/intro.md +++ b/website/docs/config_guides/intro.md @@ -30,12 +30,11 @@ config.json) and is structured as follows The most important thing to configure are your assemblies and your tracks. -:::info Note -On jbrowse desktop, a "session" refers to a config.json with a .jbrowse file extension -::: +:::info Note On jbrowse desktop, a "session" refers to a config.json with a +.jbrowse file extension ::: -:::info Note -On embedded e.g. with @jbrowse/react-linaer-genome-view, it does not accept a config file but rather an object at runtime with the config loaded. +:::info Note On embedded e.g. with @jbrowse/react-linaer-genome-view, it does +not accept a config file but rather an object at runtime with the config loaded. To fetch a config.json object on the fly in @jbrowse/react-linear-genome-view, you might use something like this: diff --git a/website/docs/config_guides/jexl.md b/website/docs/config_guides/jexl.md index 8ec82caed4..154102bce1 100644 --- a/website/docs/config_guides/jexl.md +++ b/website/docs/config_guides/jexl.md @@ -167,15 +167,15 @@ The feature in the callback is a "SimpleFeature" type object, and you can call `feature.get('start')`, `feature.get('end')`, `feature.get('refName')`, or `feature.get('other_attribute')` for e.g. maybe a field in a GFF3 column 9 -Footnote 0. See [our no-build plugin -tutorial](/docs/tutorials/no_build_plugin_tutorial/) for more info on setting -up a simple plugin for doing these customizations. +Footnote 0. See +[our no-build plugin tutorial](/docs/tutorials/no_build_plugin_tutorial/) for +more info on setting up a simple plugin for doing these customizations. -Footnote 1. `myplugin.js` does not have to use the jbrowse-plugin-template if -it is small and self contained like this, and does not import other modules. if -you import other modules from your plugin, then it can be worth it to use the +Footnote 1. `myplugin.js` does not have to use the jbrowse-plugin-template if it +is small and self contained like this, and does not import other modules. if you +import other modules from your plugin, then it can be worth it to use the jbrowse-plugin-template. -Footnote 2. if you are using embedded, there are also other methods of -including plugins, see +Footnote 2. if you are using embedded, there are also other methods of including +plugins, see https://jbrowse.org/storybook/lgv/main/?path=/story/using-plugins--page diff --git a/website/docs/config_guides/plugins.md b/website/docs/config_guides/plugins.md index d3358d0f1d..55794adcea 100644 --- a/website/docs/config_guides/plugins.md +++ b/website/docs/config_guides/plugins.md @@ -27,8 +27,8 @@ Our plugin store lists the URLs for unpkg URLs for these plugins https://jbrowse.org/jb2/plugin_store/. You can also download the plugin files from e.g. the unpkg URLs to your local server and serve them. -There are several other ways to plugins in the config, that have particular -ways of being resolved from your local server. +There are several other ways to plugins in the config, that have particular ways +of being resolved from your local server. #### umdUrl @@ -76,10 +76,10 @@ helpful for storing the plugin.js in the same folder as your config ``` `esmUrl` is resolved relative to the index.html of the file, so can be a -relative path in your root directory or an absolute URL to somewhere on the -web. Note that ESM modules are currently not supported in web workers in -firefox, so you can use MainThreadRpc, or use alternative module formats like -UMD for broad compatibility. +relative path in your root directory or an absolute URL to somewhere on the web. +Note that ESM modules are currently not supported in web workers in firefox, so +you can use MainThreadRpc, or use alternative module formats like UMD for broad +compatibility. #### esmLoc @@ -116,8 +116,9 @@ compatibility. `cjsUrl` is used for desktop plugins specifically, since Electron (as of writing) does not support ESM, and since the jbrowse-plugin-template will not output some code that is helpful for desktop like true require() calls for -desktop modules. See the [desktop plugin -tutorial](/docs/tutorials/desktop_spec_plugin_tutorial/) for more info. +desktop modules. See the +[desktop plugin tutorial](/docs/tutorials/desktop_spec_plugin_tutorial/) for +more info. ### Plugin store diff --git a/website/docs/config_guides/quantitative_track.md b/website/docs/config_guides/quantitative_track.md index fa953be24f..8fa6393f33 100644 --- a/website/docs/config_guides/quantitative_track.md +++ b/website/docs/config_guides/quantitative_track.md @@ -25,8 +25,10 @@ Example QuantitativeTrack config: #### General QuantitativeTrack options -- `scaleType` - options: linear, log, to display the coverage data. default: linear -- `adapter` - an adapter that returns numeric signal data, e.g. feature.get('score') +- `scaleType` - options: linear, log, to display the coverage data. default: + linear +- `adapter` - an adapter that returns numeric signal data, e.g. + feature.get('score') #### Autoscale options for QuantitativeTrack diff --git a/website/docs/config_guides/synteny_track.md b/website/docs/config_guides/synteny_track.md index 9bb8473dd9..6e0723059b 100644 --- a/website/docs/config_guides/synteny_track.md +++ b/website/docs/config_guides/synteny_track.md @@ -31,9 +31,9 @@ jbrowse add-track myfile.paf --type SyntenyTrack --assemblyNames \ The first assembly is the "target" and the second assembly is the "query." -See how to [configure JBrowse using the -CLI](/docs/tutorials/config_cli/#adding-a-synteny-track) for more ways to load -synteny tracks with the CLI. +See how to +[configure JBrowse using the CLI](/docs/tutorials/config_cli/#adding-a-synteny-track) +for more ways to load synteny tracks with the CLI. ### PAFAdapter config @@ -64,8 +64,8 @@ Slots ### DeltaAdapter config -The DeltaAdapter is used to load .delta files from MUMmer/nucmer. It can be -used for SyntenyTracks: +The DeltaAdapter is used to load .delta files from MUMmer/nucmer. It can be used +for SyntenyTracks: ```json { @@ -79,9 +79,9 @@ used for SyntenyTracks: Slots -- `deltaLocation` - the location of the delta file. The deltaLocation can refer to a - gzipped or unzipped delta file. It will be read into memory entirely as it is - not an indexed file format. +- `deltaLocation` - the location of the delta file. The deltaLocation can refer + to a gzipped or unzipped delta file. It will be read into memory entirely as + it is not an indexed file format. - `assemblyNames` - list of assembly names, typically two (first in list is target, second is query) - `queryAssembly` - alternative to assemblyNames: just the assemblyName of the @@ -91,8 +91,8 @@ Slots ### ChainAdapter config -The ChainAdapter is used to load .chain files from MUMmer/nucmer. It can be -used for SyntenyTracks: +The ChainAdapter is used to load .chain files from MUMmer/nucmer. It can be used +for SyntenyTracks: ```json { @@ -118,7 +118,8 @@ Slots ### MCScanAnchorsAdapter -The .anchors file from MCScan refers to pairs of homologous genes and can be loaded into synteny tracks in JBrowse 2: +The .anchors file from MCScan refers to pairs of homologous genes and can be +loaded into synteny tracks in JBrowse 2: ```json { @@ -137,18 +138,19 @@ The .anchors file from MCScan refers to pairs of homologous genes and can be loa ``` [This guide]() -shows a demonstration of how to create the anchors and bed files (the .bed -files are intermediate steps in creating the anchors files and are required by -the MCScanAnchorsAdapter). +shows a demonstration of how to create the anchors and bed files (the .bed files +are intermediate steps in creating the anchors files and are required by the +MCScanAnchorsAdapter). Slots: - `mcscanAnchorsLocation` - the location of the .anchors file from the MCScan - workflow. The .anchors file has three columns. It can be gzipped or - ungzipped, and is read into memory whole -- `bed1Location` - the location of the first assemblies .bed file from the MCScan - workflow. It can be gzipped or ungzipped, and is read into memory whole. This - would refer to the gene names on the "left" side of the .anchors file. + workflow. The .anchors file has three columns. It can be gzipped or ungzipped, + and is read into memory whole +- `bed1Location` - the location of the first assemblies .bed file from the + MCScan workflow. It can be gzipped or ungzipped, and is read into memory + whole. This would refer to the gene names on the "left" side of the .anchors + file. - `bed2Location` - the location of the second assemblies .bed file from the MCScan workflow. It can be gzipped or ungzipped, and is read into memory whole. This would refer to the gene names on the "right" side of the .anchors @@ -176,19 +178,20 @@ genes and can be loaded into synteny tracks in JBrowse 2: ``` [This guide]() -shows a demonstration of how to create the anchors and bed files (the .bed -files are intermediate steps in creating the anchors.simple files and are -required by the MCScanSimpleAnchorsAdapter) +shows a demonstration of how to create the anchors and bed files (the .bed files +are intermediate steps in creating the anchors.simple files and are required by +the MCScanSimpleAnchorsAdapter) Slots: - `mcscanSimpleAnchorsLocation` - the location of the .anchors.simple file from the MCScan workflow (this file has 5 columns, start and end gene from bed1, - start and end genes from bed2, and score). It can be gzipped or ungzipped, - and is read into memory whole -- `bed1Location` - the location of the first assemblies .bed file from the MCScan - workflow. It can be gzipped or ungzipped, and is read into memory whole. This - would refer to the gene names on the "left" side of the .anchors file. + start and end genes from bed2, and score). It can be gzipped or ungzipped, and + is read into memory whole +- `bed1Location` - the location of the first assemblies .bed file from the + MCScan workflow. It can be gzipped or ungzipped, and is read into memory + whole. This would refer to the gene names on the "left" side of the .anchors + file. - `bed2Location` - the location of the second assemblies .bed file from the MCScan workflow. It can be gzipped or ungzipped, and is read into memory whole. This would refer to the gene names on the "right" side of the .anchors diff --git a/website/docs/config_guides/text_searching.md b/website/docs/config_guides/text_searching.md index ec30ad2c13..800031a840 100644 --- a/website/docs/config_guides/text_searching.md +++ b/website/docs/config_guides/text_searching.md @@ -106,8 +106,8 @@ below for details: ### JBrowse1TextSearchAdapter config -This is more uncommon, but allows back compatibility with a JBrowse1 names -index created by `generate-names.pl`: +This is more uncommon, but allows back compatibility with a JBrowse1 names index +created by `generate-names.pl`: ```json { @@ -121,5 +121,4 @@ index created by `generate-names.pl`: } ``` -- `namesIndexLocation` - the location of the JBrowse1 names index data - directory +- `namesIndexLocation` - the location of the JBrowse1 names index data directory diff --git a/website/docs/config_guides/tracks.md b/website/docs/config_guides/tracks.md index 280377c418..042b99bbba 100644 --- a/website/docs/config_guides/tracks.md +++ b/website/docs/config_guides/tracks.md @@ -8,10 +8,10 @@ All tracks can contain: - `trackId` - internal track ID, must be unique - `name` - displayed track name -- `assemblyNames` - an array of assembly names a track is associated with, - often just a single assemblyName -- `category` - (optional) array of categories to display in a hierarchical - track selector +- `assemblyNames` - an array of assembly names a track is associated with, often + just a single assemblyName +- `category` - (optional) array of categories to display in a hierarchical track + selector Example `config.json` containing a track config for a BigBed file: diff --git a/website/docs/developer_guide.md b/website/docs/developer_guide.md index 92ca3d780b..cd27261fb3 100644 --- a/website/docs/developer_guide.md +++ b/website/docs/developer_guide.md @@ -43,8 +43,8 @@ https://github.com/GMOD/jbrowse-plugin-template. Here are some examples of working plugins: - [jbrowse-plugin-ucsc-api](https://github.com/cmdcolin/jbrowse-plugin-ucsc-api) - probably the simplest plugin example, it demonstrates accessing data from - UCSC REST API + probably the simplest plugin example, it demonstrates accessing data from UCSC + REST API - [jbrowse-plugin-gwas](https://github.com/cmdcolin/jbrowse-plugin-gwas) a custom plugin to display manhattan plot GWAS data - [jbrowse-plugin-biothings-api](https://github.com/cmdcolin/jbrowse-plugin-biothings-api) @@ -54,8 +54,8 @@ Here are some examples of working plugins: demonstrates creating a custom view type that doesn't use any conventional tracks - [jbrowse-plugin-gdc](https://github.com/GMOD/jbrowse-plugin-gdc) demonstrates - accessing GDC cancer data GraphQL API, plus a custom drawer and track type - for coloring variants by impact score + accessing GDC cancer data GraphQL API, plus a custom drawer and track type for + coloring variants by impact score - [jbrowse-plugin-systeminformation](https://github.com/garrettjstevens/jbrowse-plugin-systeminformation) demonstrates using desktop specific functionality, accessing system node libraries. This desktop specific functionality should use the CJS bundle type diff --git a/website/docs/developer_guides/config_model.md b/website/docs/developer_guides/config_model.md index e13d5a13a8..b6c8bd7eef 100644 --- a/website/docs/developer_guides/config_model.md +++ b/website/docs/developer_guides/config_model.md @@ -98,10 +98,10 @@ readConfObject(track.configuration, 'maxHeight')` ## Using config callbacks Config callbacks allow you to have a dynamic color based on some function logic -you provide. All config slots can actually become config callback. The -arguments that are given to the callback are listed by the 'contextVariable' -but must be provided by the calling code (the code reading the config slot). To -pass arguments to the a callback we say +you provide. All config slots can actually become config callback. The arguments +that are given to the callback are listed by the 'contextVariable' but must be +provided by the calling code (the code reading the config slot). To pass +arguments to the a callback we say ```js readConfObject(config, 'color', { feature }) @@ -116,8 +116,8 @@ various feature attributes. We use Jexl to express callbacks. See https://github.com/TomFrost/Jexl for more details. -There are also more examples and information in our [config -guide](/docs/config_guides/jexl). +There are also more examples and information in our +[config guide](/docs/config_guides/jexl). If you had a variant track in your config, and wanted to make a custom config callback for color, it might look like this: @@ -158,17 +158,17 @@ callback for color, it might look like this: This draws all SNV (single nucleotide variants) as green, and other types as purple (insertion, deletion, other structural variant). -You can also [write your own jexl function](../pluggable_elements) and -call it in the same way in the configuration. +You can also [write your own jexl function](../pluggable_elements) and call it +in the same way in the configuration. :::info Note It can be extremely useful to utilize a custom jexl function in the default -configuration for a pluggable element type, as you can observe in [one of the -examples above](#example-config-with-multiple-slot-types), the default value of -the `color` slot of the renderer is a jexl function. If you configure your -plugin with a custom jexl function, you can use that function as a default -value in your various pluggable elements. +configuration for a pluggable element type, as you can observe in +[one of the examples above](#example-config-with-multiple-slot-types), the +default value of the `color` slot of the renderer is a jexl function. If you +configure your plugin with a custom jexl function, you can use that function as +a default value in your various pluggable elements. ::: diff --git a/website/docs/developer_guides/creating_adapter.md b/website/docs/developer_guides/creating_adapter.md index 5f6c1e015e..e99ad1283a 100644 --- a/website/docs/developer_guides/creating_adapter.md +++ b/website/docs/developer_guides/creating_adapter.md @@ -5,22 +5,22 @@ title: Creating a custom adapter ### What is an adapter -An adapter is essentially a class that fetches and parses your data and -returns it in a format JBrowse understands. +An adapter is essentially a class that fetches and parses your data and returns +it in a format JBrowse understands. -For example, if you have some data source that contains genes, and you want -to display those genes using JBrowse's existing gene displays, you can write -a custom adapter to do so. If you want to do a custom display of your data, +For example, if you have some data source that contains genes, and you want to +display those genes using JBrowse's existing gene displays, you can write a +custom adapter to do so. If you want to do a custom display of your data, though, you'll probably need to create a custom display and/or renderer along with your adapter. ### What types of adapters are there -- **Feature adapter** - This is the most common type of adapter. Essentially, - it takes a request for a _region_ (a chromosome, starting position, and - ending position) and returns the _features_ (e.g. genes, reads, variants, - etc.) that are in that region. Examples of this in JBrowse include adapters - for [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) and +- **Feature adapter** - This is the most common type of adapter. Essentially, it + takes a request for a _region_ (a chromosome, starting position, and ending + position) and returns the _features_ (e.g. genes, reads, variants, etc.) that + are in that region. Examples of this in JBrowse include adapters for + [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) and [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf) file formats. - **Regions adapter** - This type of adapter is used to define what regions are in an assembly. It returns a list of chromosomes/contigs/scaffolds and their @@ -28,8 +28,8 @@ with your adapter. [chrome.sizes](https://software.broadinstitute.org/software/igv/chromSizes) file. - **Sequence adapter** - This is basically a combination of a regions adapter - and a feature adapter. It can give the list of regions in an assembly, and - can also return the sequence of a queried region. Examples of this in JBrowse + and a feature adapter. It can give the list of regions in an assembly, and can + also return the sequence of a queried region. Examples of this in JBrowse include adapters for [FASTA](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp) and [.2bit](https://genome.ucsc.edu/FAQ/FAQformat.html#format7) file formats. @@ -41,9 +41,11 @@ with your adapter. search indexes. Returns list of search results. An example of this in JBrowse is the trix text search adapter. -:::info Note -When using the refName alias adapter, it's important that the first column +:::info + +Note When using the refName alias adapter, it's important that the first column match what is seen in your FASTA file. + ::: ### Skeleton of a feature adapter @@ -88,7 +90,8 @@ features, discussed below) and `freeResources` (optional). To take this a little slow, let's look at each function individually. -This is a more complete description of the class interface that you can implement: +This is a more complete description of the class interface that you can +implement: ```js import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter' @@ -156,17 +159,16 @@ class MyAdapter extends BaseFeatureDataAdapter { #### getRefNames Returns the refNames that are contained in the file. This is used for "refname -renaming" and is optional, but highly useful in scenarios like human -chromosomes which have, for example, chr1 vs 1. +renaming" and is optional, but highly useful in scenarios like human chromosomes +which have, for example, chr1 vs 1. Returning the refNames used by a given file or resource allows JBrowse to -automatically smooth these small naming disparities over. See [reference -renaming](/docs/config_guide/#configuring-reference-name-aliasing). +automatically smooth these small naming disparities over. See +[reference renaming](/docs/config_guides/assemblies/#configuring-reference-name-aliasing). #### getFeatures -A function that returns features from the file given a genomic range query -e.g., +A function that returns features from the file given a genomic range query e.g., `getFeatures(region, options)` @@ -182,10 +184,10 @@ interface Region { } ``` -The `refName`, `start`, `end` specify a simple genomic range. The -`assemblyName` is used to query a specific assembly if your adapter responds to -multiple assemblies, e.g. for a synteny data file or a REST API that queries a -backend with multiple assemblies. +The `refName`, `start`, `end` specify a simple genomic range. The `assemblyName` +is used to query a specific assembly if your adapter responds to multiple +assemblies, e.g. for a synteny data file or a REST API that queries a backend +with multiple assemblies. The `originalRefName` are also passed, where `originalRefName` is the queried refname before ref renaming e.g. in BamAdapter, if the BAM file uses chr1, and @@ -221,7 +223,8 @@ except we do all those things with the `Observable` Here is a "conversion" of JBrowse-1-style `getFeatures` callbacks to JBrowse 2 observable calls -- `featureCallback(new SimpleFeature(...))` -> `observer.next(new SimpleFeature(...))` +- `featureCallback(new SimpleFeature(...))` -> + `observer.next(new SimpleFeature(...))` - `finishCallback()` -> `observer.complete()` - `errorCallback(error)` -> `observer.error(error)` diff --git a/website/docs/developer_guides/creating_addtrack_workflow.md b/website/docs/developer_guides/creating_addtrack_workflow.md new file mode 100644 index 0000000000..ec417ae807 --- /dev/null +++ b/website/docs/developer_guides/creating_addtrack_workflow.md @@ -0,0 +1,52 @@ +--- +id: creating_addtrack_workflow +title: Creating custom add-track workflows +--- + +Plugins can register their own React component to display in the "Add track" +widget for adding tracks that require custom logic. The Multi-wiggle track is an +example of this, it produces a textbox where you can paste a list of files. + +A simple addition to the add track workflow: + +```js +// plugins/wiggle/MultiWiggleAddTrackWidget/index.jsx + +import PluginManager from '@jbrowse/core/PluginManager' +import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes' +import { types } from 'mobx-state-tree' + +// locals +import MultiWiggleWidget from './AddTrackWorkflow' + +export default (pm: PluginManager) => { + pm.addAddTrackWorkflowType( + () => + new AddTrackWorkflowType({ + name: 'Multi-wiggle track', + /* in a separate file, export the react component to render within the track widget, + typically a form to collect relevant data for your track */ + ReactComponent: MultiWiggleWidget, + stateModel: types.model({}), + }), + ) +} +``` + +...and ensure you install this component into your larger plugin: + +```js +// plugins/wiggle/index.jsx + +// ... + +export default class WigglePlugin extends Plugin { + name = 'WigglePlugin' + + install(pm: PluginManager) { + // ... + MultiWiggleAddTrackWidgetF(pm) + // ... + } +} +``` diff --git a/website/docs/developer_guides/creating_display.md b/website/docs/developer_guides/creating_display.md index e6b6a38701..1e16c781d4 100644 --- a/website/docs/developer_guides/creating_display.md +++ b/website/docs/developer_guides/creating_display.md @@ -1,13 +1,13 @@ --- id: creating_display -title: Creating a display type +title: Creating a custom display type --- Display types tell JBrowse how to "display" a given track in a particular view. A track might "display" itself completely different depending on whether it is -in a dotplot or in a linear genome view. The "display" types may not actually -do the drawing of the track data: that is often done by the renderer. The -display will call the renderer though. +in a dotplot or in a linear genome view. The "display" types may not actually do +the drawing of the track data: that is often done by the renderer. The display +will call the renderer though. Here are some reasons you might want a custom display type: @@ -15,8 +15,7 @@ Here are some reasons you might want a custom display type: in the wiggle track) - Implementing custom track menu items (e.g. Show soft clipping in the alignments track) -- Adding custom widgets (e.g. custom `VariantFeatureWidget` in - variant track) +- Adding custom widgets (e.g. custom `VariantFeatureWidget` in variant track) - You want to bundle your renderer and adapter as a specific thing that is automatically initialized rather than the `BasicTrack` (which combines any adapter and renderer) diff --git a/website/docs/developer_guides/creating_renderer.md b/website/docs/developer_guides/creating_renderer.md index aadb1303dc..c5a2b6ebb0 100644 --- a/website/docs/developer_guides/creating_renderer.md +++ b/website/docs/developer_guides/creating_renderer.md @@ -8,14 +8,18 @@ import Figure from '../figure' ### What is a renderer In JBrowse 1, a track type typically would directly call the data parser and do -it's own rendering. In JBrowse 2, the data parsing and rendering is offloaded -to a web-worker or other RPC. This allows things to be faster in many cases. -This is conceptually related to "server side rendering" or SSR in React terms. +it's own rendering. In JBrowse 2, the data parsing and rendering is offloaded to +a web-worker or other RPC. This allows things to be faster in many cases. This +is conceptually related to "server side rendering" or SSR in React terms.
    -:::warning Note -You can make custom track types that do not use this workflow, but it is a built-in workflow that functions well for the core track types in JBrowse 2, and is recommended. +:::warning + +You can make custom track types that do not use this workflow, but it is a +built-in workflow that functions well for the core track types in JBrowse 2, and +is recommended. + ::: ### How to create a new renderer @@ -49,9 +53,11 @@ height that are supplied via arguments, and draw a rectangle. We then return a `React.createElement` call which creates a "rendering" component that will contain the output. -:::info Note -The above canvas operations use an `OffscreenCanvas` for Chrome, or in -other browsers serialize the drawing commands to be drawn in the main thread. +:::info + +The above canvas operations use an `OffscreenCanvas` for Chrome, or in other +browsers serialize the drawing commands to be drawn in the main thread. + ::: ### What are the props passed to the renderer @@ -72,8 +78,8 @@ export interface PileupRenderProps { ``` The layout is available on BoxRendererType renderers so that it can layout -things in pileup format, and has an addRect function to get the y-coordinate at which to -render your data. +things in pileup format, and has an addRect function to get the y-coordinate at +which to render your data. The features argument is a map of feature ID to the feature itself. To iterate over the features Map, we can use an iterator or convert to an array: @@ -150,8 +156,8 @@ export default class SVGPlugin extends Plugin { } ``` -Then, we have our Rendering component just be plain React code. This is a -highly simplified SVG renderer just to illustrate: +Then, we have our Rendering component just be plain React code. This is a highly +simplified SVG renderer just to illustrate: ```jsx export default function SvgFeatureRendering(props) { @@ -186,14 +192,14 @@ export default function SvgFeatureRendering(props) { :::info Note -1.The above SVG renderer is highly simplified, but it -shows that you can have a simple React component that leverages the existing -`BoxRendererType`, so that you do not have to necessarily create your own -renderer class +1.The above SVG renderer is highly simplified, but it shows that you can have a +simple React component that leverages the existing `BoxRendererType`, so that +you do not have to necessarily create your own renderer class 2.The renderers receive an array of regions to render, but if they are only -equipped to handle one region at a time then they can select only rendering -to `regions[0]` +equipped to handle one region at a time then they can select only rendering to +`regions[0]` + ::: ### Overriding the renderer's getFeatures method @@ -204,14 +210,14 @@ dataAdapter. If you want to drastically modify the feature fetching behavior, you can modify the renderer's `getFeatures` call. -The base `ServerSideRendererType` class has a built-in `getFeatures` function that, -in turn, calls your adapter's `getFeatures` function, but if you need +The base `ServerSideRendererType` class has a built-in `getFeatures` function +that, in turn, calls your adapter's `getFeatures` function, but if you need tighter control over how your adapter's `getFeatures` method is called, then your renderer. -The Hi-C renderer type does not operate on conventional -features and instead works with contact matrices, so the Hi-C renderer has a -custom `getFeatures` function: +The Hi-C renderer type does not operate on conventional features and instead +works with contact matrices, so the Hi-C renderer has a custom `getFeatures` +function: ```js import { toArray } from 'rxjs/operators' diff --git a/website/docs/developer_guides/creating_track.md b/website/docs/developer_guides/creating_track.md index 64e3fadac5..dbe12c6850 100644 --- a/website/docs/developer_guides/creating_track.md +++ b/website/docs/developer_guides/creating_track.md @@ -5,8 +5,8 @@ title: Creating a custom track type Important note: track types are "high level concepts", and don't do a lot of logic: instead "display" types register themselves to a track type, to display -data in a particular view. Then, the renderers are called by the display type -on e.g. a per-block basis +data in a particular view. Then, the renderers are called by the display type on +e.g. a per-block basis ## Examples of track types @@ -15,11 +15,11 @@ For examples of custom track types, refer to things like: - `HicTrack` - uses the `LinearHicDisplay` which calls the HicRenderer to draw contact matrix - `VariantTrack` uses the `ChordVariantDisplay` and `LinearVariantDisplay` to - draw itself differently in the CircularView and LinearGenomeView - respectively. display type that allows a VCF to render "chords" in the - `CircularView`. In the `LinearGenomeView`, the `LinearVariantDisplay` is - quite similar to a normal feature track, but also has a custom feature - details widget because it overrides the "selectFeature" behavior. + draw itself differently in the CircularView and LinearGenomeView respectively. + display type that allows a VCF to render "chords" in the `CircularView`. In + the `LinearGenomeView`, the `LinearVariantDisplay` is quite similar to a + normal feature track, but also has a custom feature details widget because it + overrides the "selectFeature" behavior. - `SyntenyTrack` - synteny tracks can be displayed in multiple view types like DotplotView and LinearSyntenyView. It uses the `DotplotDisplay` or `LinearSyntenyDisplay` respectively to achieve this diff --git a/website/docs/developer_guides/creating_view.md b/website/docs/developer_guides/creating_view.md index 764a78cf2c..373d2263bb 100644 --- a/website/docs/developer_guides/creating_view.md +++ b/website/docs/developer_guides/creating_view.md @@ -5,8 +5,8 @@ title: Creating a custom view type --- View types include things like our DotplotView, CircularView, SpreadsheetView, -and LinearGenomeView. At their core, views are a "panel" that can show -arbitrary contents. +and LinearGenomeView. At their core, views are a "panel" that can show arbitrary +contents. The tutorial [here](/docs/tutorials/simple_plugin) shows how to create a simple "Hello view" that says "Hello world!" diff --git a/website/docs/developer_guides/extension_points.md b/website/docs/developer_guides/extension_points.md index 575c2ac6c9..747b7a076e 100644 --- a/website/docs/developer_guides/extension_points.md +++ b/website/docs/developer_guides/extension_points.md @@ -4,6 +4,35 @@ title: Extension points toplevel: true --- +The basic API is that producers can say: + +```js +const ret = pluginManager.evaluateExtensionPoint('ExtensionPointName', { + value: 1, +}) +``` + +And consumers can say: + +```js +pluginManager.addToExtensionPoint('ExtensionPointName', arg => { + return arg.value + 1 +}) + +pluginManager.addToExtensionPoint('ExtensionPointName', arg => { + return arg.value + 1 +}) +``` + +In this case, `arg` that is passed in evaluateExtensionPoint calls all the +callbacks that have been registered by `addToExtensionPoint`. If multiple +extension points are registered, the return value of the first extension point +is passed as the new argument to the second, and so on (they are chained +together). + +So in the example above, ret would be `{value:3}` after evaluating the extension +point. + In the core codebase, we have the concept of extension points that users can call or add to. @@ -41,9 +70,9 @@ Here are the extension points in the core codebase: type: synchronous -used to add extra functionality to e.g state tree models, for example, -extra right-click context menus. your callback will receive every pluggable -element registered to the system +used to add extra functionality to e.g state tree models, for example, extra +right-click context menus. your callback will receive every pluggable element +registered to the system https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/dotplot-view/src/extensionPoints.ts#L9-L43 @@ -61,10 +90,10 @@ https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6 type: synchronous -used to infer a track type given a location type from the "Add track -workflow" +used to infer a track type given a location type from the "Add track workflow" -example https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/alignments/src/index.ts#L108-L118 +example +https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/alignments/src/index.ts#L108-L118 ### Core-extendSession @@ -79,8 +108,8 @@ used to extend the session model itself with new features type: synchronous -- `config: Record` - a snapshot of a configuration object that is - displayed in the about dialog +- `config: Record` - a snapshot of a configuration object that + is displayed in the about dialog ### TrackSelector-multiTrackMenuItems @@ -89,15 +118,16 @@ type: synchronous used to add new menu items to the "shopping cart" in the header of the hierarchical track menu when tracks are added to the selection -example https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/wiggle/src/CreateMultiWiggleExtension/index.ts#L10-L67 +example +https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/wiggle/src/CreateMultiWiggleExtension/index.ts#L10-L67 ### LaunchView-LinearGenomeView type: async -launches a linear genome view given parameters. it is not common to -extend this extension point, but you can use it as an example to create a -LaunchView type for your own view +launches a linear genome view given parameters. it is not common to extend this +extension point, but you can use it as an example to create a LaunchView type +for your own view - `session: AbstractSessionModel` - instance of the session which you can call actions on @@ -125,15 +155,16 @@ https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6 type: async -launches a sv inspector with given parameters. it is not common to -extend this extension point, but you can use it as an example to create a -LaunchView type for your own view +launches a sv inspector with given parameters. it is not common to extend this +extension point, but you can use it as an example to create a LaunchView type +for your own view - `session: AbstractSessionModel` - instance of the session which you can call actions on - `assembly: string` - assembly name - `uri: string` - a url to load -- `fileType?: string` - type of file referred to by locstring (VCF|CSV|BEDPE, etc) +- `fileType?: string` - type of file referred to by locstring (VCF|CSV|BEDPE, + etc) https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/sv-inspector/src/index.ts#L21-L61 @@ -141,15 +172,16 @@ https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6 type: async -launches a sv inspector with given parameters. it is not common to -extend this extension point, but you can use it as an example to create a -LaunchView type for your own view +launches a sv inspector with given parameters. it is not common to extend this +extension point, but you can use it as an example to create a LaunchView type +for your own view - `session: AbstractSessionModel` - instance of the session which you can call actions on - `assembly: string` - assembly name - `uri: string` - a url to load -- `fileType?: string` - type of file referred to by locstring (VCF|CSV|BEDPE, etc) +- `fileType?: string` - type of file referred to by locstring (VCF|CSV|BEDPE, + etc) https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/spreadsheet-view/src/index.ts#L26-L59 @@ -157,13 +189,14 @@ https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6 type: async -launches a dotplot with given parameters. it is not common to -extend this extension point, but you can use it as an example to create a -LaunchView type for your own view +launches a dotplot with given parameters. it is not common to extend this +extension point, but you can use it as an example to create a LaunchView type +for your own view - `session: AbstractSessionModel` - instance of the session which you can call actions on -- `views: { loc: string; assembly: string; tracks?: string[] }[]` - view params for vertical and horizontal +- `views: { loc: string; assembly: string; tracks?: string[] }[]` - view params + for vertical and horizontal - `tracks: string[]` - trackIds to turn on https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/dotplot-view/src/LaunchDotplotView.ts#L7-L46 @@ -172,13 +205,14 @@ https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6 type: async -launches a linear synteny view with given parameters. it is not common to -extend this extension point, but you can use it as an example to create a -LaunchView type for your own view +launches a linear synteny view with given parameters. it is not common to extend +this extension point, but you can use it as an example to create a LaunchView +type for your own view - `session: AbstractSessionModel` - instance of the session which you can call actions on -- `views: { loc: string; assembly: string; tracks?: string[] }[]` - view params for vertical and horizontal +- `views: { loc: string; assembly: string; tracks?: string[] }[]` - view params + for vertical and horizontal - `tracks: string[]` - trackIds to turn on https://github.com/GMOD/jbrowse-components/blob/6ceeac51f8bcecfc3b0a99e23f2277a6e5a7662e/plugins/linear-comparative-view/src/LaunchLinearSyntenyView.ts#L9-L68 @@ -192,8 +226,7 @@ adds option to provide a different component for the "About this track" dialog - `session: AbstractSessionModel` - instance of the session which you can call - `config: AnyConfigurationModel` - a configuration object for the track -Return value: -The new React component you want to use +Return value: The new React component you want to use example: replaces about dialog for a particular track ID @@ -217,8 +250,8 @@ adds option to provide a different component for the "About this track" dialog - `session: AbstractSessionModel` - instance of the session which you can call - `config: AnyConfigurationModel` - a configuration object for the track -Return value: -An object with the name of the panel and the React component to use for the panel +Return value: An object with the name of the panel and the React component to +use for the panel example: adds an extra about dialog panel for a particular track ID @@ -237,11 +270,10 @@ pluginManager.addToExtensionPoint( type: synchronous -- `config: Record` a snapshot of a configuration object for - the track, with `formatAbout` already applied to it +- `config: Record` a snapshot of a configuration object for the + track, with `formatAbout` already applied to it -Return value: -New config snapshot object +Return value: New config snapshot object ### Core-replaceWidget @@ -255,8 +287,7 @@ adds option to provide a different component for the "About this track" dialog details may be a common one. See `Core-extraFeaturePanel` also, matches the model attribute from there -Return value: -The new React component you want to use +Return value: The new React component you want to use example: replaces about feature details widget for a particular track ID @@ -288,8 +319,8 @@ type: synchronous - `feature: Record` a snapshot of a feature object - `session: AbstractSessionModel` - instance of the session which you can call -Return value: -An object with the name of the panel and the React component to use for the panel +Return value: An object with the name of the panel and the React component to +use for the panel example diff --git a/website/docs/developer_guides/modifying_menu.md b/website/docs/developer_guides/modifying_menu.md index a77dd23371..fb0bba6d72 100644 --- a/website/docs/developer_guides/modifying_menu.md +++ b/website/docs/developer_guides/modifying_menu.md @@ -15,14 +15,13 @@ existing menus and sub-menus. Sub-menus can be arbitrarily deep.
    -You add menus in the `configure` method of your plugin. Not all JBrowse -products will have top-level menus, though. JBrowse Web and JBrowse Desktop -have them, but something like JBrowse Linear View (which is an just a single -view designed to be embedded in another page) does not. This means you need to -check whether or not menus are supported using `isAbstractMenuManager` in the -`configure` method. This way the rest of the plugin will still work if there is -not a menu. Here's an example that adds an "Open My View" item to the `Add` -menu. +You add menus in the `configure` method of your plugin. Not all JBrowse products +will have top-level menus, though. JBrowse Web and JBrowse Desktop have them, +but something like JBrowse Linear View (which is an just a single view designed +to be embedded in another page) does not. This means you need to check whether +or not menus are supported using `isAbstractMenuManager` in the `configure` +method. This way the rest of the plugin will still work if there is not a menu. +Here's an example that adds an "Open My View" item to the `Add` menu. ```js import Plugin from '@jbrowse/core/Plugin' @@ -50,8 +49,9 @@ class MyPlugin extends Plugin { } ``` -This example uses `rootModel.appendToMenu`. See [top-level menu -API](/docs/api_guide#rootmodel-menu-api) for more details on available functions. +This example uses `rootModel.appendToMenu`. See +[top-level menu API](/docs/api_guide#rootmodel-menu-api) for more details on +available functions. ### Adding menu items to a custom track @@ -76,9 +76,10 @@ types })) ``` -If you'd prefer to append your track menu items onto menu items available from the -base display, you can grab the `trackMenuItems` property from the extended model -and redefine trackMenuItems with your new Menu Item appended at the end, like so: +If you'd prefer to append your track menu items onto menu items available from +the base display, you can grab the `trackMenuItems` property from the extended +model and redefine trackMenuItems with your new Menu Item appended at the end, +like so: ```js types @@ -111,8 +112,8 @@ any menu items defined for it. It's possible to add items to that menu, and you can also have different menu items based on if the click was on a feature or not, and based on what feature -is clicked. This is done by extending the `contextMenuItems` view of the -display model. Here is an example: +is clicked. This is done by extending the `contextMenuItems` view of the display +model. Here is an example: ```js class SomePlugin extends Plugin { diff --git a/website/docs/developer_guides/pluggable_elements.md b/website/docs/developer_guides/pluggable_elements.md index 9857f9026a..8625c76b2b 100644 --- a/website/docs/developer_guides/pluggable_elements.md +++ b/website/docs/developer_guides/pluggable_elements.md @@ -18,20 +18,22 @@ the browser's `window` object specifically for JBrowse plugins. **This means it is only possible to have one version of a particular plugin loaded on any given webpage, even if multiple products are loaded and using it on the same page.** -It's common for a plugin to use its `configure` method to set up [mobx autoruns -or reactions](https://mobx.js.org/refguide/autorun.html) that react to changes -in the application's state to modify its behavior. +It's common for a plugin to use its `configure` method to set up +[mobx autoruns or reactions](https://mobx.js.org/refguide/autorun.html) that +react to changes in the application's state to modify its behavior. -Plugins often also have their `install` method add "pluggable elements" into -the host JBrowse application. This is how plugins can add new kinds of views, +Plugins often also have their `install` method add "pluggable elements" into the +host JBrowse application. This is how plugins can add new kinds of views, tracks, renderers, and so forth. -:::info Note -Many of the plugins referenced in the following section are found in [the -JBrowse Github repo](https://github.com/gmod/jbrowse-components). +:::info + +Many of the plugins referenced in the following section are found in +[the JBrowse Github repo](https://github.com/gmod/jbrowse-components). We encourage you to reference and review the concepts presented here using the functional and up-to-date plugin code found there. + ::: ## Pluggable elements @@ -53,9 +55,9 @@ Examples of pluggable types include: - Extension points - Add track workflow -In additional to creating plugins that create new adapters, track types, -etc. note that you can also wrap the behavior of another track so these -elements are composable. +In additional to creating plugins that create new adapters, track types, etc. +note that you can also wrap the behavior of another track so these elements are +composable. For example, we can have adapters that perform calculations on the results of another adapter, views that contains other subviews, and tracks that contain @@ -66,8 +68,8 @@ Let's dive further into these details, and look at some examples. ### View types Creating view types is one of the most powerful features of JBrowse 2, because -it allows us to put entirely different visualizations in the same context as -the standard linear-genome-view. +it allows us to put entirely different visualizations in the same context as the +standard linear-genome-view. We have demonstrated a couple new view types in JBrowse 2 already, including: @@ -83,38 +85,37 @@ be interplay between view types e.g. popup dotplot from a linear view, etc. ### Adapters -Adapters are parsers for a given data format. We will review -what adapters the alignments plugin has (to write your own adapter, -see [creating adapters](../pluggable_elements/#creating-adapters)). +Adapters are parsers for a given data format. We will review what adapters the +alignments plugin has (to write your own adapter, see +[creating adapters](../pluggable_elements/#creating-adapters)). -Example adapters: the `@jbrowse/plugin-alignments` plugin creates -multiple adapter types: +Example adapters: the `@jbrowse/plugin-alignments` plugin creates multiple +adapter types: -- `BamAdapter` - This adapter uses the `@gmod/bam` NPM module, and adapts it - for use by the browser. +- `BamAdapter` - This adapter uses the `@gmod/bam` NPM module, and adapts it for + use by the browser. - `CramAdapter` - This adapter uses the `@gmod/cram` NPM module. Note that CramAdapter also takes a sequenceAdapter as a subadapter configuration, and uses getSubAdapter to instantiate it -- `SNPCoverageAdapter` - this adapter takes a `BamAdapter` or `CramAdapter` as a - subadapter, and calculates feature coverage from it ### Track types Track types are a high level type that controls how features are drawn. In most -cases, a track combines a renderer and an adapter, and can do additional things like: +cases, a track combines a renderer and an adapter, and can do additional things +like: - Control what widget pops up on feature click - Add extra menu items to the track menu - Create subtracks (See `AlignmentsTrack`) -- Choose "static-blocks" rendering styles, which keeps contents stable while - the user scrolls, or "dynamic-blocks" that update on each scroll +- Choose "static-blocks" rendering styles, which keeps contents stable while the + user scrolls, or "dynamic-blocks" that update on each scroll -Example tracks: the `@jbrowse/plugin-alignments` exports multiple track -types: +Example tracks: the `@jbrowse/plugin-alignments` exports multiple track types: -- `SNPCoverageTrack` - this track type actually derives from the WiggleTrack type -- `PileupTrack` - a track type that draws alignment pileup results -- `AlignmentsTrack` - combines `SNPCoverageTrack` and `PileupTrack` as "subtracks" +- `VariantTrack` - displays variant features +- `FeatureTrack` - displays generic features including gene glyphs +- `AlignmentsTrack` - shows both a pileup or reads and the coverage as a + quantiative track ### Displays @@ -135,18 +136,18 @@ Another example of a track type with multiple display types is `VariantTrack`, which has two display methods - `LinearVariantDisplay` - used in linear genome view -- `ChordVariantDisplay` - used in the circular view to draw breakends and structural variants +- `ChordVariantDisplay` - used in the circular view to draw breakends and + structural variants ### Renderers Renderers are a new concept in JBrowse 2, and are related to the concept of server side rendering (SSR), but can be used not just on the server but also in contexts like the web worker (e.g. the webworker can draw the features to an -OffscreenCanvas). For more info see [creating -renderers](../pluggable_elements/#creating-renderers). +OffscreenCanvas). For more info see +[creating renderers](../pluggable_elements/#creating-renderers). -For example, the `@jbrowse/plugin-alignments` exports several -renderer types: +For example, the `@jbrowse/plugin-alignments` exports several renderer types: - `PileupRenderer` - a renderer type that renders Pileup type display of alignments fetched from the `BamAdapter`/`CramAdapter` @@ -154,13 +155,14 @@ renderer types: renderer derives from the wiggle renderer, but does the additional step of drawing the mismatches over the coverage track -:::info Views, tracks, displays, renderers? -If you're confused about what kind of pluggable element you might need to -accomplish your development goals, a way to remember the relationship between -these four pluggable elements is as follows: +:::info + +Views, tracks, displays, renderers? If you're confused about what kind of +pluggable element you might need to accomplish your development goals, a way to +remember the relationship between these four pluggable elements is as follows: -1. A view is a container for anything, views typically _have tracks_ (the - linear genome view especially) +1. A view is a container for anything, views typically _have tracks_ (the linear + genome view especially) 2. A track controls the _what_ (kind of data, data adapters used) and _how_ (displays, renderers) of the data you'd like to display, typically within a view @@ -187,12 +189,12 @@ Widgets can do multiple types of things, including: - etc. These widgets can be extended via plugins, so for example, the -`@jbrowse/plugin-alignments` extends the `BaseFeatureDetailWidget` to -have custom display of the alignments. +`@jbrowse/plugin-alignments` extends the `BaseFeatureDetailWidget` to have +custom display of the alignments. -- `AlignmentsFeatureDetailWidget` - this provides a custom widget - for viewing the feature details of alignments features that customizes the - basic feature detail widget +- `AlignmentsFeatureDetailWidget` - this provides a custom widget for viewing + the feature details of alignments features that customizes the basic feature + detail widget ### RPC methods @@ -208,100 +210,29 @@ These methods can run in the webworker when available. ### Add track workflows -Plugins can register their own React component to display in the "Add track" -widget for adding tracks that require custom logic. The Multi-wiggle track is -an example of this, it produces a textbox where you can paste a list of files. - -A simple addition to the add track workflow: - -```js -// plugins/wiggle/MultiWiggleAddTrackWidget/index.jsx - -import PluginManager from '@jbrowse/core/PluginManager' -import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes' -import { types } from 'mobx-state-tree' - -// locals -import MultiWiggleWidget from './AddTrackWorkflow' - -export default (pm: PluginManager) => { - pm.addAddTrackWorkflowType( - () => - new AddTrackWorkflowType({ - name: 'Multi-wiggle track', - /* in a separate file, export the react component to render within the track widget, - typically a form to collect relevant data for your track */ - ReactComponent: MultiWiggleWidget, - stateModel: types.model({}), - }), - ) -} -``` - -...and ensure you install this component into your larger plugin: - -```js -// plugins/wiggle/index.jsx +Add track workflows allow users to specify a custom react component for loading +tracks into a jbrowse session. -// ... - -export default class WigglePlugin extends Plugin { - name = 'WigglePlugin' - - install(pm: PluginManager) { - // ... - MultiWiggleAddTrackWidgetF(pm) - // ... - } -} -``` +Checkout the [docs here](/docs/developer_guides/creating_addtrack_workflow). ### Extension points Extension points are a pluggable element type which allows users to add a callback that is called at an appropriate time. -Checkout the [full extension point API](/docs/api_guide/#extension-points) or -an [example for adding context menu -items](/docs/developer_guides/pluggable_elements/#adding-track-context-menu-items) +Checkout the [full extension point API](/docs/developer_guides/extension_points) +or an +[example for adding context menu items](/docs/developer_guides/pluggable_elements/#adding-track-context-menu-items) for more detailed information. -The basic API is that producers can say: - -```js -const ret = pluginManager.evaluateExtensionPoint('ExtensionPointName', { - value: 1, -}) -``` - -And consumers can say: - -```js -pluginManager.addToExtensionPoint('ExtensionPointName', arg => { - return arg.value + 1 -}) - -pluginManager.addToExtensionPoint('ExtensionPointName', arg => { - return arg.value + 1 -}) -``` - -In this case, `arg` that is passed in evaluateExtensionPoint calls all the -callbacks that have been registered by `addToExtensionPoint`. If multiple -extension points are registered, the return value of the first extension point -is passed as the new argument to the second, and so on (they are chained -together). - -So in the example above, ret would be `{value:3}` after evaluating the -extension point. - ## Next steps Now that you have an overview of the different pluggable element types that are -available to you, review your [understanding of the configuration -model](../config_model). - -Also checkout the [guided -tutorial](/docs/tutorials/simple_plugin_tutorial/01_introduction) for writing a -plugin, which will take you through everything from installation, creating a -new pluggable element, and general development tips for working with JBrowse 2. +available to you, review your +[understanding of the configuration model](../config_model). + +Also checkout the +[guided tutorial](/docs/tutorials/simple_plugin_tutorial/01_introduction) for +writing a plugin, which will take you through everything from installation, +creating a new pluggable element, and general development tips for working with +JBrowse 2. diff --git a/website/docs/embedded_components.md b/website/docs/embedded_components.md index fae5e86986..7e55ab9ff3 100644 --- a/website/docs/embedded_components.md +++ b/website/docs/embedded_components.md @@ -19,13 +19,13 @@ This component consists of a single JBrowse 2 linear view. Here is a table of different usages of the `@jbrowse/react-linear-genome-view` using different bundlers -| Bundler | Demo | Source code | Note | -| ------------------- | ----------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| create-react-app v4 | [demo](https://jbrowse.org/demos/lgv/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view)) | no polyfills needed in create-react-app v4 | -| create-react-app v5 | [demo](https://jbrowse.org/demos/lgv-cra5/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view-cra5) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-cra5)) | for create-react-app v5, we use craco to update the webpack config to polyfill some node modules. This demo also uses webworkers, which is a unique ability with webpack 5. See https://jbrowse.org/storybook/lgv/main/?path=/story/linear-view--with-web-worker for details | -| vite | [demo](https://jbrowse.org/demos/lgv-vite) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view-vite) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vite)) | for vite, we use rollup to polyfill some node polyfills similar to craco in create-react-app v5. note, may not work with newly released vite 3.x, works in dev but fails in production so this example uses vite 2.x | -| next.js | [demo](https://jbrowse.org/demos/lgv-nextjs) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view-nextjs) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-nextjs)) | uses next.js 12. Also see next.config.js to update basePath as needed | -| vanilla js | [demo](https://jbrowse.org/demos/lgv-vanillajs) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-linear-genome-view-vanillajs) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vanillajs)) | uses a script tag to include a UMD bundle, and doesn't require any transpilation or bundling. see also dev tutorial here https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view/01_introduction/ | +| Bundler | Demo | Source code | Note | +| ------------------- | ----------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| create-react-app v4 | [demo](https://jbrowse.org/demos/lgv/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view)) | no polyfills needed in create-react-app v4. on newer versions of node, you can need to use `export NODE_OPTIONS=--openssl-legacy-provider` before building cra4 apps | +| create-react-app v5 | [demo](https://jbrowse.org/demos/lgv-cra5/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-cra5) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-cra5)) | for create-react-app v5, we use craco to update the webpack config to polyfill some node modules. This demo also uses webworkers, which is a unique ability with webpack 5. See https://jbrowse.org/storybook/lgv/main/?path=/story/linear-view--with-web-worker for details | +| vite | [demo](https://jbrowse.org/demos/lgv-vite) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-vite) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-vite)) | for vite, we use rollup to polyfill some node polyfills similar to craco in create-react-app v5. | +| next.js | [demo](https://jbrowse.org/demos/lgv-nextjs) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-nextjs) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-nextjs)) | uses next.js 13. Currently is hardcoded to use /demos/lgv-nextjs/ as sub-uri, update next.config.js to customize as needed | +| vanilla js | [demo](https://jbrowse.org/demos/lgv-vanillajs) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-vanillajs) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-vanillajs)) | uses a script tag to include a UMD bundle, and doesn't require any transpilation or bundling. see also dev tutorial here https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view/01_introduction/ | ## JBrowse React Circular Genome View @@ -33,13 +33,14 @@ This component consists of a single JBrowse 2 circular view. - [@jbrowse/react-circular-genome-view](https://www.npmjs.com/package/@jbrowse/react-circular-genome-view) circular genome view React component on NPM -- [Storybook](https://jbrowse.org/storybook/cgv/main/) - docs for the circular genome view React component +- [Storybook](https://jbrowse.org/storybook/cgv/main/) - docs for the circular + genome view React component -Here is a table of different usages of the -`@jbrowse/react-circular-genome-view` using different bundlers +Here is a table of different usages of the `@jbrowse/react-circular-genome-view` +using different bundlers -| Syntax | Demo | Source code | Note | -| ------------------- | ----------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------ | -| create-react-app v4 | [demo](https://jbrowse.org/demos/cgv/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view)) | no polyfills needed in create-react-app v4 | -| create-react-app v5 | [demo](https://jbrowse.org/demos/cgv-cra5/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view-cra5) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-cra5)) | for create-react-app v5, we use craco to update the webpack config to polyfill some node modules | -| vanilla js | [demo](https://jbrowse.org/demos/cgv-vanillajs) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view-vanillajs) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-vanillajs)) | uses a script tag to include a UMD bundle, and doesn't require any transpilation or bundling | +| Syntax | Demo | Source code | Note | +| ------------------- | ----------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| create-react-app v4 | [demo](https://jbrowse.org/demos/cgv/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-circular-genome-view)) | no polyfills needed in create-react-app v4. on newer versions of node, you can need to use `export NODE_OPTIONS=--openssl-legacy-provider` before building cra4 apps | +| create-react-app v5 | [demo](https://jbrowse.org/demos/cgv-cra5/) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view-cra5) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-circular-genome-view-cra5)) | for create-react-app v5, we use craco to update the webpack config to polyfill some node modules | +| vanilla js | [demo](https://jbrowse.org/demos/cgv-vanillajs) | [source code](https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view-vanillajs) ([download](https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-circular-genome-view-vanillajs)) | uses a script tag to include a UMD bundle, and doesn't require any transpilation or bundling | diff --git a/website/docs/faq.md b/website/docs/faq.md index bec62e90e2..0579aaa0b7 100644 --- a/website/docs/faq.md +++ b/website/docs/faq.md @@ -37,7 +37,8 @@ on desktop. For the embedded components e.g. `products/jbrowse-react-linear-genome-view`, use `yarn storybook` instead of `yarn start`. -For a more extensive tutorial, see [Developing with JBrowse web and desktop](../tutorials/develop_web_and_desktop_tutorial). +For a more extensive tutorial, see +[Developing with JBrowse web and desktop](../tutorials/develop_web_and_desktop_tutorial). ## General @@ -68,21 +69,20 @@ If you use a different platform such as Django, you may want to put it in the static resources folder. Note that the server that you use should support byte-range requests (e.g. the -[Range HTTP -header](https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Range) so -that JBrowse can get small slices of large binary data files. +[Range HTTP header](https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Range) +so that JBrowse can get small slices of large binary data files. ### BAM files do not work on my server If you are using Apache then you will probably want to disable mime_magic. If mime_magic is enabled, you may see that your server responds with the HTTP header Content-Encoding: gzip which JBrowse does NOT want, because this -instructs the browser to unzip the data but JBrowse should be in charge of -this. +instructs the browser to unzip the data but JBrowse should be in charge of this. ### How can I setup JBrowse 2 on my web server -We recommend following the steps in the [quickstart web via CLI](../quickstart_cli/) guide. +We recommend following the steps in the +[quickstart web via CLI](../quickstart_web/) guide. The general procedure is using the `jbrowse create /var/www/html/jb2` and this will download the latest version of jbrowse to your web folder e.g. in @@ -103,6 +103,14 @@ using nodesource or nvm to get your nodejs for this. Also note that the @jbrowse/cli tool is just made for preparing your config.json, it is **not used to run any server-side code**. +### How can I make a header on a jbrowse-web instance + +You can edit the index.html that comes with jbrowse-web to have custom contents. +The jbrowse-web app just looks at the div that it renders into, but any contents +outside of that you can edit for custom purposes. If you need more advanced +embedding, you can consider @jbrowse/react-linear-genome-view or similar, but +the jbrowse-web app is not available as an npm installable package yet. + ### How do I update my instance of jbrowse-web You can use the command, after installing: @@ -114,7 +122,8 @@ jbrowse upgrade /path/to/your/jbrowse2 This will download the latest release from github and overwrite it onto your jbrowse-web instance. -If you've manually downloaded jbrowse-web, the newest releases can be found [here](https://github.com/GMOD/jbrowse-components/releases). +If you've manually downloaded jbrowse-web, the newest releases can be found +[here](https://github.com/GMOD/jbrowse-components/releases). ### How can I setup JBrowse 2 without the CLI tools @@ -123,9 +132,10 @@ required. Simple tasks can be done without it. -For example, for jbrowse create, you can visit the [releases -page](https://github.com/GMOD/jbrowse-components/releases) and download the -latest jbrowse-web release tag, and unzip it into your web directory. +For example, for jbrowse create, you can visit the +[releases page](https://github.com/GMOD/jbrowse-components/releases) and +download the latest jbrowse-web release tag, and unzip it into your web +directory. Checkout our [quickstart web](../quickstart_web/) guide for a speedy start to using a manually downloaded JBrowse instance. @@ -181,14 +191,15 @@ An example of a Jexl configuration callback might look like this: "color": "jexl:get(feature,'strand')==-1?'red':'blue'" ``` -See our [configuration callbacks guide](/docs/config_guides/jexl) for more information. +See our [configuration callbacks guide](/docs/config_guides/jexl) for more +information. ### My jexl is too complicated, how can I simplify it? You can create a small plugin that adds a new function to the jexl language. -See [here](../config_guide/#making-sophisticated-color-callbacks) for an example -of making a color callback. +See [here](/docs/config_guides/customizing_feature_colors/) for an example of +making a color callback. ### Adding color callbacks in the GUI @@ -215,13 +226,13 @@ In brief, to add a configuration callback to a track using the CLI, your `add-track` is going to look something like this: ```bash -jbrowse add-track somevariants.vcf --load copy --config '{"displays": [{"displayId": "my_BasicDisplay", "type": "LinearBasicDisplay", "renderer": {"color1": "jexl:get(feature, 'strand') == -1 ? 'red' : 'blue'" }}]}' +jbrowse add-track somevariants.vcf --load copy --config '{"displays": [{"displayId": "my_BasicDisplay", "type": "LinearBasicDisplay", "renderer": {"color1": "jexl:get(feature, '\''strand'\'') == -1 ? '\''red'\'' : '\''blue'\''" }}]}' ``` While adding the track to the `config.json`, you're adding additional configurations using the --config option. This additional configuration is a -"renderer" on the display that your track will be using. In this case, this -.vcf will be using the `LinearBasicDisplay`. +"renderer" on the display that your track will be using. In this case, this .vcf +will be using the `LinearBasicDisplay`. ## Curiosities @@ -236,8 +247,8 @@ where it knows which genome assembly you are working with at any given time. In JBrowse 1, the app level menu operated on the single linear genome view, but with JBrowse 2, the top level menu only performs global operations and the -linear genome view has its own hamburger menu. Note that each track also has -its own track level menu. +linear genome view has its own hamburger menu. Note that each track also has its +own track level menu. ### Why do some of my reads not display soft clipping @@ -248,7 +259,8 @@ The soft clipping indicators on these reads will appear black. ### Do you have any tips for learning React and mobx-state-tree -Here is a short guide to React and mobx-state-tree that could help get you oriented: +Here is a short guide to React and mobx-state-tree that could help get you +oriented: https://gist.github.com/cmdcolin/94d1cbc285e6319cc3af4b9a8556f03f @@ -266,31 +278,33 @@ We build on a lot of great open source technology, some main ones include: Yes! JBrowse 2 may load ~5MB of JS resources (2.5MB for main thread bundle, 2.5MB for worker bundle). If you have gzip enabled, the amount of data the user -has to download though is only 1.4MB. We have worked on making bundle size -small with lazy loading and other methods but adding gzip will help your users. +has to download though is only 1.4MB. We have worked on making bundle size small +with lazy loading and other methods but adding gzip will help your users. It will depend on your particular server setup e.g. apache, nginx, cloudfront, etc. how this may be done, but it is recommended to look into this. ### How does JBrowse know when to display the "Zoom in to see more features" message -The rules that JBrowse uses to determine when to display the "Zoom in to see more features" message are called stats estimation rules +The rules that JBrowse uses to determine when to display the "Zoom in to see +more features" message are called stats estimation rules The general outline is: - It doesn't display a zoom in message if zoomed in closer than 20kb - It performs byte size estimation for BAM and CRAM type files (you will see a - byte size estimation displayed alongside the "Zoom in to see features" - message -- Other data types that don't use byte size estimation use feature density - based calculation -- Hi-C, BigWig, and sequence adapters are hardcoded to return `{ featureDensity:0 }` to always render + byte size estimation displayed alongside the "Zoom in to see features" message +- Other data types that don't use byte size estimation use feature density based + calculation +- Hi-C, BigWig, and sequence adapters are hardcoded to return + `{ featureDensity:0 }` to always render If you need to customize your particular track, you can set config variables on the "display" section of your config - `maxFeatureScreenDensity` - number of features times bpPerPx -- `fetchSizeLimit` - this config variable exists on the adapters (can increase size limit) +- `fetchSizeLimit` - this config variable exists on the adapters (can increase + size limit) Example config with a small feature screen density: @@ -361,9 +375,9 @@ alternative temporary directory using the environment variable The `jbrowse text-index` command creates text searching indexes using trix. The trix indexes are based on the format described by UCSC here -https://genome.ucsc.edu/goldenPath/help/trix.html, but we re-implemented the code -the create these index formats in the JBrowse CLI so you do not have to install -the UCSC tools. +https://genome.ucsc.edu/goldenPath/help/trix.html, but we re-implemented the +code the create these index formats in the JBrowse CLI so you do not have to +install the UCSC tools. The main idea is that you give trix: @@ -381,31 +395,31 @@ Pax6 GENE002 Wnt GENE001 ``` -Then a second file, the .ixx file, tells us at what byte offset certain lines -in the file are e.g.: +Then a second file, the .ixx file, tells us at what byte offset certain lines in +the file are e.g.: ``` signa000000435 ``` Note that JBrowse creates a specialized trix index also. Instead of creating a -ix file with just the gene names, it also provides their name and location in -an encoded format. +ix file with just the gene names, it also provides their name and location in an +encoded format. ## URL params ### Why can't I copy and paste my URL bar to share it with another user -In JBrowse Web, the current session can become too long to store in the URL -bar, so instead, we store it in localStorage and only keep the key to the +In JBrowse Web, the current session can become too long to store in the URL bar, +so instead, we store it in localStorage and only keep the key to the localStorage entry in the URL var. This is because otherwise URLs can get -prohibitively long, and break server side navigations, intermediate caches, -etc. Therefore, we make "sharing a session" a manual step that generates a -shortened URL by default. +prohibitively long, and break server side navigations, intermediate caches, etc. +Therefore, we make "sharing a session" a manual step that generates a shortened +URL by default. -Note 1: users of @jbrowse/react-linear-genome-view have to re-implement any -URL query param logic themselves, as this component makes no attempt to access -URL query params. +Note 1: users of @jbrowse/react-linear-genome-view have to re-implement any URL +query param logic themselves, as this component makes no attempt to access URL +query params. Note 2: You can copy and paste your URL bar and put it in another tab on your own computer, and JBrowse will restore the session using BroadcastChannel @@ -423,9 +437,9 @@ This process, generates a URL with the format: &session=share-<DYNAMODBID>&password=<DECODEKEY> -The DECODEKEY is never transmitted to the server, but you can copy and paste -the share URL, the person you shared automatically downloads the DynamoDB -entry, and decodes it with the DECODEKEY from the URL that you provide +The DECODEKEY is never transmitted to the server, but you can copy and paste the +share URL, the person you shared automatically downloads the DynamoDB entry, and +decodes it with the DECODEKEY from the URL that you provide With this system, the contents of the dynamoDB are safe and unable to be read, even by JBrowse administrators. diff --git a/website/docs/introduction.md b/website/docs/introduction.md index 25873c4bfb..66d586e565 100644 --- a/website/docs/introduction.md +++ b/website/docs/introduction.md @@ -7,12 +7,12 @@ toplevel: true Welcome to the JBrowse 2 documentation. -- [Quick start for JBrowse desktop](quickstart_desktop) - a quick start guide - to getting JBrowse desktop running on your machine -- [Quick start for JBrowse web](quickstart_web) - a quick start guide to - running JBrowse 2 in a browser -- [Quick start for JBrowse web via CLI](quickstart_cli) - a quick start guide - to intalling the JBrowse 2 CLI and getting JBrowse web running locally on a +- [Quick start for JBrowse desktop](quickstart_desktop) - a quick start guide to + getting JBrowse desktop running on your machine +- [Quick start for JBrowse web](quickstart_web) - a quick start guide to running + JBrowse 2 in a browser +- [Quick start for JBrowse web via CLI](quickstart_web) - a quick start guide to + installing the JBrowse 2 CLI and getting JBrowse web running locally on a browser ### User and developer guides @@ -24,16 +24,15 @@ Welcome to the JBrowse 2 documentation. #### Tutorials -- [Config editing via graphical interface](./tutorials/config_gui) - a guide - for configuring JBrowse via the GUI +- [Config editing via graphical interface](./tutorials/config_gui) - a guide for + configuring JBrowse via the GUI - [Config editing via command-line interface](./tutorials/config_cli) - a guide for configuring JBrowse via CLI -- [Writing a simple plugin for JBrowse - 2](./tutorials/simple_plugin_tutorial/01_introduction/) -- [Developing with JBrowse web and - desktop](./tutorials/develop_web_and_desktop_tutorial/) +- [Writing a simple plugin for JBrowse 2](./tutorials/simple_plugin_tutorial/01_introduction/) +- [Developing with JBrowse web and desktop](./tutorials/develop_web_and_desktop_tutorial/) -...and more! Use the left panel to browse some of the other guide docs available. +...and more! Use the left panel to browse some of the other guide docs +available. ### Other resources @@ -44,8 +43,10 @@ Welcome to the JBrowse 2 documentation. command line image generator - [Embedded components, JBrowseR, and JBrowse Jupyter](embedded_components) - docs for our reusable React components -- [JBrowseR](https://gmod.github.io/JBrowseR/) - docs for our R htmlwidget usable in Shiny apps -- [JBrowse Jupyter](https://gmod.github.io/jbrowse-jupyter/docs/html/index.html) - docs for our Python dash component usable in Jupyter +- [JBrowseR](https://gmod.github.io/JBrowseR/) - docs for our R htmlwidget + usable in Shiny apps +- [JBrowse Jupyter](https://gmod.github.io/jbrowse-jupyter/docs/html/index.html) - + docs for our Python dash component usable in Jupyter ### PDF download diff --git a/website/docs/jbrowse_jupyter.md b/website/docs/jbrowse_jupyter.md index 860ecf8731..41ccfc7ccf 100644 --- a/website/docs/jbrowse_jupyter.md +++ b/website/docs/jbrowse_jupyter.md @@ -6,5 +6,5 @@ title: JBrowse Jupyter Comprehensive documentation for JBrowse Jupyter is found off-site, [here](https://gmod.github.io/jbrowse-jupyter/docs/html/index.html). -Also check out the JBrowse Jupyter [GitHub -repo](https://github.com/GMOD/jbrowse-jupyter). +Also check out the JBrowse Jupyter +[GitHub repo](https://github.com/GMOD/jbrowse-jupyter). diff --git a/website/docs/jbrowser.md b/website/docs/jbrowser.md index 69e923e631..8d062c979e 100644 --- a/website/docs/jbrowser.md +++ b/website/docs/jbrowser.md @@ -6,5 +6,5 @@ id: jbrowser Comprehensive documentation for JBrowseR is found off-site, [here](https://gmod.github.io/JBrowseR/). -Also check out the JBrowse Jupyter [GitHub -repo](https://github.com/GMOD/JBrowseR/). +Also check out the JBrowse Jupyter +[GitHub repo](https://github.com/GMOD/JBrowseR/). diff --git a/website/docs/links.js b/website/docs/links.js new file mode 100644 index 0000000000..7ebc1a531a --- /dev/null +++ b/website/docs/links.js @@ -0,0 +1,15 @@ +import config from '../docusaurus.config.json' + +const ver = `${config.customFields.currentVersion}` + +const baseURL = `https://github.com/GMOD/jbrowse-components/releases/download` + +const baseVer = `${baseURL}/${ver}` + +const winDL = `${baseVer}/jbrowse-desktop-${ver}-win.exe` + +const macDL = `${baseVer}/jbrowse-desktop-${ver}-mac.dmg` + +const linDL = `${baseVer}/jbrowse-desktop-${ver}-linux.AppImage` + +export { linDL, macDL, winDL } diff --git a/website/docs/md_parser.js b/website/docs/md_parser.js index 87a9b6c793..5916f769bf 100755 --- a/website/docs/md_parser.js +++ b/website/docs/md_parser.js @@ -9,6 +9,7 @@ let readingHeader = false let title = '' let topLevel = false +// eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { for await (const line of rl) { if (line.startsWith('import Figure')) { diff --git a/website/docs/models/Base1DView.md b/website/docs/models/Base1DView.md new file mode 100644 index 0000000000..7dacacb8ad --- /dev/null +++ b/website/docs/models/Base1DView.md @@ -0,0 +1,264 @@ +--- +id: base1dview +title: Base1DView +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +used in non-lgv view representations of a 1d view e.g. the two axes of the +dotplot use this + +### Base1DView - Properties + +#### property: id + +```js +// type signature +IOptionalIType, [undefined]> +// code +id: ElementId +``` + +#### property: displayedRegions + +```js +// type signature +IArrayType; start: ISimpleType; end: ISimpleType; reversed: IOptionalIType, [...]>; } & { ...; }, { ...; }, _NotCustomized, _NotCustomized>> +// code +displayedRegions: types.array(Region) +``` + +#### property: bpPerPx + +```js +// type signature +number +// code +bpPerPx: 0 +``` + +#### property: offsetPx + +```js +// type signature +number +// code +offsetPx: 0 +``` + +#### property: interRegionPaddingWidth + +```js +// type signature +IOptionalIType, [undefined]> +// code +interRegionPaddingWidth: types.optional(types.number, 0) +``` + +#### property: minimumBlockWidth + +```js +// type signature +IOptionalIType, [undefined]> +// code +minimumBlockWidth: types.optional(types.number, 0) +``` + +### Base1DView - Getters + +#### getter: width + +```js +// type +number +``` + +#### getter: assemblyNames + +```js +// type +any[] +``` + +#### getter: displayedRegionsTotalPx + +```js +// type +number +``` + +#### getter: maxOffset + +```js +// type +number +``` + +#### getter: minOffset + +```js +// type +number +``` + +#### getter: totalBp + +```js +// type +number +``` + +#### getter: dynamicBlocks + +```js +// type +BlockSet +``` + +#### getter: staticBlocks + +```js +// type +BlockSet +``` + +#### getter: currBp + +```js +// type +any +``` + +### Base1DView - Methods + +#### method: pxToBp + +```js +// type signature +pxToBp: (px: number) => { + coord: number + index: number + refName: string + oob: boolean + assemblyName: string + offset: number + start: number + end: number + reversed: boolean +} +``` + +#### method: bpToPx + +```js +// type signature +bpToPx: ({ + refName, + coord, + regionNumber, +}: { + refName: string, + coord: number, + regionNumber?: number, +}) => number +``` + +### Base1DView - Actions + +#### action: setDisplayedRegions + +```js +// type signature +setDisplayedRegions: (regions: Region[]) => void +``` + +#### action: setBpPerPx + +```js +// type signature +setBpPerPx: (val: number) => void +``` + +#### action: setVolatileWidth + +```js +// type signature +setVolatileWidth: (width: number) => void +``` + +#### action: setFeatures + +```js +// type signature +setFeatures: (features: Feature[]) => void +``` + +#### action: showAllRegions + +this makes a zoomed out view that shows all displayedRegions that makes the +overview bar square with the scale bar + +```js +// type signature +showAllRegions: () => void +``` + +#### action: zoomOut + +```js +// type signature +zoomOut: () => void +``` + +#### action: zoomIn + +```js +// type signature +zoomIn: () => void +``` + +#### action: zoomTo + +```js +// type signature +zoomTo: (newBpPerPx: number, offset?: number) => number +``` + +#### action: scrollTo + +```js +// type signature +scrollTo: (offsetPx: number) => number +``` + +#### action: centerAt + +```js +// type signature +centerAt: (coord: number, refName: string, regionNumber: number) => void +``` + +#### action: scroll + +note: the scroll is clamped to keep the view on the main screen + +```js +// type signature +scroll: (distance: number) => number +``` + +#### action: moveTo + +offset is the base-pair-offset in the displayed region, index is the index of +the displayed region in the linear genome view + +```js +// type signature +moveTo: (start?: BpOffset, end?: BpOffset) => void +``` diff --git a/website/docs/models/BaseChordDisplay.md b/website/docs/models/BaseChordDisplay.md index ea5d20f660..aa57a185fe 100644 --- a/website/docs/models/BaseChordDisplay.md +++ b/website/docs/models/BaseChordDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs extends `BaseDisplay` @@ -41,8 +44,7 @@ any #### getter: rendererType -the pluggable element type object for this diplay's -renderer +the pluggable element type object for this display's renderer ```js // type @@ -51,8 +53,8 @@ RendererType #### getter: selectedFeatureId -returns a string feature ID if the globally-selected object -is probably a feature +returns a string feature ID if the globally-selected object is probably a +feature ```js // type @@ -95,7 +97,7 @@ renderStarted: () => void ```js // type signature -renderSuccess: ({ message, data, reactElement, renderingComponent, }: { message: string; data: any; reactElement: React.ReactElement; renderingComponent: React.ComponentType; }) => void +renderSuccess: ({ message, data, reactElement, html, renderingComponent, }: { message: string; data: any; html: string; reactElement: React.ReactElement; renderingComponent: React.ComponentType; }) => void ``` #### action: renderError diff --git a/website/docs/models/BaseConnectionModel.md b/website/docs/models/BaseConnectionModel.md new file mode 100644 index 0000000000..1d11d21066 --- /dev/null +++ b/website/docs/models/BaseConnectionModel.md @@ -0,0 +1,66 @@ +--- +id: baseconnectionmodel +title: BaseConnectionModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +### BaseConnectionModel - Properties + +#### property: name + +```js +// type signature +ISimpleType +// code +name: types.identifier +``` + +#### property: tracks + +```js +// type signature +IArrayType +// code +tracks: types.array(pluginManager.pluggableConfigSchemaType('track')) +``` + +### BaseConnectionModel - Actions + +#### action: addTrackConf + +```js +// type signature +addTrackConf: ( + trackConf: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, +) => any +``` + +#### action: addTrackConfs + +```js +// type signature +addTrackConfs: (trackConfs: ({ [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode)[]) => any[] +``` + +#### action: setTrackConfs + +```js +// type signature +setTrackConfs: (trackConfs: ({ [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode)[]) => IMSTArray<...> & IStateTreeNode<...> +``` + +#### action: clear + +```js +// type signature +clear: () => void +``` diff --git a/website/docs/models/BaseDisplay.md b/website/docs/models/BaseDisplay.md index 4626b9d29f..f5618b96a1 100644 --- a/website/docs/models/BaseDisplay.md +++ b/website/docs/models/BaseDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs ### BaseDisplay - Properties @@ -69,8 +72,7 @@ any #### getter: rendererType -the pluggable element type object for this display's -renderer +the pluggable element type object for this display's renderer ```js // type @@ -79,8 +81,8 @@ RendererType #### getter: DisplayMessageComponent -if a display-level message should be displayed instead, -make this return a react component +if a display-level message should be displayed instead, make this return a react +component ```js // type @@ -98,8 +100,8 @@ MenuItem[] #### method: renderProps -the react props that are passed to the Renderer when data -is rendered in this display +the react props that are passed to the Renderer when data is rendered in this +display ```js // type signature diff --git a/website/docs/models/BaseInternetAccountModel.md b/website/docs/models/BaseInternetAccountModel.md new file mode 100644 index 0000000000..dba845c41e --- /dev/null +++ b/website/docs/models/BaseInternetAccountModel.md @@ -0,0 +1,219 @@ +--- +id: baseinternetaccountmodel +title: BaseInternetAccountModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +### BaseInternetAccountModel - Properties + +#### property: id + +```js +// type signature +IOptionalIType, [undefined]> +// code +id: ElementId +``` + +#### property: type + +```js +// type signature +ISimpleType +// code +type: types.string +``` + +### BaseInternetAccountModel - Getters + +#### getter: name + +```js +// type +string +``` + +#### getter: description + +```js +// type +string +``` + +#### getter: internetAccountId + +```js +// type +string +``` + +#### getter: authHeader + +```js +// type +string +``` + +#### getter: tokenType + +```js +// type +string +``` + +#### getter: domains + +```js +// type +string[] +``` + +#### getter: toggleContents + +Can use this to customize what is displayed in fileSelector's toggle box + +```js +// type +React.ReactNode +``` + +#### getter: SelectorComponent + +Can use this to customize what the fileSelector. It takes a prop called +`setLocation` that should be used to set a UriLocation + +```js +// type +any +``` + +#### getter: selectorLabel + +Can use this to add a label to the UrlChooser. Has no effect if a custom +SelectorComponent is supplied + +```js +// type +string +``` + +#### getter: tokenKey + +The key used to store this internetAccount's token in sessionStorage + +```js +// type +string +``` + +### BaseInternetAccountModel - Methods + +#### method: handlesLocation + +Determine whether this internetAccount provides credentials for a URL + +```js +// type signature +handlesLocation: (location: UriLocation) => boolean +``` + +### BaseInternetAccountModel - Actions + +#### action: getTokenFromUser + +Must be implemented by a model extending or composing this one. Pass the user's +token to `resolve`. + +```js +// type signature +getTokenFromUser: (resolve: (token: string) => void, reject: (error: Error) => void) => void +``` + +#### action: storeToken + +```js +// type signature +storeToken: (token: string) => void +``` + +#### action: removeToken + +```js +// type signature +removeToken: () => void +``` + +#### action: retrieveToken + +```js +// type signature +retrieveToken: () => string +``` + +#### action: validateToken + +This can be used by an internetAccount to validate a token works before it is +used. This is run when preAuthorizationInformation is requested, so it can be +used to check that a token is valid before sending it to a worker thread. It +expects the token to be returned so that this action can also be used to +generate a new token (e.g. by using a refresh token) if the original one was +invalid. Should throw an error if a token is invalid. + +```js +// type signature +validateToken: (token: string, loc: UriLocation) => Promise +``` + +#### action: getToken + +Try to get the token from the location pre-auth, from local storage, or from a +previously cached promise. If token is not available, uses `getTokenFromUser`. + +```js +// type signature +getToken: (location?: UriLocation) => Promise +``` + +#### action: addAuthHeaderToInit + +```js +// type signature +addAuthHeaderToInit: (init: RequestInit, token: string) => { headers: Headers; body?: BodyInit; cache?: RequestCache; credentials?: RequestCredentials; ... 8 more ...; window?: null; } +``` + +#### action: getPreAuthorizationInformation + +Gets the token and returns it along with the information needed to create a new +internetAccount. + +```js +// type signature +getPreAuthorizationInformation: (location: UriLocation) => Promise<{ internetAccountType: string; authInfo: { token: string; configuration: any; }; }> +``` + +#### action: getFetcher + +Get a fetch method that will add any needed authentication headers to the +request before sending it. If location is provided, it will be checked to see if +it includes a token in it pre-auth information. + +```js +// type signature +getFetcher: (loc?: UriLocation) => (input: RequestInfo, init?: RequestInit) => Promise +``` + +#### action: openLocation + +Gets a filehandle that uses a fetch that adds auth headers + +```js +// type signature +openLocation: (location: UriLocation) => RemoteFileWithRangeCache +``` diff --git a/website/docs/models/BaseLinearDisplay.md b/website/docs/models/BaseLinearDisplay.md index 2f60f13f9c..4bdcc9fd12 100644 --- a/website/docs/models/BaseLinearDisplay.md +++ b/website/docs/models/BaseLinearDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs extends `BaseDisplay` @@ -75,8 +78,8 @@ any #### getter: renderDelay -how many milliseconds to wait for the display to -"settle" before re-rendering a block +how many milliseconds to wait for the display to "settle" before re-rendering a +block ```js // type @@ -92,8 +95,8 @@ React.FC #### getter: selectedFeatureId -returns a string feature ID if the globally-selected object -is probably a feature +returns a string feature ID if the globally-selected object is probably a +feature ```js // type @@ -102,8 +105,8 @@ string #### getter: DisplayMessageComponent -if a display-level message should be displayed instead of the blocks, -make this return a react component +if a display-level message should be displayed instead of the blocks, make this +return a react component ```js // type @@ -112,8 +115,8 @@ any #### getter: features -a CompositeMap of `featureId -> feature obj` that -just looks in all the block data for that feature +a CompositeMap of `featureId -> feature obj` that just looks in all the block +data for that feature ```js // type @@ -189,7 +192,8 @@ region is too large if: - stats are ready - region is greater than 20kb (don't warn when zoomed in less than that) -- and bytes is greater than max allowed bytes or density greater than max density +- and bytes is greater than max allowed bytes or density greater than max + density ```js // type @@ -198,8 +202,8 @@ boolean #### getter: regionTooLargeReason -only shows a message of bytes requested is defined, the feature density -based stats don't produce any helpful message besides to zoom in +only shows a message of bytes requested is defined, the feature density based +stats don't produce any helpful message besides to zoom in ```js // type diff --git a/website/docs/models/BaseTrackModel.md b/website/docs/models/BaseTrackModel.md new file mode 100644 index 0000000000..5e03f7e5e5 --- /dev/null +++ b/website/docs/models/BaseTrackModel.md @@ -0,0 +1,155 @@ +--- +id: basetrackmodel +title: BaseTrackModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +these MST models only exist for tracks that are _shown_. they should contain +only UI state for the track, and have a reference to a track configuration. note +that multiple displayed tracks could use the same configuration. + +### BaseTrackModel - Properties + +#### property: id + +```js +// type signature +IOptionalIType, [undefined]> +// code +id: ElementId +``` + +#### property: type + +```js +// type signature +ISimpleType +// code +type: types.literal(trackType) +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(baseTrackConfig) +``` + +#### property: minimized + +```js +// type signature +false +// code +minimized: false +``` + +#### property: displays + +```js +// type signature +IArrayType +// code +displays: types.array(pm.pluggableMstType('display', 'stateModel')) +``` + +### BaseTrackModel - Getters + +#### getter: rpcSessionId + +determines which webworker to send the track to, currently based on trackId + +```js +// type +any +``` + +#### getter: name + +```js +// type +any +``` + +#### getter: textSearchAdapter + +```js +// type +any +``` + +#### getter: adapterType + +```js +// type +AdapterType +``` + +#### getter: viewMenuActions + +```js +// type +MenuItem[] +``` + +#### getter: canConfigure + +```js +// type +any +``` + +### BaseTrackModel - Methods + +#### method: trackMenuItems + +```js +// type signature +trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; })[] +``` + +### BaseTrackModel - Actions + +#### action: setMinimized + +```js +// type signature +setMinimized: (flag: boolean) => void +``` + +#### action: activateConfigurationUI + +```js +// type signature +activateConfigurationUI: () => void +``` + +#### action: showDisplay + +```js +// type signature +showDisplay: (displayId: string, initialSnapshot?: {}) => void +``` + +#### action: hideDisplay + +```js +// type signature +hideDisplay: (displayId: string) => number +``` + +#### action: replaceDisplay + +```js +// type signature +replaceDisplay: (oldId: string, newId: string, initialSnapshot?: {}) => void +``` diff --git a/website/docs/models/BaseViewModel.md b/website/docs/models/BaseViewModel.md new file mode 100644 index 0000000000..e9c2c059e3 --- /dev/null +++ b/website/docs/models/BaseViewModel.md @@ -0,0 +1,84 @@ +--- +id: baseviewmodel +title: BaseViewModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +### BaseViewModel - Properties + +#### property: id + +```js +// type signature +IOptionalIType, [undefined]> +// code +id: ElementId +``` + +#### property: displayName + +displayName is displayed in the header of the view, or assembly names being used +if none is specified + +```js +// type signature +IMaybe> +// code +displayName: types.maybe(types.string) +``` + +#### property: minimized + +```js +// type signature +false +// code +minimized: false +``` + +### BaseViewModel - Getters + +#### getter: menuItems + +```js +// type +() => MenuItem[] +``` + +### BaseViewModel - Actions + +#### action: setDisplayName + +```js +// type signature +setDisplayName: (name: string) => void +``` + +#### action: setWidth + +width is an important attribute of the view model, when it becomes set, it often +indicates when the app can start drawing to it. certain views like lgv are +strict about this because if it tries to draw before it knows the width it +should draw to, it may start fetching data for regions it doesn't need to + +setWidth is updated by a ResizeObserver generally, the views often need to know +how wide they are to properly draw genomic regions + +```js +// type signature +setWidth: (newWidth: number) => void +``` + +#### action: setMinimized + +```js +// type signature +setMinimized: (flag: boolean) => void +``` diff --git a/website/docs/models/CircularView.md b/website/docs/models/CircularView.md index bf18aa9004..917cbdc45d 100644 --- a/website/docs/models/CircularView.md +++ b/website/docs/models/CircularView.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs extends `BaseViewModel` @@ -38,7 +41,7 @@ offsetRadians: -Math.PI / 2 // type signature number // code -bpPerPx: 2000000 +bpPerPx: 200 ``` #### property: tracks @@ -129,6 +132,13 @@ scrollY: 0 ### CircularView - Getters +#### getter: width + +```js +// type +number +``` + #### getter: staticSlices ```js @@ -253,12 +263,12 @@ any #### getter: elidedRegions -this is displayedRegions, post-processed to -elide regions that are too small to see reasonably +this is displayedRegions, post-processed to elide regions that are too small to +see reasonably ```js // type -any[] +({ elided: true; widthBp: number; regions: Region[]; } | { elided: false; widthBp: number; start: number; end: number; refName: string; })[] ``` #### getter: assemblyNames diff --git a/website/docs/models/DotplotDisplay.md b/website/docs/models/DotplotDisplay.md index 9dd23ddbc4..03f7f7a83e 100644 --- a/website/docs/models/DotplotDisplay.md +++ b/website/docs/models/DotplotDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs ### DotplotDisplay - Properties diff --git a/website/docs/models/DotplotView.md b/website/docs/models/DotplotView.md index 3e4546f1e2..27de6c8257 100644 --- a/website/docs/models/DotplotView.md +++ b/website/docs/models/DotplotView.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs ### DotplotView - Properties @@ -140,7 +143,7 @@ cursorMode: 'crosshair' ```js // type signature -IArrayType, [undefined]>; type: ISimpleType; configuration: ITypeUnion; displays: IArrayType<...>; }, { ...; } & ... 1 more ... & { ...; }, _NotCustomized, _NotCustomized>> +IArrayType, [undefined]>; type: ISimpleType; configuration: ITypeUnion; minimized: IType<...>; displays: IArrayType<...>; }, { ...; } & ... 1 more ... & { ...; }, _NotCustomized, _NotCustomized>> // code tracks: types.array( pm.pluggableMstType('track', 'stateModel') as BaseTrackStateModel, @@ -149,9 +152,8 @@ tracks: types.array( #### property: viewTrackConfigs -this represents tracks specific to this view specifically used -for read vs ref dotplots where this track would not really apply -elsewhere +this represents tracks specific to this view specifically used for read vs ref +dotplots where this track would not really apply elsewhere ```js // type signature @@ -317,7 +319,8 @@ setError: (e: unknown) => void #### action: closeView -removes the view itself from the state tree entirely by calling the parent removeView +removes the view itself from the state tree entirely by calling the parent +removeView ```js // type signature diff --git a/website/docs/models/JBrowseDesktopSessionModel.md b/website/docs/models/JBrowseDesktopSessionModel.md new file mode 100644 index 0000000000..9a6c63f105 --- /dev/null +++ b/website/docs/models/JBrowseDesktopSessionModel.md @@ -0,0 +1,617 @@ +--- +id: jbrowsedesktopsessionmodel +title: JBrowseDesktopSessionModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +inherits SnackbarModel + +### JBrowseDesktopSessionModel - Properties + +#### property: name + +```js +// type signature +ISimpleType +// code +name: types.identifier +``` + +#### property: margin + +```js +// type signature +number +// code +margin: 0 +``` + +#### property: drawerWidth + +```js +// type signature +IOptionalIType, [undefined]> +// code +drawerWidth: types.optional( + types.refinement(types.integer, width => width >= minDrawerWidth), + 384, + ) +``` + +#### property: views + +```js +// type signature +IArrayType +// code +views: types.array(pluginManager.pluggableMstType('view', 'stateModel')) +``` + +#### property: widgets + +```js +// type signature +IMapType +// code +widgets: types.map( + pluginManager.pluggableMstType('widget', 'stateModel'), + ) +``` + +#### property: activeWidgets + +```js +// type signature +IMapType>> +// code +activeWidgets: types.map( + types.safeReference( + pluginManager.pluggableMstType('widget', 'stateModel'), + ), + ) +``` + +#### property: connectionInstances + +```js +// type signature +IArrayType +// code +connectionInstances: types.array( + pluginManager.pluggableMstType('connection', 'stateModel'), + ) +``` + +#### property: sessionAssemblies + +```js +// type signature +IArrayType> +// code +sessionAssemblies: types.array(assemblyConfigSchemasType) +``` + +#### property: temporaryAssemblies + +```js +// type signature +IArrayType> +// code +temporaryAssemblies: types.array(assemblyConfigSchemasType) +``` + +#### property: minimized + +```js +// type signature +IOptionalIType, [undefined]> +// code +minimized: types.optional(types.boolean, false) +``` + +#### property: drawerPosition + +```js +// type signature +IOptionalIType, [undefined]> +// code +drawerPosition: types.optional( + types.string, + localStorage.getItem('drawerPosition') || 'right', + ) +``` + +### JBrowseDesktopSessionModel - Getters + +#### getter: DialogComponent + +```js +// type +any +``` + +#### getter: DialogProps + +```js +// type +any +``` + +#### getter: rpcManager + +```js +// type +any +``` + +#### getter: configuration + +```js +// type +any +``` + +#### getter: assemblies + +```js +// type +any +``` + +#### getter: assemblyNames + +```js +// type +any +``` + +#### getter: tracks + +```js +// type +any +``` + +#### getter: textSearchManager + +```js +// type +TextSearchManager +``` + +#### getter: connections + +```js +// type +any +``` + +#### getter: savedSessions + +```js +// type +any +``` + +#### getter: savedSessionNames + +```js +// type +any +``` + +#### getter: history + +```js +// type +any +``` + +#### getter: menus + +```js +// type +any +``` + +#### getter: assemblyManager + +```js +// type +any +``` + +#### getter: version + +```js +// type +any +``` + +#### getter: visibleWidget + +```js +// type +any +``` + +#### getter: adminMode + +```js +// type +boolean +``` + +### JBrowseDesktopSessionModel - Methods + +#### method: renderProps + +```js +// type signature +renderProps: () => { + theme: any +} +``` + +#### method: getReferring + +See if any MST nodes currently have a types.reference to this object. + +```js +// type signature +getReferring: (object: IAnyStateTreeNode) => ReferringNode[] +``` + +#### method: getTrackActionMenuItems + +```js +// type signature +getTrackActionMenuItems: (config: any) => ({ label: string; onClick: () => void; icon: OverridableComponent> & { muiName: string; }; disabled?: undefined; } | { ...; })[] +``` + +### JBrowseDesktopSessionModel - Actions + +#### action: moveViewUp + +```js +// type signature +moveViewUp: (id: string) => void +``` + +#### action: moveViewDown + +```js +// type signature +moveViewDown: (id: string) => void +``` + +#### action: setDrawerPosition + +```js +// type signature +setDrawerPosition: (arg: string) => void +``` + +#### action: queueDialog + +```js +// type signature +queueDialog: (callback: (doneCallback: () => void) => [any, any]) => void +``` + +#### action: makeConnection + +```js +// type signature +makeConnection: ( + configuration: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, + initialSnapshot?: {}, +) => any +``` + +#### action: prepareToBreakConnection + +```js +// type signature +prepareToBreakConnection: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => (Record<...> | (() => void))[] +``` + +#### action: breakConnection + +```js +// type signature +breakConnection: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void +``` + +#### action: deleteConnection + +```js +// type signature +deleteConnection: ( + configuration: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, +) => any +``` + +#### action: updateDrawerWidth + +```js +// type signature +updateDrawerWidth: (drawerWidth: number) => number +``` + +#### action: resizeDrawer + +```js +// type signature +resizeDrawer: (distance: number) => number +``` + +#### action: addView + +```js +// type signature +addView: (typeName: string, initialState?: {}) => any +``` + +#### action: removeView + +```js +// type signature +removeView: (view: any) => void +``` + +#### action: addAssembly + +```js +// type signature +addAssembly: (assemblyConfig: any) => void +``` + +#### action: removeAssembly + +```js +// type signature +removeAssembly: (assemblyName: string) => void +``` + +#### action: removeTemporaryAssembly + +```js +// type signature +removeTemporaryAssembly: (assemblyName: string) => void +``` + +#### action: addTemporaryAssembly + +used for read vs ref type assemblies + +```js +// type signature +addTemporaryAssembly: ( + assemblyConfig: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, +) => any +``` + +#### action: addAssemblyConf + +```js +// type signature +addAssemblyConf: (assemblyConf: any) => any +``` + +#### action: addTrackConf + +```js +// type signature +addTrackConf: (trackConf: any) => any +``` + +#### action: hasWidget + +```js +// type signature +hasWidget: (widget: any) => boolean +``` + +#### action: removeReferring + +```js +// type signature +removeReferring: (referring: any, track: any, callbacks: Function[], dereferenceTypeCount: Record) => void +``` + +#### action: deleteTrackConf + +```js +// type signature +deleteTrackConf: ( + trackConf: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, +) => any +``` + +#### action: addConnectionConf + +```js +// type signature +addConnectionConf: (connectionConf: any) => any +``` + +#### action: addLinearGenomeViewOfAssembly + +```js +// type signature +addLinearGenomeViewOfAssembly: (assemblyName: string, initialState?: {}) => any +``` + +#### action: addViewOfAssembly + +```js +// type signature +addViewOfAssembly: (viewType: any, assemblyName: string, initialState?: any) => + any +``` + +#### action: addViewFromAnotherView + +```js +// type signature +addViewFromAnotherView: ( + viewType: string, + otherView: any, + initialState?: { displayedRegions?: Region[] }, +) => any +``` + +#### action: addWidget + +```js +// type signature +addWidget: ( + typeName: string, + id: string, + initialState?: {}, + configuration?: { type: string }, +) => any +``` + +#### action: showWidget + +```js +// type signature +showWidget: (widget: any) => void +``` + +#### action: hideWidget + +```js +// type signature +hideWidget: (widget: any) => void +``` + +#### action: minimizeWidgetDrawer + +```js +// type signature +minimizeWidgetDrawer: () => void +``` + +#### action: showWidgetDrawer + +```js +// type signature +showWidgetDrawer: () => void +``` + +#### action: hideAllWidgets + +```js +// type signature +hideAllWidgets: () => void +``` + +#### action: setSelection + +set the global selection, i.e. the globally-selected object. can be a feature, a +view, just about anything + +```js +// type signature +setSelection: (thing: any) => void +``` + +#### action: clearSelection + +clears the global selection + +```js +// type signature +clearSelection: () => void +``` + +#### action: editConfiguration + +opens a configuration editor to configure the given thing, and sets the current +task to be configuring it + +```js +// type signature +editConfiguration: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void +``` + +#### action: editTrackConfiguration + +```js +// type signature +editTrackConfiguration: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void +``` + +#### action: clearConnections + +```js +// type signature +clearConnections: () => void +``` + +#### action: addSavedSession + +```js +// type signature +addSavedSession: (sessionSnapshot: ModelCreationType; margin: IType; drawerWidth: IOptionalIType, [undefined]>; ... 7 more ...; drawerPosition: IOptionalIType<...>; }>>) => any +``` + +#### action: removeSavedSession + +```js +// type signature +removeSavedSession: (sessionSnapshot: any) => any +``` + +#### action: renameCurrentSession + +```js +// type signature +renameCurrentSession: (sessionName: string) => any +``` + +#### action: duplicateCurrentSession + +```js +// type signature +duplicateCurrentSession: () => any +``` + +#### action: activateSession + +```js +// type signature +activateSession: (sessionName: any) => any +``` + +#### action: setDefaultSession + +```js +// type signature +setDefaultSession: () => any +``` + +#### action: setSession + +```js +// type signature +setSession: (sessionSnapshot: ModelCreationType; margin: IType; drawerWidth: IOptionalIType, [undefined]>; ... 7 more ...; drawerPosition: IOptionalIType<...>; }>>) => any +``` diff --git a/website/docs/models/JBrowseReactCGVSessionModel.md b/website/docs/models/JBrowseReactCGVSessionModel.md new file mode 100644 index 0000000000..5e2dace82b --- /dev/null +++ b/website/docs/models/JBrowseReactCGVSessionModel.md @@ -0,0 +1,338 @@ +--- +id: jbrowsereactcgvsessionmodel +title: JBrowseReactCGVSessionModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +### JBrowseReactCGVSessionModel - Properties + +#### property: name + +```js +// type signature +ISimpleType +// code +name: types.identifier +``` + +#### property: view + +```js +// type signature +IAnyModelType +// code +view: pluginManager.getViewType('CircularView').stateModel +``` + +#### property: widgets + +```js +// type signature +IMapType +// code +widgets: types.map( + pluginManager.pluggableMstType('widget', 'stateModel'), + ) +``` + +#### property: activeWidgets + +```js +// type signature +IMapType>> +// code +activeWidgets: types.map( + types.safeReference( + pluginManager.pluggableMstType('widget', 'stateModel'), + ), + ) +``` + +#### property: connectionInstances + +```js +// type signature +IArrayType +// code +connectionInstances: types.array( + pluginManager.pluggableMstType('connection', 'stateModel'), + ) +``` + +### JBrowseReactCGVSessionModel - Getters + +#### getter: DialogComponent + +```js +// type +any +``` + +#### getter: DialogProps + +```js +// type +any +``` + +#### getter: rpcManager + +```js +// type +any +``` + +#### getter: configuration + +```js +// type +any +``` + +#### getter: assemblies + +```js +// type +any[] +``` + +#### getter: assemblyNames + +```js +// type +any[] +``` + +#### getter: tracks + +```js +// type +any +``` + +#### getter: aggregateTextSearchAdapters + +```js +// type +any +``` + +#### getter: connections + +```js +// type +any +``` + +#### getter: adminMode + +```js +// type +boolean +``` + +#### getter: assemblyManager + +```js +// type +any +``` + +#### getter: version + +```js +// type +any +``` + +#### getter: views + +```js +// type +any[] +``` + +#### getter: visibleWidget + +```js +// type +any +``` + +### JBrowseReactCGVSessionModel - Methods + +#### method: renderProps + +```js +// type signature +renderProps: () => { + theme: any +} +``` + +#### method: getReferring + +See if any MST nodes currently have a types.reference to this object. + +```js +// type signature +getReferring: (object: IAnyStateTreeNode) => ReferringNode[] +``` + +#### method: getTrackActionMenuItems + +```js +// type signature +getTrackActionMenuItems: (config: any) => { label: string; onClick: () => void; icon: OverridableComponent> & { muiName: string; }; }[] +``` + +### JBrowseReactCGVSessionModel - Actions + +#### action: queueDialog + +```js +// type signature +queueDialog: (callback: (doneCallback: () => void) => [any, any]) => void +``` + +#### action: removeActiveDialog + +```js +// type signature +removeActiveDialog: () => void +``` + +#### action: makeConnection + +```js +// type signature +makeConnection: ( + configuration: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, + initialSnapshot?: {}, +) => any +``` + +#### action: removeReferring + +```js +// type signature +removeReferring: (referring: any, track: any, callbacks: Function[], dereferenceTypeCount: Record) => void +``` + +#### action: prepareToBreakConnection + +```js +// type signature +prepareToBreakConnection: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => (Record<...> | (() => void))[] +``` + +#### action: breakConnection + +```js +// type signature +breakConnection: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void +``` + +#### action: addView + +replaces view in this case + +```js +// type signature +addView: (typeName: string, initialState?: {}) => any +``` + +#### action: removeView + +does nothing + +```js +// type signature +removeView: () => void +``` + +#### action: addWidget + +does nothing + +```js +// type signature +addWidget: ( + typeName: string, + id: string, + initialState?: {}, + configuration?: { type: string }, +) => any +``` + +#### action: showWidget + +does nothing + +```js +// type signature +showWidget: (widget: any) => void +``` + +#### action: hasWidget + +```js +// type signature +hasWidget: (widget: any) => boolean +``` + +#### action: hideWidget + +```js +// type signature +hideWidget: (widget: any) => void +``` + +#### action: hideAllWidgets + +```js +// type signature +hideAllWidgets: () => void +``` + +#### action: setSelection + +set the global selection, i.e. the globally-selected object. can be a feature, a +view, just about anything + +```js +// type signature +setSelection: (thing: any) => void +``` + +#### action: clearSelection + +clears the global selection + +```js +// type signature +clearSelection: () => void +``` + +#### action: clearConnections + +```js +// type signature +clearConnections: () => void +``` + +#### action: renameCurrentSession + +```js +// type signature +renameCurrentSession: (sessionName: string) => any +``` diff --git a/website/docs/models/JBrowseReactLGVSessionModel.md b/website/docs/models/JBrowseReactLGVSessionModel.md new file mode 100644 index 0000000000..e0a805010f --- /dev/null +++ b/website/docs/models/JBrowseReactLGVSessionModel.md @@ -0,0 +1,371 @@ +--- +id: jbrowsereactlgvsessionmodel +title: JBrowseReactLGVSessionModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +inherits SnackbarModel + +### JBrowseReactLGVSessionModel - Properties + +#### property: name + +```js +// type signature +ISimpleType +// code +name: types.identifier +``` + +#### property: margin + +```js +// type signature +number +// code +margin: 0 +``` + +#### property: view + +```js +// type signature +IModelType<{ id: IOptionalIType, [undefined]>; displayName: IMaybe>; minimized: IType; } & { ...; }, { ...; } & ... 14 more ... & { ...; }, _NotCustomized, _NotCustomized> +// code +view: pluginManager.getViewType('LinearGenomeView') + .stateModel as LinearGenomeViewStateModel +``` + +#### property: widgets + +```js +// type signature +IMapType +// code +widgets: types.map( + pluginManager.pluggableMstType('widget', 'stateModel'), + ) +``` + +#### property: activeWidgets + +```js +// type signature +IMapType>> +// code +activeWidgets: types.map( + types.safeReference( + pluginManager.pluggableMstType('widget', 'stateModel'), + ), + ) +``` + +#### property: connectionInstances + +```js +// type signature +IArrayType +// code +connectionInstances: types.array( + pluginManager.pluggableMstType('connection', 'stateModel'), + ) +``` + +#### property: sessionTracks + +```js +// type signature +IArrayType +// code +sessionTracks: types.array( + pluginManager.pluggableConfigSchemaType('track'), + ) +``` + +### JBrowseReactLGVSessionModel - Getters + +#### getter: disableAddTracks + +```js +// type +any +``` + +#### getter: DialogComponent + +```js +// type +any +``` + +#### getter: DialogProps + +```js +// type +any +``` + +#### getter: textSearchManager + +```js +// type +TextSearchManager +``` + +#### getter: rpcManager + +```js +// type +any +``` + +#### getter: configuration + +```js +// type +any +``` + +#### getter: assemblies + +```js +// type +any[] +``` + +#### getter: assemblyNames + +```js +// type +any[] +``` + +#### getter: tracks + +```js +// type +any +``` + +#### getter: aggregateTextSearchAdapters + +```js +// type +any +``` + +#### getter: connections + +```js +// type +any +``` + +#### getter: adminMode + +```js +// type +boolean +``` + +#### getter: assemblyManager + +```js +// type +any +``` + +#### getter: version + +```js +// type +any +``` + +#### getter: views + +```js +// type +({ id: string; displayName: string; minimized: boolean; type: string; offsetPx: number; bpPerPx: number; displayedRegions: IMSTArray; start: ISimpleType; end: ISimpleType<...>; reversed: IOptionalIType<...>; } & { ...; }, { ...; }, _NotCustomized, _NotCustomized>> & ... +``` + +#### getter: visibleWidget + +```js +// type +any +``` + +### JBrowseReactLGVSessionModel - Methods + +#### method: renderProps + +```js +// type signature +renderProps: () => { + theme: any +} +``` + +#### method: getReferring + +See if any MST nodes currently have a types.reference to this object. + +```js +// type signature +getReferring: (object: IAnyStateTreeNode) => ReferringNode[] +``` + +#### method: getTrackActionMenuItems + +```js +// type signature +getTrackActionMenuItems: (config: any) => { label: string; onClick: () => void; icon: OverridableComponent> & { muiName: string; }; }[] +``` + +### JBrowseReactLGVSessionModel - Actions + +#### action: addTrackConf + +```js +// type signature +addTrackConf: ( + trackConf: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, +) => any +``` + +#### action: queueDialog + +```js +// type signature +queueDialog: (callback: (doneCallback: () => void) => [any, any]) => void +``` + +#### action: removeActiveDialog + +```js +// type signature +removeActiveDialog: () => void +``` + +#### action: makeConnection + +```js +// type signature +makeConnection: ( + configuration: { [x: string]: any } & NonEmptyObject & { + setSubschema(slotName: string, data: unknown): any, + } & IStateTreeNode, + initialSnapshot?: {}, +) => any +``` + +#### action: removeReferring + +```js +// type signature +removeReferring: (referring: any, track: any, callbacks: Function[], dereferenceTypeCount: Record) => void +``` + +#### action: prepareToBreakConnection + +```js +// type signature +prepareToBreakConnection: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => (Record<...> | (() => void))[] +``` + +#### action: breakConnection + +```js +// type signature +breakConnection: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void +``` + +#### action: addView + +```js +// type signature +addView: (typeName: string, initialState?: {}) => { id: string; displayName: string; minimized: boolean; type: string; offsetPx: number; bpPerPx: number; displayedRegions: IMSTArray; start: ISimpleType<...>; end: ISimpleType<...>; reversed: IOptionalIType<...>; } & { ...; }, { ...; }... +``` + +#### action: addWidget + +```js +// type signature +addWidget: ( + typeName: string, + id: string, + initialState?: {}, + configuration?: { type: string }, +) => any +``` + +#### action: showWidget + +```js +// type signature +showWidget: (widget: any) => void +``` + +#### action: hasWidget + +```js +// type signature +hasWidget: (widget: any) => boolean +``` + +#### action: hideWidget + +```js +// type signature +hideWidget: (widget: any) => void +``` + +#### action: hideAllWidgets + +```js +// type signature +hideAllWidgets: () => void +``` + +#### action: setSelection + +set the global selection, i.e. the globally-selected object. can be a feature, a +view, just about anything + +```js +// type signature +setSelection: (thing: any) => void +``` + +#### action: clearSelection + +clears the global selection + +```js +// type signature +clearSelection: () => void +``` + +#### action: clearConnections + +```js +// type signature +clearConnections: () => void +``` + +#### action: renameCurrentSession + +```js +// type signature +renameCurrentSession: (sessionName: string) => any +``` diff --git a/website/docs/models/JBrowseWebRootModel.md b/website/docs/models/JBrowseWebRootModel.md index 90569c498a..5ba4932a1b 100644 --- a/website/docs/models/JBrowseWebRootModel.md +++ b/website/docs/models/JBrowseWebRootModel.md @@ -5,11 +5,15 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info -note that many properties of the root model are available through the session, which -may be preferable since using getSession() is better relied on than getRoot() +## Docs + +note that many properties of the root model are available through the session, +which may be preferable since using getSession() is better relied on than +getRoot() ### JBrowseWebRootModel - Properties @@ -35,8 +39,8 @@ configPath: types.maybe(types.string) #### property: session -`session` encompasses the currently active state of the app, including -views open, tracks open in those views, etc. +`session` encompasses the currently active state of the app, including views +open, tracks open in those views, etc. ```js // type signature @@ -49,7 +53,7 @@ session: types.maybe(Session) ```js // type signature -IOptionalIType>; }, { error: Error; regions: BasicRegion[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; } & { ...; } & { ...; } & { ...; } & { ...; }, _NotCustomized, _No... +IOptionalIType>; }, { error: unknown; loaded: boolean; loadingP: Promise; volatileRegions: BasicRegion[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; } & ... 4 more... // code assemblyManager: types.optional(AssemblyManager, {}) ``` diff --git a/website/docs/models/JBrowseWebSessionModel.md b/website/docs/models/JBrowseWebSessionModel.md index dea47dd41d..0e247a8de2 100644 --- a/website/docs/models/JBrowseWebSessionModel.md +++ b/website/docs/models/JBrowseWebSessionModel.md @@ -5,8 +5,13 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +inherits SnackbarModel ### JBrowseWebSessionModel - Properties @@ -327,6 +332,20 @@ getTrackActionMenuItems: (config: { [x: string]: any; } & NonEmptyObject & { set ### JBrowseWebSessionModel - Actions +#### action: moveViewUp + +```js +// type signature +moveViewUp: (id: string) => void +``` + +#### action: moveViewDown + +```js +// type signature +moveViewDown: (id: string) => void +``` + #### action: setDrawerPosition ```js @@ -578,8 +597,8 @@ hideAllWidgets: () => void #### action: setSelection -set the global selection, i.e. the globally-selected object. -can be a feature, a view, just about anything +set the global selection, i.e. the globally-selected object. can be a feature, a +view, just about anything ```js // type signature @@ -667,8 +686,8 @@ setSession: (sessionSnapshot: ModelCreationType +// code +type: types.literal('LGVSyntenyDisplay') +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(schema) +``` diff --git a/website/docs/models/LinearAlignmentsDisplay.md b/website/docs/models/LinearAlignmentsDisplay.md index bdce0c522e..f21eeaa7be 100644 --- a/website/docs/models/LinearAlignmentsDisplay.md +++ b/website/docs/models/LinearAlignmentsDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs extends `BaseDisplay` @@ -18,11 +21,9 @@ refers to LinearPileupDisplay sub-display model ```js // type signature -IMaybe +IMaybe // code -PileupDisplay: types.maybe( - pluginManager.getDisplayType('LinearPileupDisplay').stateModel, - ) +PileupDisplay: types.maybe(types.union(...lowerPanelDisplays)) ``` #### property: SNPCoverageDisplay @@ -34,8 +35,8 @@ refers to LinearSNPCoverageDisplay sub-display model IMaybe // code SNPCoverageDisplay: types.maybe( - pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel, - ) + pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel, + ) ``` #### property: snpCovHeight @@ -74,36 +75,27 @@ number height: 250 ``` -#### property: showCoverage +#### property: userFeatureScreenDensity ```js // type signature -true +IMaybe> // code -showCoverage: true +userFeatureScreenDensity: types.maybe(types.number) ``` -#### property: showPileup +#### property: lowerPanelType ```js // type signature -true +string // code -showPileup: true -``` - -#### property: userFeatureScreenDensity - -```js -// type signature -IMaybe> -// code -userFeatureScreenDensity: types.maybe(types.number) +lowerPanelType: 'LinearPileupDisplay' ``` ### LinearAlignmentsDisplay - Getters -#### getter: pileupDisplayConfig +#### getter: pileupConf ```js // type @@ -131,21 +123,7 @@ any any ``` -#### getter: sortedByPosition - -```js -// type -any -``` - -#### getter: sortedByRefName - -```js -// type -any -``` - -#### getter: snpCoverageDisplayConfig +#### getter: coverageConf ```js // type @@ -177,20 +155,6 @@ trackMenuItems: () => MenuItem[] ### LinearAlignmentsDisplay - Actions -#### action: toggleCoverage - -```js -// type signature -toggleCoverage: () => void -``` - -#### action: togglePileup - -```js -// type signature -togglePileup: () => void -``` - #### action: setScrollTop ```js @@ -209,28 +173,35 @@ setSNPCoverageHeight: (n: number) => void ```js // type signature -setSNPCoverageDisplay: (displayConfig: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void +setSNPCoverageDisplay: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void ``` -#### action: setUserFeatureScreenDensity +#### action: updateStatsLimit ```js // type signature -setUserFeatureScreenDensity: (limit: number) => void +updateStatsLimit: (stats: unknown) => void ``` #### action: setPileupDisplay ```js // type signature -setPileupDisplay: (displayConfig: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void +setPileupDisplay: (configuration: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode) => void ``` #### action: setHeight ```js // type signature -setHeight: (displayHeight: number) => number +setHeight: (n: number) => number +``` + +#### action: setLowerPanelType + +```js +// type signature +setLowerPanelType: (type: string) => void ``` #### action: resizeHeight diff --git a/website/docs/models/LinearBareDisplay.md b/website/docs/models/LinearBareDisplay.md index 756ffba30a..4f688fefee 100644 --- a/website/docs/models/LinearBareDisplay.md +++ b/website/docs/models/LinearBareDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs extends `BaseLinearDisplay` diff --git a/website/docs/models/LinearBasicDisplay.md b/website/docs/models/LinearBasicDisplay.md index 6be75b026b..4f430ed8a0 100644 --- a/website/docs/models/LinearBasicDisplay.md +++ b/website/docs/models/LinearBasicDisplay.md @@ -5,10 +5,14 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info -used by `FeatureTrack`, has simple settings like "show/hide feature labels", etc. +## Docs + +used by `FeatureTrack`, has simple settings like "show/hide feature labels", +etc. ### LinearBasicDisplay - Properties diff --git a/website/docs/models/LinearComparativeDisplay.md b/website/docs/models/LinearComparativeDisplay.md new file mode 100644 index 0000000000..a695149fac --- /dev/null +++ b/website/docs/models/LinearComparativeDisplay.md @@ -0,0 +1,95 @@ +--- +id: linearcomparativedisplay +title: LinearComparativeDisplay +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +### LinearComparativeDisplay - Properties + +#### property: type + +```js +// type signature +ISimpleType<"LinearComparativeDisplay"> +// code +type: types.literal('LinearComparativeDisplay') +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(configSchema) +``` + +#### property: height + +```js +// type signature +number +// code +height: 100 +``` + +### LinearComparativeDisplay - Getters + +#### getter: rendererTypeName + +```js +// type +any +``` + +#### getter: renderProps + +```js +// type +() => { rpcDriverName: string; displayModel: { id: string; type: "LinearComparativeDisplay"; rpcDriverName: string; configuration: any; height: number; } & NonEmptyObject & ... 4 more ... & IStateTreeNode<...>; highResolutionScaling: number; } +``` + +### LinearComparativeDisplay - Actions + +#### action: setLoading + +controlled by a reaction + +```js +// type signature +setLoading: (abortController: AbortController) => void +``` + +#### action: setMessage + +controlled by a reaction + +```js +// type signature +setMessage: (messageText: string) => void +``` + +#### action: setRendered + +controlled by a reaction + +```js +// type signature +setRendered: (args?: { data: unknown; reactElement: React.ReactElement; renderingComponent: React.Component; }) => void +``` + +#### action: setError + +controlled by a reaction + +```js +// type signature +setError: (error: unknown) => void +``` diff --git a/website/docs/models/LinearComparativeView.md b/website/docs/models/LinearComparativeView.md index 9ba7ba313b..2e0b8be771 100644 --- a/website/docs/models/LinearComparativeView.md +++ b/website/docs/models/LinearComparativeView.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs ### LinearComparativeView - Properties @@ -99,7 +102,7 @@ currently this is limited to an array of two ```js // type signature -IArrayType, [undefined]>; displayName: IMaybe>; } & { id: IOptionalIType, [...]>; ... 12 more ...; showGridlines: IType<...>; }, { ...; } & ... 14 more ... & { ...; }, _NotCustomized, _NotCustomized>> +IArrayType, [undefined]>; displayName: IMaybe>; minimized: IType; } & { ...; }, { ...; } & ... 14 more ... & { ...; }, _NotCustomized, _NotCustomized>> // code views: types.array( pluginManager.getViewType('LinearGenomeView') @@ -109,9 +112,8 @@ views: types.array( #### property: viewTrackConfigs -this represents tracks specific to this view specifically used -for read vs ref dotplots where this track would not really apply -elsewhere +this represents tracks specific to this view specifically used for read vs ref +dotplots where this track would not really apply elsewhere ```js // type signature @@ -188,19 +190,20 @@ setHeight: (newHeight: number) => void ```js // type signature -setViews: (views: ModelCreationType, [undefined]>; displayName: IMaybe>; } & { id: IOptionalIType, [...]>; ... 12 more ...; showGridlines: IType<...>; }>>[]) => void +setViews: (views: ModelCreationType, [undefined]>; displayName: IMaybe>; minimized: IType; } & { ...; }>>[]) => void ``` #### action: removeView ```js // type signature -removeView: (view: { id: string; displayName: string; type: "LinearGenomeView"; offsetPx: number; bpPerPx: number; displayedRegions: IMSTArray; start: ISimpleType; end: ISimpleType<...>; reversed: IOptionalIType<...>; } & { ...; }, { ...; }, _NotCustomized, _NotCustomized>> & IS... +removeView: (view: { id: string; displayName: string; minimized: boolean; type: string; offsetPx: number; bpPerPx: number; displayedRegions: IMSTArray; start: ISimpleType; end: ISimpleType<...>; reversed: IOptionalIType<...>; } & { ...; }, { ...; }, _NotCustomized, _NotCustomize... ``` #### action: closeView -removes the view itself from the state tree entirely by calling the parent removeView +removes the view itself from the state tree entirely by calling the parent +removeView ```js // type signature diff --git a/website/docs/models/LinearGCContentDisplay.md b/website/docs/models/LinearGCContentDisplay.md new file mode 100644 index 0000000000..b88f576eb8 --- /dev/null +++ b/website/docs/models/LinearGCContentDisplay.md @@ -0,0 +1,37 @@ +--- +id: lineargccontentdisplay +title: LinearGCContentDisplay +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +base model BaseWiggleDisplayModel + +### LinearGCContentDisplay - Properties + +#### property: type + +```js +// type signature +ISimpleType<"LinearGCContentDisplay"> +// code +type: types.literal('LinearGCContentDisplay') +``` + +### LinearGCContentDisplay - Methods + +#### method: renderProps + +retrieves the sequence adapter from parent track, and puts it as a subadapter on +a GCContentAdapter + +```js +// type signature +renderProps: () => any +``` diff --git a/website/docs/models/LinearGenomeView.md b/website/docs/models/LinearGenomeView.md index 60961eda3d..439f1f1086 100644 --- a/website/docs/models/LinearGenomeView.md +++ b/website/docs/models/LinearGenomeView.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs ### LinearGenomeView - Properties @@ -21,11 +24,15 @@ id: ElementId #### property: type +this is a string instead of the const literal 'LinearGenomeView' to reduce some +typescripting strictness, but you should pass the string 'LinearGenomeView' to +the model explicitly + ```js // type signature -ISimpleType<"LinearGenomeView"> +string // code -type: types.literal('LinearGenomeView') +type: types.literal('LinearGenomeView') as unknown as string ``` #### property: offsetPx @@ -139,10 +146,9 @@ show the "center line" // type signature IOptionalIType, [undefined]> // code -showCenterLine: types.optional(types.boolean, () => { - const setting = localStorageGetItem('lgv-showCenterLine') - return setting !== undefined && setting !== null ? !!+setting : false - }) +showCenterLine: types.optional(types.boolean, () => + JSON.parse(localStorageGetItem('lgv-showCenterLine') || 'false'), + ) ``` #### property: showCytobandsSetting @@ -153,10 +159,9 @@ show the "cytobands" in the overview scale bar // type signature IOptionalIType, [undefined]> // code -showCytobandsSetting: types.optional(types.boolean, () => { - const setting = localStorageGetItem('lgv-showCytobands') - return setting !== undefined && setting !== null ? !!+setting : true - }) +showCytobandsSetting: types.optional(types.boolean, () => + JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true'), + ) ``` #### property: showGridlines @@ -193,6 +198,132 @@ number any[] ``` +#### getter: assemblyErrors + +```js +// type +string +``` + +#### getter: assembliesInitialized + +```js +// type +boolean +``` + +#### getter: initialized + +```js +// type +any +``` + +#### getter: hasDisplayedRegions + +```js +// type +boolean +``` + +#### getter: isSearchDialogDisplayed + +```js +// type +boolean +``` + +#### getter: scaleBarHeight + +```js +// type +number +``` + +#### getter: headerHeight + +```js +// type +number +``` + +#### getter: trackHeights + +```js +// type +any +``` + +#### getter: trackHeightsWithResizeHandles + +```js +// type +any +``` + +#### getter: height + +```js +// type +any +``` + +#### getter: totalBp + +```js +// type +number +``` + +#### getter: maxBpPerPx + +```js +// type +number +``` + +#### getter: minBpPerPx + +```js +// type +number +``` + +#### getter: error + +```js +// type +any +``` + +#### getter: maxOffset + +```js +// type +number +``` + +#### getter: minOffset + +```js +// type +number +``` + +#### getter: displayedRegionsTotalPx + +```js +// type +number +``` + +#### getter: trackTypeActions + +```js +// type +Map +``` + #### getter: canShowCytobands ```js @@ -216,8 +347,8 @@ boolean #### getter: cytobandOffset -the cytoband is displayed to the right of the chromosome name, -and that offset is calculated manually with this method +the cytoband is displayed to the right of the chromosome name, and that offset +is calculated manually with this method ```js // type @@ -226,12 +357,11 @@ number #### getter: staticBlocks -static blocks are an important concept jbrowse uses to avoid -re-rendering when you scroll to the side. when you horizontally -scroll to the right, old blocks to the left may be removed, and -new blocks may be instantiated on the right. tracks may use the -static blocks to render their data for the region represented by -the block +static blocks are an important concept jbrowse uses to avoid re-rendering when +you scroll to the side. when you horizontally scroll to the right, old blocks to +the left may be removed, and new blocks may be instantiated on the right. tracks +may use the static blocks to render their data for the region represented by the +block ```js // type @@ -240,10 +370,9 @@ BlockSet #### getter: dynamicBlocks -dynamic blocks represent the exact coordinates of the currently -visible genome regions on the screen. they are similar to static -blocks, but statcic blocks can go offscreen while dynamic blocks -represent exactly what is on screen +dynamic blocks represent the exact coordinates of the currently visible genome +regions on the screen. they are similar to static blocks, but statcic blocks can +go offscreen while dynamic blocks represent exactly what is on screen ```js // type @@ -261,8 +390,7 @@ any #### getter: visibleLocStrings -a single "combo-locstring" representing all the regions visible -on the screen +a single "combo-locstring" representing all the regions visible on the screen ```js // type @@ -287,14 +415,65 @@ any ### LinearGenomeView - Methods +#### method: MiniControlsComponent + +```js +// type signature +MiniControlsComponent: () => React.FC +``` + +#### method: HeaderComponent + +```js +// type signature +HeaderComponent: () => React.FC +``` + +#### method: renderProps + +```js +// type signature +renderProps: () => any +``` + +#### method: searchScope + +```js +// type signature +searchScope: (assemblyName: string) => { assemblyName: string; includeAggregateIndexes: boolean; tracks: IMSTArray & IStateTreeNode>; } +``` + +#### method: getTrack + +```js +// type signature +getTrack: (id: string) => any +``` + +#### method: rankSearchResults + +```js +// type signature +rankSearchResults: (results: BaseResult[]) => BaseResult[] +``` + +#### method: rewriteOnClicks + +modifies view menu action onClick to apply to all tracks of same type + +```js +// type signature +rewriteOnClicks: (trackType: string, viewMenuActions: MenuItem[]) => void +``` + #### method: getSelectedRegions -Helper method for the fetchSequence. -Retrieves the corresponding regions that were selected by the rubberband +Helper method for the fetchSequence. Retrieves the corresponding regions that +were selected by the rubberband ```js // type signature -getSelectedRegions: (leftOffset?: BpOffset, rightOffset?: BpOffset) => BaseBlock[] +getSelectedRegions: (leftOffset?: BpOffset, rightOffset?: BpOffset) => { start: number; end: number; regionNumber?: number; reversed?: boolean; refName: string; assemblyName: string; key: string; offsetPx: number; widthPx: number; variant?: string; isLeftEndOfDisplayedRegion?: boolean; }[] ``` #### method: menuItems @@ -333,8 +512,8 @@ bpToPx: ({ #### method: centerAt -scrolls the view to center on the given bp. if that is not in any -of the displayed regions, does nothing +scrolls the view to center on the given bp. if that is not in any of the +displayed regions, does nothing ```js // type signature @@ -471,6 +650,13 @@ showTrack: ( ) => any ``` +#### action: hideTrack + +```js +// type signature +hideTrack: (trackId: string) => number +``` + #### action: moveTrack ```js @@ -616,8 +802,8 @@ setCoarseDynamicBlocks: (blocks: BlockSet) => void #### action: moveTo -offset is the base-pair-offset in the displayed region, index is the index of the -displayed region in the linear genome view +offset is the base-pair-offset in the displayed region, index is the index of +the displayed region in the linear genome view ```js // type signature @@ -630,16 +816,15 @@ navigate to the given locstring ```js // type signature -navToLocString: (locString: string, optAssemblyName?: string) => void +navToLocString: (locString: string, optAssemblyName?: string) => Promise ``` #### action: navTo -Navigate to a location based on its refName and optionally start, end, -and assemblyName. Can handle if there are multiple displayedRegions -from same refName. Only navigates to a location if it is entirely -within a displayedRegion. Navigates to the first matching location -encountered. +Navigate to a location based on its refName and optionally start, end, and +assemblyName. Can handle if there are multiple displayedRegions from same +refName. Only navigates to a location if it is entirely within a +displayedRegion. Navigates to the first matching location encountered. Throws an error if navigation was unsuccessful diff --git a/website/docs/models/LinearPileupDisplay.md b/website/docs/models/LinearPileupDisplay.md index d4001962f6..57bc605f1b 100644 --- a/website/docs/models/LinearPileupDisplay.md +++ b/website/docs/models/LinearPileupDisplay.md @@ -5,8 +5,13 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +extends `BaseLinearDisplay` ### LinearPileupDisplay - Properties @@ -114,6 +119,15 @@ colorBy: types.maybe( ) ``` +#### property: filterBy + +```js +// type signature +IOptionalIType, [undefined]>; flagExclude: IOptionalIType, [undefined]>; readName: IMaybe<...>; tagFilter: IMaybe<...>; }, {}, _NotCustomized, _NotCustomized>, [...]> +// code +filterBy: types.optional(FilterModel, {}) +``` + ### LinearPileupDisplay - Getters #### getter: maxHeight @@ -197,6 +211,13 @@ trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMe setReady: (flag: boolean) => void ``` +#### action: setCurrSortBpPerPx + +```js +// type signature +setCurrSortBpPerPx: (n: number) => void +``` + #### action: setMaxHeight ```js @@ -208,14 +229,14 @@ setMaxHeight: (n: number) => void ```js // type signature -setFeatureHeight: (n: number) => void +setFeatureHeight: (n?: number) => void ``` #### action: setNoSpacing ```js // type signature -setNoSpacing: (flag: boolean) => void +setNoSpacing: (flag?: boolean) => void ``` #### action: setColorScheme diff --git a/website/docs/models/LinearReadArcsDisplay.md b/website/docs/models/LinearReadArcsDisplay.md new file mode 100644 index 0000000000..76f301b441 --- /dev/null +++ b/website/docs/models/LinearReadArcsDisplay.md @@ -0,0 +1,235 @@ +--- +id: linearreadarcsdisplay +title: LinearReadArcsDisplay +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +extends `BaseLinearDisplay` + +### LinearReadArcsDisplay - Properties + +#### property: type + +```js +// type signature +ISimpleType<"LinearReadArcsDisplay"> +// code +type: types.literal('LinearReadArcsDisplay') +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(configSchema) +``` + +#### property: filterBy + +```js +// type signature +IOptionalIType, [undefined]>; flagExclude: IOptionalIType, [undefined]>; readName: IMaybe<...>; tagFilter: IMaybe<...>; }, {}, _NotCustomized, _NotCustomized>, [...]> +// code +filterBy: types.optional(FilterModel, {}) +``` + +#### property: lineWidth + +```js +// type signature +IMaybe> +// code +lineWidth: types.maybe(types.number) +``` + +#### property: jitter + +```js +// type signature +IMaybe> +// code +jitter: types.maybe(types.number) +``` + +#### property: colorBy + +```js +// type signature +IMaybe; tag: IMaybe>; extra: IType; }, {}, _NotCustomized, _NotCustomized>> +// code +colorBy: types.maybe( + types.model({ + type: types.string, + tag: types.maybe(types.string), + extra: types.frozen(), + }), + ) +``` + +#### property: drawInter + +```js +// type signature +true +// code +drawInter: true +``` + +#### property: drawLongRange + +```js +// type signature +true +// code +drawLongRange: true +``` + +### LinearReadArcsDisplay - Getters + +#### getter: lineWidthSetting + +```js +// type +any +``` + +#### getter: jitterVal + +```js +// type +number +``` + +#### getter: ready + +```js +// type +boolean +``` + +### LinearReadArcsDisplay - Methods + +#### method: trackMenuItems + +```js +// type signature +trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; } | { ...; })[] +``` + +#### method: renderSvg + +```js +// type signature +renderSvg: (opts: ExportSvgOptions) => Promise +``` + +### LinearReadArcsDisplay - Actions + +#### action: reload + +internal, a reference to a HTMLCanvas because we use a autorun to draw the +canvas + +```js +// type signature +reload: () => void +``` + +#### action: setRef + +internal, a reference to a HTMLCanvas because we use a autorun to draw the +canvas + +```js +// type signature +setRef: (ref: HTMLCanvasElement) => void +``` + +#### action: setColorScheme + +```js +// type signature +setColorScheme: (s: { type: string; }) => void +``` + +#### action: setChainData + +```js +// type signature +setChainData: (args: ChainData) => void +``` + +#### action: setDrawInter + +```js +// type signature +setDrawInter: (f: boolean) => void +``` + +#### action: setDrawLongRange + +```js +// type signature +setDrawLongRange: (f: boolean) => void +``` + +#### action: setLoading + +```js +// type signature +setLoading: (f: boolean) => void +``` + +#### action: setDrawn + +used during tests to detect when we can complete a snapshot test + +```js +// type signature +setDrawn: (f: boolean) => void +``` + +#### action: setFilterBy + +```js +// type signature +setFilterBy: (filter: Filter) => void +``` + +#### action: setLastDrawnOffsetPx + +allows the drawing to slide around a little bit if it takes a long time to +refresh + +```js +// type signature +setLastDrawnOffsetPx: (n: number) => void +``` + +#### action: setLineWidth + +thin, bold, extrabold, etc + +```js +// type signature +setLineWidth: (n: number) => void +``` + +#### action: setJitter + +jitter val, helpful to jitter the x direction so you see better evidence when +e.g. 100 long reads map to same x position + +```js +// type signature +setJitter: (n: number) => void +``` diff --git a/website/docs/models/LinearReadCloudDisplay.md b/website/docs/models/LinearReadCloudDisplay.md new file mode 100644 index 0000000000..57b772f4a1 --- /dev/null +++ b/website/docs/models/LinearReadCloudDisplay.md @@ -0,0 +1,137 @@ +--- +id: linearreadclouddisplay +title: LinearReadCloudDisplay +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +extends `BaseLinearDisplay` + +### LinearReadCloudDisplay - Properties + +#### property: type + +```js +// type signature +ISimpleType<"LinearReadCloudDisplay"> +// code +type: types.literal('LinearReadCloudDisplay') +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(configSchema) +``` + +#### property: filterBy + +```js +// type signature +IOptionalIType, [undefined]>; flagExclude: IOptionalIType, [undefined]>; readName: IMaybe<...>; tagFilter: IMaybe<...>; }, {}, _NotCustomized, _NotCustomized>, [...]> +// code +filterBy: types.optional(FilterModel, {}) +``` + +#### property: colorBy + +```js +// type signature +IMaybe; tag: IMaybe>; extra: IType; }, {}, _NotCustomized, _NotCustomized>> +// code +colorBy: types.maybe( + types.model({ + type: types.string, + tag: types.maybe(types.string), + extra: types.frozen(), + }), + ) +``` + +### LinearReadCloudDisplay - Getters + +#### getter: ready + +```js +// type +boolean +``` + +### LinearReadCloudDisplay - Methods + +#### method: trackMenuItems + +```js +// type signature +trackMenuItems: () => MenuItem[] +``` + +#### method: renderSvg + +```js +// type signature +renderSvg: (opts: ExportSvgOptions) => Promise +``` + +### LinearReadCloudDisplay - Actions + +#### action: reload + +internal, a reference to a HTMLCanvas because we use a autorun to draw the +canvas + +```js +// type signature +reload: () => void +``` + +#### action: setRef + +```js +// type signature +setRef: (ref: HTMLCanvasElement) => void +``` + +#### action: setChainData + +```js +// type signature +setChainData: (args: ChainData) => void +``` + +#### action: setLoading + +```js +// type signature +setLoading: (f: boolean) => void +``` + +#### action: setDrawn + +```js +// type signature +setDrawn: (f: boolean) => void +``` + +#### action: setFilterBy + +```js +// type signature +setFilterBy: (filter: Filter) => void +``` + +#### action: setLastDrawnOffsetPx + +```js +// type signature +setLastDrawnOffsetPx: (n: number) => void +``` diff --git a/website/docs/models/LinearReferenceSequenceDisplay.md b/website/docs/models/LinearReferenceSequenceDisplay.md new file mode 100644 index 0000000000..a8da8f7abd --- /dev/null +++ b/website/docs/models/LinearReferenceSequenceDisplay.md @@ -0,0 +1,116 @@ +--- +id: linearreferencesequencedisplay +title: LinearReferenceSequenceDisplay +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +base model `BaseLinearDisplay` + +### LinearReferenceSequenceDisplay - Properties + +#### property: type + +```js +// type signature +ISimpleType<"LinearReferenceSequenceDisplay"> +// code +type: types.literal('LinearReferenceSequenceDisplay') +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(configSchema) +``` + +#### property: showForward + +```js +// type signature +true +// code +showForward: true +``` + +#### property: showReverse + +```js +// type signature +true +// code +showReverse: true +``` + +#### property: showTranslation + +```js +// type signature +true +// code +showTranslation: true +``` + +### LinearReferenceSequenceDisplay - Getters + +#### getter: rendererTypeName + +```js +// type +any +``` + +### LinearReferenceSequenceDisplay - Methods + +#### method: renderProps + +```js +// type signature +renderProps: () => any +``` + +#### method: regionCannotBeRendered + +```js +// type signature +regionCannotBeRendered: () => 'Zoom in to see sequence' +``` + +#### method: trackMenuItems + +```js +// type signature +trackMenuItems: () => { label: string; type: string; checked: boolean; onClick: () => void; }[] +``` + +### LinearReferenceSequenceDisplay - Actions + +#### action: toggleShowForward + +```js +// type signature +toggleShowForward: () => void +``` + +#### action: toggleShowReverse + +```js +// type signature +toggleShowReverse: () => void +``` + +#### action: toggleShowTranslation + +```js +// type signature +toggleShowTranslation: () => void +``` diff --git a/website/docs/models/LinearSNPCoverageDisplay.md b/website/docs/models/LinearSNPCoverageDisplay.md index 210bdb8835..bdee8ce3c7 100644 --- a/website/docs/models/LinearSNPCoverageDisplay.md +++ b/website/docs/models/LinearSNPCoverageDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs extends `LinearWiggleDisplay` @@ -54,17 +57,7 @@ drawArcs: types.maybe(types.boolean) // type signature IOptionalIType, [undefined]>; flagExclude: IOptionalIType, [undefined]>; readName: IMaybe<...>; tagFilter: IMaybe<...>; }, {}, _NotCustomized, _NotCustomized>, [...]> // code -filterBy: types.optional( - types.model({ - flagInclude: types.optional(types.number, 0), - flagExclude: types.optional(types.number, 1540), - readName: types.maybe(types.string), - tagFilter: types.maybe( - types.model({ tag: types.string, value: types.string }), - ), - }), - {}, - ) +filterBy: types.optional(FilterModel, {}) ``` #### property: colorBy diff --git a/website/docs/models/LinearSyntenyDisplay.md b/website/docs/models/LinearSyntenyDisplay.md new file mode 100644 index 0000000000..6cf8ac4bb0 --- /dev/null +++ b/website/docs/models/LinearSyntenyDisplay.md @@ -0,0 +1,68 @@ +--- +id: linearsyntenydisplay +title: LinearSyntenyDisplay +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +extends `LinearComparativeDisplay` model + +### LinearSyntenyDisplay - Properties + +#### property: type + +```js +// type signature +ISimpleType<"LinearSyntenyDisplay"> +// code +type: types.literal('LinearSyntenyDisplay') +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(configSchema) +``` + +### LinearSyntenyDisplay - Getters + +#### getter: rendererTypeName + +```js +// type +any +``` + +#### getter: adapterConfig + +```js +// type +any +``` + +#### getter: trackIds + +unused + +```js +// type +string[] +``` + +### LinearSyntenyDisplay - Methods + +#### method: renderProps + +```js +// type signature +renderProps: () => { rpcDriverName: string; displayModel: { id: string; type: never; rpcDriverName: string; configuration: any; height: number; } & NonEmptyObject & { rendererTypeName: string; error: unknown; } & ... 6 more ... & IStateTreeNode<...>; config: any; width: number; height: number; } +``` diff --git a/website/docs/models/LinearSyntenyView.md b/website/docs/models/LinearSyntenyView.md index 53d5c0f4dd..6349b59917 100644 --- a/website/docs/models/LinearSyntenyView.md +++ b/website/docs/models/LinearSyntenyView.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs extends the `LinearComparativeView` base model diff --git a/website/docs/models/LinearVariantDisplay.md b/website/docs/models/LinearVariantDisplay.md index 23fe629813..0388f46a77 100644 --- a/website/docs/models/LinearVariantDisplay.md +++ b/website/docs/models/LinearVariantDisplay.md @@ -5,11 +5,14 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info -extends `LinearBasicDisplay` -very similar to basic display, but provides custom widget on feature click +## Docs + +extends `LinearBasicDisplay` very similar to basic display, but provides custom +widget on feature click ### LinearVariantDisplay - Properties diff --git a/website/docs/models/LinearWiggleDisplay.md b/website/docs/models/LinearWiggleDisplay.md index cbdf2b46e0..2246db4f2f 100644 --- a/website/docs/models/LinearWiggleDisplay.md +++ b/website/docs/models/LinearWiggleDisplay.md @@ -5,8 +5,11 @@ toplevel: true --- Note: this document is automatically generated from mobx-state-tree objects in -our source code. See [Core concepts and intro to pluggable -elements](/docs/developer_guide/) for more info +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs Extends `BaseLinearDisplay` @@ -375,9 +378,9 @@ setLoading: (aborter: AbortController) => void #### action: selectFeature -this overrides the BaseLinearDisplayModel to avoid popping up a -feature detail display, but still sets the feature selection on the -model so listeners can detect a click +this overrides the BaseLinearDisplayModel to avoid popping up a feature detail +display, but still sets the feature selection on the model so listeners can +detect a click ```js // type signature diff --git a/website/docs/models/SnackbarModel.md b/website/docs/models/SnackbarModel.md new file mode 100644 index 0000000000..46f2aa2bd1 --- /dev/null +++ b/website/docs/models/SnackbarModel.md @@ -0,0 +1,55 @@ +--- +id: snackbarmodel +title: SnackbarModel +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Docs + +### SnackbarModel - Getters + +#### getter: snackbarMessages + +```js +// type +IObservableArray +``` + +### SnackbarModel - Actions + +#### action: notify + +```js +// type signature +notify: (message: string, level?: NotificationLevel, action?: SnackAction) => void +``` + +#### action: pushSnackbarMessage + +```js +// type signature +pushSnackbarMessage: ( + message: string, + level?: NotificationLevel, + action?: SnackAction, +) => number +``` + +#### action: popSnackbarMessage + +```js +// type signature +popSnackbarMessage: () => any +``` + +#### action: removeSnackbarMessage + +```js +// type signature +removeSnackbarMessage: (message: string) => void +``` diff --git a/website/docs/quickstart_cli.md b/website/docs/quickstart_cli.md index 0215c2930f..981a7603e8 100644 --- a/website/docs/quickstart_cli.md +++ b/website/docs/quickstart_cli.md @@ -9,118 +9,8 @@ import Figure from './figure' In this guide, we'll get an instance of JBrowse web running on your computer's browser. -Just want to download JBrowse web and get started? Follow our [JBrowse web -quick start](../quickstart_web). +Just want to download JBrowse web and get started? Follow our +[JBrowse web quick start](../quickstart_web). -Want JBrowse desktop? Follow our [JBrowse desktop quick -start](../quickstart_desktop). - -## Prerequisites - -- Ability to run commands on the command line -- A stable and recent version of [node](https://nodejs.org/en/) - -:::caution - -If you are using `apt` as your package manager, we recommend not using it to -install Node.js. Good alternatives include -[NodeSource](https://github.com/nodesource) or -[NVM](https://github.com/nvm-sh/nvm). - -::: - -## Downloading JBrowse 2 using the JBrowse CLI - -The JBrowse CLI can help perform many tasks to help you manage JBrowse 2, such -as: - -- create a new instance of JBrowse 2 automatically -- update an existing instance of JBrowse 2 with the latest released version -- configure your JBrowse 2 instance - -### Installing the CLI tools - -To globally install the JBrowse CLI, run - -```sh-session -npm install -g @jbrowse/cli -``` - -After running this command you can then test the installation with - -```sh-session -jbrowse --version -``` - -which will output the current version of the JBrowse CLI. - -:::note - -If you can't or don't want to globally install the JBrowse CLI, you can also use -the [npx](https://nodejs.dev/learn/the-npx-nodejs-package-runner) command, which -is included with Node.js, to run JBrowse CLI without installing it. Simply -replace `jbrowse` with `npx @jbrowse/cli` in any command, e.g. - -```sh-session -npx @jbrowse/cli --version -``` - -::: - -### Using `jbrowse create` to download JBrowse 2 - -In the directory where you would like to download JBrowse 2, run - -```sh-session -jbrowse create jbrowse2 -``` - -### Checking the download - -The directory where you downloaded JBrowse should look something like this: - -```txt -jbrowse2/ -├── asset-manifest.json -├── favicon.ico -├── index.html -├── manifest.json -├── robots.txt -├── static/ -├── test_data/ -└── version.txt -``` - -## Running JBrowse 2 - -JBrowse 2 requires a web server to run. It won't work if you try to directly -open the `index.html` in your web browser. We can use a simple server to check -that JBrowse 2 has been downloaded properly. Run - -```sh-session -cd jbrowse2/ -npx serve . # use npx serve -S . if you want to refer to symlinked data later on -``` - -which will start a web server in our JBrowse 2 directory. - -Navigate to the location specified in the CLI's output (likely -`http://localhost:3000`). - -Your page should look something like this: - -
    - -Click on the sample config to see JBrowse 2 running with a demo -configuration. It should look like this: - -
    - -Congratulations! You're running JBrowse 2. - -## Next steps - -Now that JBrowse 2 is set up, you can configure it with your own genomes and -tracks. There are two ways you can configure JBrowse 2: with the JBrowse CLI -(tutorial [here](../tutorials/config_cli)) or with JBrowse 2's built-in graphical -configuration editing (guide [here](../tutorials/config_gui)). +Want JBrowse desktop? Follow our +[JBrowse desktop quick start](../quickstart_desktop). diff --git a/website/docs/quickstart_desktop.md b/website/docs/quickstart_desktop.md index f1c749d0a5..380652a59e 100644 --- a/website/docs/quickstart_desktop.md +++ b/website/docs/quickstart_desktop.md @@ -5,11 +5,10 @@ toplevel: true --- import Figure from './figure' -import config from '../docusaurus.config.json' + +import {winDL,macDL,linDL} from './links' + import PlaylistAddIcon from '@mui/icons-material/PlaylistAdd' -const winDownloadLink = `https://github.com/GMOD/jbrowse-components/releases/download/${config.customFields.currentVersion}/jbrowse-desktop-${config.customFields.currentVersion}-win.exe` -const macDownloadLink = `https://github.com/GMOD/jbrowse-components/releases/download/${config.customFields.currentVersion}/jbrowse-desktop-${config.customFields.currentVersion}-mac.dmg` -const linDownloadLink = `https://github.com/GMOD/jbrowse-components/releases/download/${config.customFields.currentVersion}/jbrowse-desktop-${config.customFields.currentVersion}-linux.AppImage` In this guide, we'll get the JBrowse desktop application running on your computer. @@ -18,16 +17,15 @@ computer. ### Installing on Windows -Click here to download the latest Windows -installer executable. +Click here to download the latest Windows installer +executable. Double-click the downloaded installer and it will install and open JBrowse. You can now open JBrowse like any other program. ### Installing on MacOS -Click here to download the latest MacOS release -artifact. +Click here to download the latest MacOS release artifact. When the .dmg file is downloaded, double click, and drag JBrowse 2 into 'applications'. @@ -36,8 +34,7 @@ You can now open JBrowse 2 like any other application on your Mac. ### Installing on Linux -Click here to download the latest Linux AppImage -release. +Click here to download the latest Linux AppImage release. Start it in one of two ways: @@ -66,19 +63,20 @@ You can now double-click the AppImage file to launch JBrowse. ## JBrowse Desktop start screen -After you have installed and started JBrowse Desktop you will see a start -screen like this: +After you have installed and started JBrowse Desktop you will see a start screen +like this:
    -**On the left hand panel,** "Launch new session" can launch a new session -using either your own custom genome (which you can load using an indexed FASTA -or a twobit file via `open sequence file`) or a pre-loaded genome via the "Quickstart list". +**On the left hand panel,** "Launch new session" can launch a new session using +either your own custom genome (which you can load using an indexed FASTA or a +twobit file via `open sequence file`) or a pre-loaded genome via the "Quickstart +list". **On the right hand panel** is the "Recently opened sessions". This includes -sessions that you have explicitly saved, and sessions that were autosaved -(i.e. ones that you didn't explicitly use "Save as" on). You can re-open your -sessions by clicking on the session name. +sessions that you have explicitly saved, and sessions that were autosaved (i.e. +ones that you didn't explicitly use "Save as" on). You can re-open your sessions +by clicking on the session name. ### Special features on the start screen @@ -89,15 +87,14 @@ quickstart panel. You can convert a session in the "Recently opened sessions" into an entry that appears in the quickstart list. **To do this:** Click a checkbox next to a session in the "Recently opened -sessions" table, and then hit the icon next to the trash -can icon. This is helpful if you want to make your own custom organism a -template for quickstarts in the future. +sessions" table, and then hit the icon next to the trash can +icon. This is helpful if you want to make your own custom organism a template +for quickstarts in the future. #### Selecting multiple entries from the quickstart panel -Users can also hit the checkbox for multiple species in the quickstart list, -and then the sessions are combined which can be helpful for comparative -genomics. +Users can also hit the checkbox for multiple species in the quickstart list, and +then the sessions are combined which can be helpful for comparative genomics. ### Next steps diff --git a/website/docs/quickstart_web.md b/website/docs/quickstart_web.md index bbc91e1696..297d255f24 100644 --- a/website/docs/quickstart_web.md +++ b/website/docs/quickstart_web.md @@ -1,28 +1,76 @@ --- id: quickstart_web -title: JBrowse web quick start +title: JBrowse web setup using the CLI toplevel: true --- import Figure from './figure' + import config from '../docusaurus.config.json' -In this guide, we'll get an instance of JBrowse web running on your computer's -browser. +## Prerequisites + +- Node.js 12+. Note: we recommend not using `apt` to install Node.js, it often + installs old versions. Good alternatives include + [NodeSource](https://github.com/nodesource) or + [NVM](https://github.com/nvm-sh/nvm). +- [Samtools](http://www.htslib.org/) installed e.g. `sudo apt install samtools` + or `brew install samtools`, used for creating FASTA index and BAM/CRAM + processing for creating tabix GFF +- [tabix](http://www.htslib.org/doc/tabix.html) installed e.g. + `sudo apt install tabix` and `brew install htslib`, used for creating tabix + indexes for BED/VCF/GFF files +- (optional) [`genometools`](http://genometools.org/) installed e.g. + `sudo apt install genometools` or `brew install brewsci/bio/genometools` used + for sorting GFF3. can use awk instead of `genometools` instead + +## Installing the JBrowse CLI + +The JBrowse CLI can help perform many tasks to help you manage JBrowse 2, such +as: + +- create a new instance of JBrowse 2 automatically +- update an existing instance of JBrowse 2 with the latest released version +- configure your JBrowse 2 instance + +To globally install the JBrowse CLI, run + +```sh-session +npm install -g @jbrowse/cli +``` -Are you an **administrator**, or want to install via CLI to get access to -configuration tools? Follow our [CLI quick start](../quickstart_cli). +After running this command you can then test the installation with -Want JBrowse desktop? Follow our [JBrowse desktop quick -start](../quickstart_desktop). +```sh-session +jbrowse --version +``` -## Downloading manually +which will output the current version of the JBrowse CLI. -Download JBrowse 2 manually here. +:::note -Once you have downloaded the ZIP file, extract it to the directory where you -would like to have JBrowse 2. +If you can't or don't want to globally install the JBrowse CLI, you can also use +the [npx](https://nodejs.dev/learn/the-npx-nodejs-package-runner) command, which +is included with Node.js, to run JBrowse CLI without installing it. Simply +replace `jbrowse` with `npx @jbrowse/cli` in any command, e.g. + +```sh-session +npx @jbrowse/cli --version +``` + +::: + +### Using `jbrowse create` to download JBrowse 2 + +In the directory where you would like to download JBrowse 2, run + +```sh-session +jbrowse create jbrowse2 +``` + +This fetches the latest version of jbrowse-web and unzips it to a folder named +"jbrowse2" from github (https://github.com/GMOD/jbrowse-components/releases), +you could run this step manually if you wanted to instead. ### Checking the download @@ -43,12 +91,20 @@ jbrowse2/ ## Running JBrowse 2 JBrowse 2 requires a web server to run. It won't work if you try to directly -open the `index.html` in your web browser. We can use a simple server to check -that JBrowse 2 has been downloaded properly. Run +open the `index.html` in your web browser. + +Oftentimes, you may put the folder on a web server in the static html folder +e.g. /var/www/html/jbrowse2/ once in place, you can then visit +http://yourserver/jbrowse2 + +You could also use a simple server to check that JBrowse 2 has been downloaded +properly. Run ```sh-session cd jbrowse2/ -npx serve . # use npx serve -S . if you want to refer to symlinked data later on +npx serve . +# or +npx serve -S . # if you want to refer to symlinked data later on ``` which will start a web server in our JBrowse 2 directory. @@ -60,16 +116,245 @@ Your page should look something like this:
    -Click on the sample config to see JBrowse 2 running with a demo -configuration. It should look like this: +Click on the sample config to see JBrowse 2 running with a demo configuration. +It should look like this:
    Congratulations! You're running JBrowse 2. -## Next steps +## Adding tracks Now that JBrowse 2 is set up, you can configure it with your own genomes and -tracks. There are two ways you can configure JBrowse 2: with the JBrowse CLI -(guide [here](../tutorials/config_cli/)) or with JBrowse 2's built-in graphical -configuration editing (guide [here](../tutorials/config_gui/)). +tracks. + +### Adding a genome assembly in FASTA format + +The first step to creating a jbrowse config is to load a genome assembly. This +is normally in FASTA format, and we will start by creating a "FASTA index" with +`samtools`: + +```bash +samtools faidx genome.fa +jbrowse add-assembly genome.fa --load copy --out /var/www/html/jbrowse/ +``` + +This will output a configuration snippet to a file named +/var/www/html/jbrowse/config.json if it does not already exist, or append a new +assembly to that config file if it does exist. It will also copy genome.fa and +genome.fa.fai to the /var/www/html/jbrowse/ folder because we used --load copy. +If you wanted to symlink instead, can use --load symlink + +JBrowse 2 also supports other assembly file formats, including bgzip-compressed +indexed FASTA, and 2bit files. + +
    + +### Adding a BAM or CRAM track + +For this example we will use a BAM file to add an alignments track. As with +assemblies, you can add a track using local files or remote locations of your +files. + +```bash +samtools index file.bam +jbrowse add-track file.bam --load copy --out /var/www/html/jbrowse +samtools index file.cram +jbrowse add-track file.cram --load copy --out /var/www/html/jbrowse +``` + +This will add a track configuration entry to /var/www/html/jbrowse/config.json +and copy the files into the folder as well. If you use --load symlink, it can +symlink the files instead. To see more options adding the track, such as +specifying a name, run `jbrowse add-track --help`. + +If you have JBrowse 2 +[running as described](/docs/quickstart_web/#running-jbrowse-2) in the JBrowse +web quickstart, you can refresh the page and an add a linear genome view of the +volvox assembly. Then open track selector, and you will see the alignments +track. + +
    + +### Adding a VCF track + +Adding a variant track is similar to adding an alignments track. For this +example, we will use a VCF file for the track. JBrowse 2 expects VCFs to be +compressed with `bgzip` and `tabix` indexed. + +To add the track, run + +```bash +bgzip file.vcf +tabix file.vcf.gz +jbrowse add-track file.vcf.gz --load copy --out /var/www/html/jbrowse +``` + +:::note + +Note if you get errors about your VCF file not being sorted when using tabix, +you can use bcftools to sort your VCF. + +```bash +bcftools sort file.vcf > file.sorted.vcf +bgzip file.sorted.vcf +tabix file.sorted.vcf.gz +``` + +You can also bgzip and index with the `bcftools` tool. + +```bash +bcftools view volvox.vcf --output-type z > volvox.vcf.gz +rm volvox.vcf +bcftools index --tbi volvox.vcf.gz +``` + +For more info about `bgzip`, `tabix`, and `bcftools`, see +https://www.htslib.org/. + +::: + +
    + +### Adding a BigWig/BigBed track + +Probably one of the most simple track types to load is a BigWig/BigBed file +since it does not have any external index file, it is just a single file. + +```bash +jbrowse add-track file.bw --load copy --out /var/www/html/jbrowse +``` + +### Adding a GFF3 file with GFF3Tabix + +To load a GFF3 file, we can sort and index it with tabix, make sure you have +[GenomeTools](http://genometools.org/) (to install can use +`sudo apt install genometools`). + +```bash +gt gff3 -sortlines -tidy -retainids yourfile.gff > yourfile.sorted.gff +bgzip yourfile.sorted.gff +tabix yourfile.sorted.gff.gz +jbrowse add-track yourfile.sorted.gff.gz --load copy +``` + +As an alternative to `gt gff3 -sortlines`, use `awk` and GNU `sort`, as follows: + +```bash +awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -t\"\t\" -k1,1 -k4,4n"}' file.gff > file.sorted.gff +bgzip file.sorted.gff +tabix file.sorted.gff.gz +``` + +The `awk` command is inspired by the method in the +[tabix documentation](http://www.htslib.org/doc/tabix.html), but avoids +subshells and properly sets the tab delimiter for GNU sort in case there are +spaces in the GFF. + +### Adding a synteny track from a PAF file + +Loading synteny data makes use of all the previous functions we've used so far +in this guide. + +Here, we make use of the +[grape](https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz) +and +[peach](https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz) +genome assemblies, but replace with your own data if applicable. + +Use [minimap2](https://github.com/lh3/minimap2) to create a PAF file from FASTA +files: + +```bash +## Use minimap2 to create a PAF from your assemblies +minimap2 grape.fa peach.fa > peach_vs_grape.paf + +## add each assembly to jbrowse config +## the -n flag names the assemblies explicitly +jbrowse add-assembly grape.fa --load copy -n grape --out /var/www/html/jbrowse +jbrowse add-assembly peach.fa --load copy -n peach --out /var/www/html/jbrowse +``` + +Next, we'll load the synteny "track" from the PAF file. + +**Order matters here for the `--assemblyNames` parameter:** + +If minimap2 is run as `minimap2 grape.fa peach.fa`, then you need to load as +`--assemblyNames peach,grape`. + +The order is reversed between the `minimap2` and `jbrowse` tools. + +```bash +jbrowse add-track peach_vs_grape.paf --assemblyNames peach,grape --load copy --out /var/www/html/jbrowse +``` + +## Indexing feature names for searching + +The final step of loading your JBrowse instance may include adding a "search +index" so that you can search by genes or other features by their name or ID. + +To do this we can use the `jbrowse text-index` command: + +```bash +jbrowse text-index --out /var/www/html/jbrowse +``` + +This will index relevant track types e.g. any track with Gff3TabixAdapter (gene +names and IDs) or VcfTabixAdapter (e.g. variant IDs). The command will print out +a progress bar for each track that it is indexing. + +This will also update your `config.json` so that after it completes, you can +type a gene name into the "search box" in the linear genome view or other views +and quickly navigate to genes by gene name. + +See the [text-index](/docs/cli#jbrowse-text-index) command docs for more info. +Also see the [FAQ entries for text searching](/docs/faq#text-searching) + +## Conclusion + +Now that you have JBrowse configured with an assembly and a couple of tracks, +you can start customizing it further. Check out the rest of the docs for more +information, especially the [JBrowse CLI](/docs/cli) docs for more details on +some of the steps shown here. + +## Miscellaneous tips + +You can use `--subDir` to organize your data directory: + +```bash +mkdir my_bams +## Copies .bam and .bai files to my_bams folder +jbrowse add-track myfile.bam --subDir my_bams --load copy --out /var/www/html/jbrowse +``` + +### Upgrade JBrowse Web to the latest version + +You can upgrade your JBrowse release to the latest version with: + +```bash +# run this command in an existing jbrowse 2 installation +jbrowse upgrade +``` + +The above command downloads the latest jbrowse-web from github and unzips it +into the current directory + +### Upgrade @jbrowse/cli to the latest + +To upgrade the CLI tools, you can re-run the install command + +```bash +npm install -g @jbrowse/cli +``` + +### Output to a custom named config file, and output to subfolders + +You can use filenames other than config.json, and put configs in subfolders of +your jbrowse 2 installation too + +```bash +jbrowse add-assembly mygenome.fa --out /path/to/my/jbrowse2/subfolder/alt_config.json --load copy +``` + +This would then be accessible at e.g. +http://localhost/jbrowse2/?config=subfolder/alt_config.json diff --git a/website/docs/superquickstart_web.md b/website/docs/superquickstart_web.md index 89a68708cc..f53c011535 100644 --- a/website/docs/superquickstart_web.md +++ b/website/docs/superquickstart_web.md @@ -4,5 +4,6 @@ title: Super-quick start guide for JBrowse web toplevel: true --- -The contents of this page have been moved and merged into the [Configure -JBrowse using the CLI](../tutorials/config_cli) guide under User tutorials. +The contents of this page have been moved and merged into the +[Configure JBrowse using the CLI](/docs/tutorials/config_cli) guide under User +tutorials. diff --git a/website/docs/tex_parser.js b/website/docs/tex_parser.js index cbe49a93d3..6cdf1dcd04 100755 --- a/website/docs/tex_parser.js +++ b/website/docs/tex_parser.js @@ -11,6 +11,7 @@ let readingHeader = false let title = '' let topLevel = false +// eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { for await (const line of rl) { if (line.startsWith('import Figure')) { diff --git a/website/docs/title.md b/website/docs/title.md index 384e5037ed..2168a9378b 100644 --- a/website/docs/title.md +++ b/website/docs/title.md @@ -3,5 +3,12 @@ title: JBrowse 2 guide date: \today subtitle: jbrowse-version git-commit-sha geometry: 'left=2cm,right=2cm,top=2cm,bottom=2cm' -abstract: JBrowse 2 is a platform for genomics data visualization. JBrowse 2 is packaged as a web-app that can be setup on your server or as a executable that can be run on your desktop. It also has re-usable components that can be embedded in your web apps. This document includes a user manual with screenshots of how to use the app, a configuration guide for administrators, and developer documentation for programmers making JBrowse 2 plugins or core code modifications. +abstract: + JBrowse 2 is a platform for genomics data visualization. JBrowse 2 is packaged + as a web-app that can be setup on your server or as a executable that can be + run on your desktop. It also has re-usable components that can be embedded in + your web apps. This document includes a user manual with screenshots of how to + use the app, a configuration guide for administrators, and developer + documentation for programmers making JBrowse 2 plugins or core code + modifications. --- diff --git a/website/docs/tutorials/config_cli.md b/website/docs/tutorials/config_cli.md index ae1702cc1b..0b0972f67e 100644 --- a/website/docs/tutorials/config_cli.md +++ b/website/docs/tutorials/config_cli.md @@ -6,304 +6,4 @@ toplevel: true import Figure from '../figure' -In order to display your data, JBrowse 2 needs to know about the reference -genome for your organism of interest and needs to have tracks created that -reference your data sources. This guide will show you how to set those up using -the JBrowse CLI. - -:::note -You can also do this configuration with graphical configuration editing -interface built into JBrowse 2. See that guide [here](/docs/config_gui). -::: - -:::info -If you are an administrator configuring JBrowse on a webserver, you can add -the `--out` command followed by your target directory, e.g. `--out /var/www/html/jbrowse2` to write each JBrowse CLI configuration command to the -`config.json` in that target directory for your webserver to read from. - -::: - -## Pre-requisites - -- Installed and created your JBrowse environment using the [quickstart CLI - guide](/docs/quickstart_cli) -- Some bioinformatics tools: - - [Samtools](http://www.htslib.org/) installed e.g. `sudo apt install samtools` or `brew install samtools`, used for creating FASTA index and - BAM/CRAM processing - - [Genometools](http://genometools.org/) installed e.g. `sudo apt install genometools` or `brew install genometools`, (further, `brew install brewsci` and `brew install bio`) used for sorting GFF3 for creating tabix - GFF - - [tabix](http://www.htslib.org/doc/tabix.html) installed e.g. `sudo apt intall tabix` and `brew install htslib`, used for creating tabix indexes - for BED/VCF/GFF files - -### Loading a local FASTA file - -To use your own local data (in the following, replace "genome.fa" with your -FASTA file), you'll have to first create an index with samtools, then add it to -the `config.json` using a local reference: - -```bash -## Create an indexed (.fai) FASTA file using samtools -samtools faidx genome.fa -## Then, load it using the add-assembly command -## and add your genome assembly to the config -jbrowse add-assembly genome.fa --load copy --out /var/www/html/jbrowse -``` - -JBrowse 2 also supports other assembly file formats, including bgzip-compressed -indexed FASTA, and 2bit files. See [configuring -assemblies](/docs/config_guide#assembly-config) for more info on formats -supported for the sequence file. - -If you have your JBrowse 2 [running as -described](/docs/quickstart_cli/#running-jbrowse-2) in the JBrowse web -quickstart, you can refresh the page and an add a linear genome view. You will -now see your config in the Assembly dropdown. - -
    - -## Adding a track - -Now we will show you how to add an alignments track and a variant track to -JBrowse 2. - -### Adding an alignments track - -For this example we will use a BAM file to add an alignments track. - -As with assemblies, you can add a track using local files or remote locations -of your files. - -This example uses the following -[BAM](https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox.bam) and [BAM -index](https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox.bam.bai) -files downloaded locally as `/data/volvox.bam` and `/data/volvox.bam.bai` -respectively: - -```bash -## Replace with the location of your BAM file -jbrowse add-track /data/volvox.bam --load copy --out /var/www/html/jbrowse -``` - -:::note -If you're using your own local BAM file and need to generate an index, use samtools as follows: - -```bash -## Create an indexed BAM file using samtools -samtools index file.bam -## Add the BAM and BAI files to the JBrowse config -jbrowse add-track file.bam --load copy --out /var/www/html/jbrowse -``` - -::: - -This will copy the BAM and BAM index into the JBrowse 2 directory and add a -track pointing at those files to the config file. To see more options adding -the track, such as specifying a name, run `jbrowse add-track --help`. - -If you don't want to copy your BAM file, you can use `--move` to move the file -into the JBrowse 2 directory or `--symlink` to add a symlink to the file to the -JBrowse 2 directory. If you want more control over the location, you can use -`inPlace` to point the track at the file where it is, but be careful with this -option because on a traditional server you will need to ensure that the file is -in a place where the web server is serving it. - -If you have your JBrowse 2 [running as -described](../../quickstart_cli/#running-jbrowse-2) in the JBrowse web -quickstart, you can refresh the page and an add a linear genome view of the -volvox assembly. Then open track selector, and you will see the alignments -track. - -
    - -### Adding a variant track - -Adding a variant track is similar to adding an alignments track. For this -example, we will use a VCF file for the track. JBrowse 2 expects VCFs to be -compressed with `bgzip` and indexed. Similar to the above example, we will -assume the files are at `/data/volvox.vcf.gz` and `/data/volvox.vcf.gz.tbi`. -You can download these file here: -[VCF](https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox.vcf.gz) and -[VCF -index](https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox.vcf.gz.tbi). - -To add the track, run - -```bash -jbrowse add-track /data/volvox.vcf.gz --load copy --out /var/www/html/jbrowse -``` - -:::note - -If your VCF is not indexed, you can use the `bgzip` and `tabix` tools to -compress index it. - -```bash -bgzip yourfile.vcf -tabix yourfile.vcf.gz -``` - -Alternatively, you can do the same thing with the `bcftools` tool. - -```bash -bcftools view volvox.vcf --output-type z > volvox.vcf.gz -rm volvox.vcf -bcftools index --tbi volvox.vcf.gz -``` - -Note if you get errors about your VCF file not being sorted when using tabix, -you can use bcftools to sort your VCF. - -```bash -bcftools sort file.vcf > file.sorted.vcf -bgzip file.sorted.vcf -tabix file.sorted.vcf.gz -``` - -For more info about `bgzip`, `tabix`, and `bcftools`, see -https://www.htslib.org/. - -::: - -If you have your JBrowse 2 -[running as described](../../quickstart_cli/#running-jbrowse-2) in the JBrowse web -quickstart, you can refresh the page and an add a linear genome view of the -volvox assembly. Then open track selector, and you will see the variant track. - -
    - -### Adding a BigWig/BigBed track - -Probably one of the most simple track types to load is a BigWig/BigBed file -since it does not have any external index file, it is just a single file. - -Make use of this [example file](https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox-sorted.bam.coverage.bw) if you do not currently have your own data to add. - -```bash -## Download bigwig or bigbed file -jbrowse add-track volvox-sorted.bam.coverage.bw --load copy --out /var/www/html/jbrowse -``` - -### Adding a GFF3 file with GFF3Tabix - -To load a GFF3 file, we can sort and index it with tabix, make sure you have -[GenomeTools](http://genometools.org/) (to install can use `sudo apt install genometools`). - -```bash -gt gff3 -sortlines -tidy -retainids yourfile.gff > yourfile.sorted.gff -bgzip yourfile.sorted.gff -tabix yourfile.sorted.gff.gz -jbrowse add-track yourfile.sorted.gff.gz --load copy -``` - -As an alternative to `gt gff3 -sortlines`, use `awk` and GNU `sort`, as -follows: - -```bash -awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -t\"\t\" -k1,1 -k4,4n"}' file.gff > file.sorted.gff -bgzip file.sorted.gff -tabix file.sorted.gff.gz -``` - -The `awk` command is inspired by the method in the [tabix -documentation](http://www.htslib.org/doc/tabix.html), but avoids subshells and -properly sets the tab delimiter for GNU sort in case there are spaces in the -GFF. - -### Adding a synteny track - -Loading synteny data makes use of all the previous functions we've used so far -in this guide. - -Here, we make use of the -[grape](https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz) -and -[peach](https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz) -genome assemblies, but replace with your own data if applicable. - -Use [minimap2](https://github.com/lh3/minimap2) to create a PAF file from FASTA -files: - -```bash -## Use minimap2 to create a PAF from your assemblies -minimap2 grape.fa peach.fa > peach_vs_grape.paf - -## add each assembly to jbrowse config -## the -n flag names the assemblies explicitly -jbrowse add-assembly grape.fa --load copy -n grape --out /var/www/html/jbrowse -jbrowse add-assembly peach.fa --load copy -n peach --out /var/www/html/jbrowse -``` - -Next, we'll load the synteny "track" from the PAF file. - -**Order matters here for the `--assemblyNames` parameter:** - -If minimap2 is run as `minimap2 grape.fa peach.fa`, then you need to load as -`--assemblyNames peach,grape`. - -The order is reversed between the `minimap2` and `jbrowse` tools. - -```bash -jbrowse add-track peach_vs_grape.paf --assemblyNames peach,grape --load copy --out /var/www/html/jbrowse -``` - -## Indexing feature names for searching - -The final step of loading your JBrowse instance may include adding a "search -index" so that you can search by genes or other features by their name or ID. - -To do this we can use the `jbrowse text-index` command: - -```bash -jbrowse text-index --out /var/www/html/jbrowse -``` - -This will index relevant track types e.g. any track with Gff3TabixAdapter (gene -names and IDs) or VcfTabixAdapter (e.g. variant IDs). The command will print -out a progress bar for each track that it is indexing. - -This will also update your `config.json` so that after it completes, you can -type a gene name into the "search box" in the linear genome view or other views -and quickly navigate to genes by gene name. - -See the [text-index](/docs/cli#jbrowse-text-index) command docs for more info. -Also see the [FAQ entries for text searching](../../faq#text-searching) - -## Conclusion - -Now that you have JBrowse configured with an assembly and a couple of tracks, -you can start customizing it further. Check out the rest of the docs for more -information, especially the [JBrowse CLI](/docs/cli) docs for more details on -some of the steps shown here. - -## Miscellaneous tips - -You can use `--subDir` to organize your data directory: - -```bash -mkdir my_bams -## Copies .bam and .bai files to my_bams folder -jbrowse add-track myfile.bam --subDir my_bams --load copy --out /var/www/html/jbrowse -``` - -You can upgrade your JBrowse release to the latest version with: - -```bash -jbrowse upgrade -``` - -The above command downloads the latest jbrowse-web from github. - -To upgrade the CLI tools, you can re-run the install command - -```bash -npm install -g @jbrowse/CLI -``` - -You can use filenames that are different than config.json, and put them in -subfolders too - -```bash -## The following adds an assembly to the alt_config.json file specified -## To run JBrowse using this alt_config.json, navigate to http://localhost/jbrowse2/?config=subfolder/alt_config.json -jbrowse add-assembly mygenome.fa --out /path/to/my/jbrowse2/subfolder/alt_config.json --load copy -``` +Contents moved [/docs/quickstart_web](here) diff --git a/website/docs/tutorials/config_gui.md b/website/docs/tutorials/config_gui.md index d854e75094..1c03622386 100644 --- a/website/docs/tutorials/config_gui.md +++ b/website/docs/tutorials/config_gui.md @@ -1,6 +1,6 @@ --- id: config_gui -title: Configure JBrowse using the GUI +title: JBrowse web setup using the GUI toplevel: true --- @@ -22,9 +22,9 @@ You can also do this configuration with JBrowse CLI. See that guide This tutorial requires having the following software installed -- [JBrowse CLI](../../quickstart_cli/#installing-the-cli-tools) +- [JBrowse CLI](/docs/quickstart_web/#installing-the-cli-tools) -- [JBrowse 2 web application](../../quickstart_cli/#using-jbrowse-create-to-download-jbrowse-2) +- [JBrowse 2 web application](/docs/quickstart_web/#using-jbrowse-create-to-download-jbrowse-2) ## Starting JBrowse 2 admin server @@ -32,9 +32,11 @@ The JBrowse CLI contains a tool called `admin-server`. This will act as a web server for JBrowse 2 and will write any changes made in JBrowse 2 to a config file. -:::warning Note -The `admin-server` is meant to be used temporarily for configuration, **not in -production.** +:::warning + +Note The `admin-server` is meant to be used temporarily for configuration, **not +in production.** + ::: The `admin-server` launches an instance of JBrowse 2 in "admin mode", which then @@ -85,8 +87,8 @@ form:
    -Click on "Create New Assembly". Great, we've added an assembly! -We can see that we have successfully added the hg38 assembly: +Click on "Create New Assembly". Great, we've added an assembly! We can see that +we have successfully added the hg38 assembly:
    @@ -130,8 +132,8 @@ The following file formats are supported in core JBrowse 2: - 2bit - .hic (Hi-C contact matrix visualization) -Additional data formats can be supported via plugins; checkout the [plugin -store](/plugin_store). +Additional data formats can be supported via plugins; checkout the +[plugin store](/plugin_store). For tabix files, TBI or CSI indexes are allowed. CSI or BAI is allowed for BAM. Only CRAI is allowed for CRAM. The index will be inferred for BAI or TBI files @@ -140,43 +142,42 @@ index file explicitly. ### Editing a track -First, open a Linear Genome View using the navigation bar (`File > Add > Linear Genome View`), and click on the "Select Tracks" button. +First, open a Linear Genome View using the navigation bar +(`File > Add > Linear Genome View`), and click on the "Select Tracks" button. The configuration settings are accessible by clicking on the ellipses by each track.
    -Open the configuration editor for the track by clicking on the "Settings" -button shown above. You can use the configuration editor to live-edit any -configurable value for a given track. +Open the configuration editor for the track by clicking on the "Settings" button +shown above. You can use the configuration editor to live-edit any configurable +value for a given track. ## Setting a default session -It is also possible to use the graphical admin server to set the default -session of your JBrowse 2 instance. This is the session that will appear when -JBrowse 2 is first visited. To do so, open the form to set the default session +It is also possible to use the graphical admin server to set the default session +of your JBrowse 2 instance. This is the session that will appear when JBrowse 2 +is first visited. To do so, open the form to set the default session (`Admin > Set default session`):
    -You can use the form to clear your default session, -select the currently open session, or any of your previously saved sessions. +You can use the form to clear your default session, select the currently open +session, or any of your previously saved sessions. ## Additional resources There are a number of additional features for configuring JBrowse 2. Make sure -to refer to the [config guide](/docs/config_guide) for topics such as [adding -tracks](/docs/config_guide/#track-configurations) or [adding an assembly with -the CLI](/docs/config_guide/#adding-an-assembly-with-the-cli). +to refer to the [config guide](/docs/config_guide) for more topics. ## Conclusion -This guide showed how to launch the `admin-server` in the JBrowse CLI to -perform graphical configuration of your application. Specifically, we looked at -how to access and use the assembly manager, as well as how to access the -configuration editor for tracks. Importantly, all tracks have different -configuration options available in the configuration editor. +This guide showed how to launch the `admin-server` in the JBrowse CLI to perform +graphical configuration of your application. Specifically, we looked at how to +access and use the assembly manager, as well as how to access the configuration +editor for tracks. Importantly, all tracks have different configuration options +available in the configuration editor. Make sure to take a look at any tracks you add to JBrowse 2 that you might want to further configure! diff --git a/website/docs/tutorials/desktop_spec_plugin_tutorial.md b/website/docs/tutorials/desktop_spec_plugin_tutorial.md index 1f7cb9d70f..d51aae204d 100644 --- a/website/docs/tutorials/desktop_spec_plugin_tutorial.md +++ b/website/docs/tutorials/desktop_spec_plugin_tutorial.md @@ -6,7 +6,8 @@ toplevel: true import Figure from '../figure' -The following tutorial will demonstrate making a desktop-specific JBrowse plugin to run external tools such as bcftools and tabix on a VCF file. +The following tutorial will demonstrate making a desktop-specific JBrowse plugin +to run external tools such as bcftools and tabix on a VCF file. ## Prerequisites @@ -14,32 +15,53 @@ The following tutorial will demonstrate making a desktop-specific JBrowse plugin - A stable and recent version of [node](https://nodejs.org/en/) - yarn or npm - basic familiarity with the command line, React, package management, and npm -- bcftools installed `brew install bcftool`s or `sudo apt install bcftools` -- tabix installed `brew install htslib` or `sudo apt install htslib` +- `bcftools` installed `brew install bcftools` or `sudo apt install bcftools` +- `tabix` installed `brew install htslib` or `sudo apt install htslib` ## Why might I need a desktop-specific plugin -If you've developed a plugin before, you know that much of JBrowse 2's functionality can operate across both web and desktop instances of JBrowse. The main difference between the two applications has to do with JBrowse desktop's ability to run jobs on the machine it is running on, where web instances are beholden to the browser and the resources provided to it as a traditional web application. +If you've developed a plugin before, you know that much of JBrowse 2's +functionality can operate across both web and desktop instances of JBrowse. The +main difference between the two applications has to do with JBrowse desktop's +ability to run jobs on the machine it is running on, where web instances are +beholden to the browser and the resources provided to it as a traditional web +application. -JBrowse desktop utilizes [electron](https://www.electronjs.org/docs/latest) to distribute the Javascript application as a cross-platform desktop application. +JBrowse desktop utilizes [electron](https://www.electronjs.org/docs/latest) to +distribute the Javascript application as a cross-platform desktop application. -You might decide to build a desktop specific plugin if you need additional resources that are not distributed over the web to process data, if you need to run CLI operations, or otherwise run machine-specific tools through JBrowse. +You might decide to build a desktop specific plugin if you need additional +resources that are not distributed over the web to process data, if you need to +run CLI operations, or otherwise run machine-specific tools through JBrowse. ## Writing a desktop-specific plugin -In this tutorial, we are going to write a plugin that performs some of the file preparation steps outlined in the [CLI tutorial](../config_cli). Specifically, our plugin will provide users with an interface to submit their file, the simple script will accept the file, then the script will run the appropriate operations against it, and then it will provide JBrowse with the files in an acceptable format. This kind of workflow can only be done on JBrowse desktop. +In this tutorial, we are going to write a plugin that performs some of the file +preparation steps outlined in the [CLI tutorial](../config_cli). Specifically, +our plugin will provide users with an interface to submit their file, the simple +script will accept the file, then the script will run the appropriate operations +against it, and then it will provide JBrowse with the files in an acceptable +format. This kind of workflow can only be done on JBrowse desktop. -A completed version of this plugin can be found [here](https://github.com/carolinebridge-oicr/jbrowse-plugin-desktop-tools) if you get stuck following along. +A completed version of this plugin can be found +[here](https://github.com/carolinebridge-oicr/jbrowse-plugin-desktop-tools) if +you get stuck following along. + +:::info + +Presently there is no formal procedure to differentiate desktop-specific plugins +from universal plugins. Please include this information in the README of your +repository if making a public-facing plugin, and follow the outlined steps for +restricting plugin behaviour to desktop only. -:::info Note -Presently there is no formal procedure to differentiate desktop-specific plugins from universal plugins. Please include this information in the README of your repository if making a public-facing plugin, and follow the outlined steps for restricting plugin behaviour to desktop only. ::: ### Setup #### Use git to clone the plugin template -The easiest way to start developing your plugin for JBrowse 2 is to use the [plugin template](https://github.com/gmod/jbrowse-plugin-template). +The easiest way to start developing your plugin for JBrowse 2 is to use the +[plugin template](https://github.com/gmod/jbrowse-plugin-template). To clone the plugin template project, on the command line run: @@ -59,11 +81,14 @@ yarn init You'll be asked a few questions relating to your new project. -Most fields can be left blank, but **make sure to enter a descriptive name for your plugin** in the first field. +Most fields can be left blank, but **make sure to enter a descriptive name for +your plugin** in the first field. :::note Tip -A typical naming convention for JBrowse plugins is **"jbrowse-plugin-"**, or, if you are going to publish to an NPM organization, we advise **"@myscope/jbrowse-plugin-"**. +A typical naming convention for JBrowse plugins is **"jbrowse-plugin-"**, or, if +you are going to publish to an NPM organization, we advise +**"@myscope/jbrowse-plugin-"**. ::: @@ -75,7 +100,8 @@ yarn # or npm i #### Create a .jbrowse configuration file -To make things easier for testing, you're encouraged to make a simple .jbrowse configuration file. +To make things easier for testing, you're encouraged to make a simple .jbrowse +configuration file. It should look something like this: @@ -143,19 +169,32 @@ It should look something like this: } ``` -Ensure you change the assembly to one that coordinates with your own files, or use our [testing file](https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox.vcf.gz) (unzip it to get the raw vcf) with the configuration as shown above. You can download the [volvox sample assembly](https://github.com/carolinebridge-oicr/jbrowse-plugin-desktop-tools/blob/main/volvox.2bit) and place it in your root directory of your plugin running at localhost:9000. +Ensure you change the assembly to one that coordinates with your own files, or +use our +[testing file](https://jbrowse.org.s3.amazonaws.com/genomes/volvox/volvox.vcf.gz) +(unzip it to get the raw vcf) with the configuration as shown above. You can +download the +[volvox sample assembly](https://github.com/carolinebridge-oicr/jbrowse-plugin-desktop-tools/blob/main/volvox.2bit) +and place it in your root directory of your plugin running at localhost:9000. Place your myconfig.jbrowse file somewhere convenient; we'll open it later. #### Run JBrowse Desktop -Follow the [developing with JBrowse web and desktop tutorial](../develop_web_and_desktop_tutorial) to create a running instance of JBrowse 2 desktop. The tutorial will also have you run your template plugin on the app to test. +Follow the +[developing with JBrowse web and desktop tutorial](../develop_web_and_desktop_tutorial) +to create a running instance of JBrowse 2 desktop. The tutorial will also have +you run your template plugin on the app to test. ### Running CLI operations through JBrowse desktop #### Creating the UI -We'll need some way to accept the file from the user through the JBrowse UI. Adding a new widget here is the same as doing it for a typical JBrowse plugin (see the [simple JBrowse 2 plugin guide](../simple_plugin_tutorial/01_introduction) if you haven't already). +We'll need some way to accept the file from the user through the JBrowse UI. +Adding a new widget here is the same as doing it for a typical JBrowse plugin +(see the +[simple JBrowse 2 plugin guide](../simple_plugin_tutorial/01_introduction) if +you haven't already). 1. Create a basic component and add it through the plugin manager @@ -230,13 +269,22 @@ export default class DesktopToolsPlugin extends Plugin { } ``` -It is critical to include the `isElectron` check before installing your plugin. This method verifies that the process running the application is an electron app (i.e. desktop), and our plugin will (eventually) crash JBrowse if it is attempted to be run on web. By using this method where necessary, we ensure that if an individual runs JBrowse with a config file that includes this plugin on JBrowse web, the application will simply not install the plugin. +It is critical to include the `isElectron` check before installing your plugin. +This method verifies that the process running the application is an electron app +(i.e. desktop), and our plugin will (eventually) crash JBrowse if it is +attempted to be run on web. By using this method where necessary, we ensure that +if an individual runs JBrowse with a config file that includes this plugin on +JBrowse web, the application will simply not install the plugin. Try running your plugin as-is now: -`yarn start` your plugin, then, in your running instance of JBrowse desktop, navigate: `Open > select your myconfig.jbrowse file`. +`yarn start` your plugin, then, in your running instance of JBrowse desktop, +navigate: `Open > select your myconfig.jbrowse file`. -If you navigate `Add > Linear genome view > Open > Open track selector > + icon button > Add track` you should see your simple message display after selecting the "Raw variant track" option in the dropdown. +If you navigate +`Add > Linear genome view > Open > Open track selector > + icon button > Add track` +you should see your simple message display after selecting the "Raw variant +track" option in the dropdown. We'll add some more UI elements that allow us to do something more interesting: @@ -379,13 +427,17 @@ function LocalFileChooser(props: { } ``` -Above, we added a component that allows us to select a local file for processing. Its information is propagated, and we have access to its data through the model. +Above, we added a component that allows us to select a local file for +processing. Its information is propagated, and we have access to its data +through the model. -In the `onClick` method of our Submit button, we want to execute our CLI operations. +In the `onClick` method of our Submit button, we want to execute our CLI +operations. #### Setting up the script -To run a simple script, we're going to import the 'child_process' module from node: +To run a simple script, we're going to import the 'child_process' module from +node: **./src/MyToolWidget/MyToolWidget.tsx** @@ -404,7 +456,8 @@ function execute(command: any, callback: any) { // ... ``` -Now, we can provide a command through the command parameter after the "Submit" button is clicked on our UI: +Now, we can provide a command through the command parameter after the "Submit" +button is clicked on our UI: **./src/MyToolWidget/MyToolWidget.tsx** @@ -434,15 +487,20 @@ onClick={() => { // ... ``` -You can see how easy the execute function is to use now. Where we currently have "echo ${localPath}" is where we're going to write our CLI commands. +You can see how easy the execute function is to use now. Where we currently have +"echo ${localPath}" is where we're going to write our CLI commands. -If relevant when writing your own plugin, you can put any string of valid CLI commands here and your child process will execute them to the best of its ability. +If relevant when writing your own plugin, you can put any string of valid CLI +commands here and your child process will execute them to the best of its +ability. -Try refreshing your desktop instance and get the script to echo the localpath of your selected file. +Try refreshing your desktop instance and get the script to echo the localpath of +your selected file. #### Adding functionality to the script -For this plugin, the script we will run against the plain .vcf files provided through the JBrowse desktop UI will look like the following: +For this plugin, the script we will run against the plain .vcf files provided +through the JBrowse desktop UI will look like the following: ```bash bcftools sort "myfile.vcf" > "myfile.vcf.sorted.vcf" @@ -450,7 +508,9 @@ bgzip "myfile.vcf.sorted.vcf" tabix "myfile.vcf.sorted.vcf.gz ``` -Remember to install these libraries (detailed in the [prerequisites](#prerequisites)) before running your plugin operation. If a CLI operation cannot be executed, simply nothing happens. +Remember to install these libraries (detailed in the +[prerequisites](#prerequisites)) before running your plugin operation. If a CLI +operation cannot be executed, simply nothing happens. **./src/MyToolWidget/MyToolWidget.tsx** @@ -502,7 +562,9 @@ onClick={() => { ### Running the plugin on JBrowse desktop -We have all the necessary infrastructure to run our plugin completely now. If you haven't been testing and running your plugin along with the tutorial, remember you can run it with the following steps: +We have all the necessary infrastructure to run our plugin completely now. If +you haven't been testing and running your plugin along with the tutorial, +remember you can run it with the following steps: ```bash yarn serve # in the `~/jbrowse-components/products/jbrowse-desktop` directory @@ -516,9 +578,11 @@ yarn develop # in another terminal tab in the same `~/jbrowse-components/product yarn start # in another terminal tab in your plugin `~/jbrowse-plugin-my-plugin/` directory, or similar ``` -Then open your `.jbrowse` configuration file containing your plugin details, and navigate to the Add track workflow. +Then open your `.jbrowse` configuration file containing your plugin details, and +navigate to the Add track workflow. -Try using our volvox raw vcf file and volvox assembly for testing if you do not have your own data. +Try using our volvox raw vcf file and volvox assembly for testing if you do not +have your own data. Your final product should look something like the following: @@ -526,19 +590,33 @@ Your final product should look something like the following: ## Distributing the plugin -Distributing a desktop plugin is very similar to the [publishing steps outlined in the simple plugin tutorial](../simple_plugin_tutorial/04_publishing). +Distributing a desktop plugin is very similar to the +[publishing steps outlined in the simple plugin tutorial](../simple_plugin_tutorial/04_publishing). -As stated before, we encourage you to clearly indicate when a plugin is intended for desktop use only, as desktop-only operations are likely to crash when used on a web application. +As stated before, we encourage you to clearly indicate when a plugin is intended +for desktop use only, as desktop-only operations are likely to crash when used +on a web application. ## Next steps -After this tutorial you should have a general understanding of the capabilities and potential desktop-only workflows that can be developed for a plugin for JBrowse 2. +After this tutorial you should have a general understanding of the capabilities +and potential desktop-only workflows that can be developed for a plugin for +JBrowse 2. -It should be reiterated that the functionality outlined in this tutorial is a simple example to get you started with working on more complicated workflows with more tools -- virtually anything you might do with a script or on the command line can be integrated into the JBrowse UI to streamline a workflow, for example, creating BigWig files from BAM/CRAM files with mosdepth, gunzip, and bedGraphToBigWig tools. +It should be reiterated that the functionality outlined in this tutorial is a +simple example to get you started with working on more complicated workflows +with more tools -- virtually anything you might do with a script or on the +command line can be integrated into the JBrowse UI to streamline a workflow, for +example, creating BigWig files from BAM/CRAM files with mosdepth, gunzip, and +bedGraphToBigWig tools. -If you'd like some general development information, checkout the series of [developer guides](../../developer_guide) available. +If you'd like some general development information, checkout the series of +[developer guides](/docs/developer_guide) available. ### Core takeaways -- developing a plugin specifically for desktop can allow you to run operations locally or on a private process through JBrowse to assist in data display or development -- the `isElectron` function exported by `@jbrowse/core/util` is critical in identifying codeblocks that can only be executed when running on JBrowse +- developing a plugin specifically for desktop can allow you to run operations + locally or on a private process through JBrowse to assist in data display or + development +- the `isElectron` function exported by `@jbrowse/core/util` is critical in + identifying codeblocks that can only be executed when running on JBrowse diff --git a/website/docs/tutorials/develop_web_and_desktop_tutorial.md b/website/docs/tutorials/develop_web_and_desktop_tutorial.md index 81228b1717..1f62d616ab 100644 --- a/website/docs/tutorials/develop_web_and_desktop_tutorial.md +++ b/website/docs/tutorials/develop_web_and_desktop_tutorial.md @@ -6,9 +6,13 @@ toplevel: true import Figure from '../figure' -The following guide will walk you through setting up a developer environment for development with JBrowse web and JBrowse desktop. +The following guide will walk you through setting up a developer environment for +development with JBrowse web and JBrowse desktop. -This guide will provide some steps from the perspective of a plugin developer, but if you are interested in contributing to [jbrowse-components](https://github.com/GMOD/jbrowse-components/), the setup steps are equally relevant. +This guide will provide some steps from the perspective of a plugin developer, +but if you are interested in contributing to +[jbrowse-components](https://github.com/GMOD/jbrowse-components/), the setup +steps are equally relevant. ## Prerequisites @@ -19,7 +23,9 @@ This guide will provide some steps from the perspective of a plugin developer, b ## Setup JBrowse 2 using the latest developer build -The code for both JBrowse web and JBrowse desktop is found in the [jbrowse-components](https://github.com/GMOD/jbrowse-components/) repository. First we're going to clone the repo and install the dependencies. +The code for both JBrowse web and JBrowse desktop is found in the +[jbrowse-components](https://github.com/GMOD/jbrowse-components/) repository. +First we're going to clone the repo and install the dependencies. ```bash git clone https://github.com/GMOD/jbrowse-components @@ -38,7 +44,11 @@ JBrowse web will by default spin up on http://localhost:3000.
    -You can select one of the sample configs to poke around with or to immediately start seeing changes you make in the codebase, or you can run JBrowse against a config with the plugin you're developing. See [the plugin tutorial](../simple_plugin_tutorial/01_introduction) if you need help starting with plugin development. +You can select one of the sample configs to poke around with or to immediately +start seeing changes you make in the codebase, or you can run JBrowse against a +config with the plugin you're developing. See +[the plugin tutorial](../simple_plugin_tutorial/01_introduction) if you need +help starting with plugin development. If you have a plugin running on port 9000 from the plugin tutorial, navigate to @@ -46,7 +56,8 @@ If you have a plugin running on port 9000 from the plugin tutorial, navigate to http://localhost:3000/?config=http://localhost:9000/jbrowse_config.json ``` -and you'll see the pluggable elements you've added through your plugin on your running JBrowse session. +and you'll see the pluggable elements you've added through your plugin on your +running JBrowse session.
    @@ -66,23 +77,33 @@ cd products/jbrowse-desktop yarn develop ``` -Doing this, you can quickly restart the "react app" part of JBrowse (the tab where you ran `yarn develop`) during your development without having to wait for the electron app (`yarn serve` tab) to restart, as you would if you simply ran `yarn start` in one tab. +Doing this, you can quickly restart the "react app" part of JBrowse (the tab +where you ran `yarn develop`) during your development without having to wait for +the electron app (`yarn serve` tab) to restart, as you would if you simply ran +`yarn start` in one tab. A new window running JBrowse desktop will open. ### Running JBrowse desktop with a plugin in development -The following assumes your plugin is running on port `9000`, as shown in the [the plugin tutorial](../simple_plugin_tutorial/02_installation_and_setup). +The following assumes your plugin is running on port `9000`, as shown in the +[the plugin tutorial](../simple_plugin_tutorial/02_installation_and_setup). -JBrowse will open on the splash screen when first spun up. The easiest way to see your local plugin running on JBrowse desktop is to select a quickstart assembly (under "Launch new session" on the left side of the screen) and then press "Go". +JBrowse will open on the splash screen when first spun up. The easiest way to +see your local plugin running on JBrowse desktop is to select a quickstart +assembly (under "Launch new session" on the left side of the screen) and then +press "Go".
    -Then navigate: `Tools` -> `Plugin Store` and press the button at the top of the Plugin Store widget "Add Custom Plugin." +Then navigate: `Tools` -> `Plugin Store` and press the button at the top of the +Plugin Store widget "Add Custom Plugin."
    -It's important to fill these fields in correctly, if you've followed the [the plugin tutorial](../simple_plugin_tutorial/01_introduction), the information you need will be in the `jbrowse_config.json` file. +It's important to fill these fields in correctly, if you've followed the +[the plugin tutorial](../simple_plugin_tutorial/01_introduction), the +information you need will be in the `jbrowse_config.json` file. You might see something like the following in your `jbrowse_config.json` file: @@ -101,30 +122,38 @@ To which you would fill the fields in like so:
    -After pressing "Submit" on this form, your plugin should be added to your session. +After pressing "Submit" on this form, your plugin should be added to your +session. -For easy access to this session, navigate `File` -> `Save as..` to save the `.jbrowse` file somewhere you can easily open it. +For easy access to this session, navigate `File` -> `Save as..` to save the +`.jbrowse` file somewhere you can easily open it. -:::warning Note -When developing your plugin using JBrowse desktop, the app will not automatically reload when you make changes to your plugin code. To see these changes applied, **press `F5` to refresh the desktop react application**. +:::warning Note When developing your plugin using JBrowse desktop, the app will +not automatically reload when you make changes to your plugin code. To see these +changes applied, **press `F5` to refresh the desktop react application**. -You can also abort the running process under the "yarn develop" tab we set up earlier, and start it again. -::: +You can also abort the running process under the "yarn develop" tab we set up +earlier, and start it again. ::: -:::info -If you would like to see your `console.log` output under the "yarn develop" tab of your desktop development environment, follow these steps: +:::info If you would like to see your `console.log` output under the "yarn +develop" tab of your desktop development environment, follow these steps: -1. Create or edit the `.bash_profile` file typically found in the root directory of your profile +1. Create or edit the `.bash_profile` file typically found in the root directory + of your profile 2. Add `export ELECTRON_ENABLE_LOGGING=1` on a new line to the file 3. Restart your terminal and JBrowse `yarn develop` process -You should now be able to see console log statements in your terminal when developing on JBrowse desktop (denoted by a message prefixed with something like INFO:CONSOLE). -::: +You should now be able to see console log statements in your terminal when +developing on JBrowse desktop (denoted by a message prefixed with something like +INFO:CONSOLE). ::: ## Next Steps -Now that you have your environments and your plugin running, you can start developing for JBrowse 2. +Now that you have your environments and your plugin running, you can start +developing for JBrowse 2. -If you took a detour from the plugin tutorial, [head back to where you left off](../simple_plugin_tutorial/03_adding_pluggable_element). +If you took a detour from the plugin tutorial, +[head back to where you left off](../simple_plugin_tutorial/03_adding_pluggable_element). -If you'd like some general development information, checkout the series of [developer guides](../../developer_guide) available. +If you'd like some general development information, checkout the series of +[developer guides](../../developer_guide) available. diff --git a/website/docs/tutorials/embed_linear_genome_view/01_introduction.md b/website/docs/tutorials/embed_linear_genome_view/01_introduction.md index 67da3cc6be..c9d0af53d2 100644 --- a/website/docs/tutorials/embed_linear_genome_view/01_introduction.md +++ b/website/docs/tutorials/embed_linear_genome_view/01_introduction.md @@ -6,16 +6,16 @@ title: Introduction ## Welcome! This tutorial will show you how to get a JBrowse 2 linear genome view embedded -in a website. It is similar to a [tutorial given a -BCC2020](../../archive/bcc2020_embedding_jbrowse_01_getting_started), but has -been updated to reflect the final, released version of the interface. +in a website. It is similar to a +[tutorial given a BCC2020](../../archive/bcc2020_embedding_jbrowse_01_getting_started), +but has been updated to reflect the final, released version of the interface. ## What is JBrowse 2 JBrowse 2 is a pluggable open-source platform for visualizing and integrating -biological data. At its core, it is a [genome -browser](https://en.wikipedia.org/wiki/Genome_browser), but it has also been -built as an extensible platform to enable visualization of all kinds of +biological data. At its core, it is a +[genome browser](https://en.wikipedia.org/wiki/Genome_browser), but it has also +been built as an extensible platform to enable visualization of all kinds of biological data. For those of you who have used the original JBrowse, you'll recognize many of @@ -49,16 +49,15 @@ This tutorial is a good fit if you have an existing web page and you'd like to have JBrowse running inside that page, although in the tutorial we'll create a page from scratch so you don't need an existing page to do this tutorial. -If your web page is built with React, you can install our [JBrowse Linear -Genome View React -Component](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) +If your web page is built with React, you can install our +[JBrowse Linear Genome View React Component](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) from NPM instead of adding it like is done in this guide. A lot of the content -of this tutorial would still be relevant to setting up and configuring the -view, though. +of this tutorial would still be relevant to setting up and configuring the view, +though. Also, another option for your web site is to add the full JBrowse Web app as a -new page in your site. This might be an option if the JBrowse Linear Genome -View is missing features you need. +new page in your site. This might be an option if the JBrowse Linear Genome View +is missing features you need. ## What you need @@ -68,12 +67,12 @@ installers [here](https://nodejs.org/en/download/), or if you are on Mac or Linux and plan on doing more extensive JavaScript development, we recommend using [NVM](https://github.com/nvm-sh/nvm). -You can do most of this tutorial with a simple text editor and some way to -serve files (just opening the HTML files we create in a browser won't work, -you'll need a server). If you have Node.js installed, you can run a simple -server by opening your terminal in the directory you want to serve and running -`npx serve` (or you can install it globally with `npm install -g serve` and -then run `serve`). +You can do most of this tutorial with a simple text editor and some way to serve +files (just opening the HTML files we create in a browser won't work, you'll +need a server). If you have Node.js installed, you can run a simple server by +opening your terminal in the directory you want to serve and running `npx serve` +(or you can install it globally with `npm install -g serve` and then run +`serve`). We'll also be using the JBrowse CLI, although you can technically complete the tutorial without it. You can install it after installing Node.js by running diff --git a/website/docs/tutorials/embed_linear_genome_view/02_simple_site.md b/website/docs/tutorials/embed_linear_genome_view/02_simple_site.md index 98df71dab9..499df7b403 100644 --- a/website/docs/tutorials/embed_linear_genome_view/02_simple_site.md +++ b/website/docs/tutorials/embed_linear_genome_view/02_simple_site.md @@ -5,11 +5,11 @@ title: Beginnings of a simple site ## Create a simple web page -Let's get started! The first thing we're going to do is create a simple web -page into which we can embed JBrowse Linear Genome View. First, create a folder -to the files in. Inside that folder, create a new file called "index.html" and -open it in your preferred text editor/IDE. Paste the following into the file -and save it: +Let's get started! The first thing we're going to do is create a simple web page +into which we can embed JBrowse Linear Genome View. First, create a folder to +the files in. Inside that folder, create a new file called "index.html" and open +it in your preferred text editor/IDE. Paste the following into the file and save +it: ```html title="index.html" @@ -46,10 +46,10 @@ way to adding JBrowse Linear Genome View to a web site! To add JBrowse Linear Genome View, you need to add the source to your page and then render the component. Since JBrowse Linear Genome View uses React for -rendering, you'll also need to load the React source, too. We'll start by -adding a `head` to our page and use it to load the sources and a `div` that -will hold JBrowse. Update your "index.html" so matches what's below, then save -it, switch over to your browser, and refresh the page. +rendering, you'll also need to load the React source, too. We'll start by adding +a `head` to our page and use it to load the sources and a `div` that will hold +JBrowse. Update your "index.html" so matches what's below, then save it, switch +over to your browser, and refresh the page. ```html {2-16,19} title="index.html" @@ -77,11 +77,10 @@ it, switch over to your browser, and refresh the page. Now we can check if the script loaded properly. In your browser, open the developer tools (You can use F12 or -Ctrl+Shift+I or right-click the page and -select "Inspect") and go to the "Network" tab. If you see something like the -below with a status of 200 for "react-linear-genome-view.umd.development.js," -"react-dom.development.js," and "react.development.js," then you are good to -go! +Ctrl+Shift+I or right-click the page and select +"Inspect") and go to the "Network" tab. If you see something like the below with +a status of 200 for "react-linear-genome-view.umd.development.js," +"react-dom.development.js," and "react.development.js," then you are good to go! ![Network tab of developer tools showing that scripts have loaded correctly](./img/network_success.png) diff --git a/website/docs/tutorials/embed_linear_genome_view/03_assemblies.md b/website/docs/tutorials/embed_linear_genome_view/03_assemblies.md index 4d40ddc5f6..3c1ba1c5de 100644 --- a/website/docs/tutorials/embed_linear_genome_view/03_assemblies.md +++ b/website/docs/tutorials/embed_linear_genome_view/03_assemblies.md @@ -6,11 +6,11 @@ title: About assemblies ## What is an assembly? An assembly in JBrowse 2 is a collection of information that describes the -organism you are working with, such as its name and its reference sequence. -This is what JBrowse 2 uses to set up the coordinate system for the genome -browser and keep tracks organized. In JBrowse Web, you are able to have -multiple assemblies on screen at the same time. JBrowse Linear Genome View, -however, is more focused and allows just one assembly. +organism you are working with, such as its name and its reference sequence. This +is what JBrowse 2 uses to set up the coordinate system for the genome browser +and keep tracks organized. In JBrowse Web, you are able to have multiple +assemblies on screen at the same time. JBrowse Linear Genome View, however, is +more focused and allows just one assembly. These are the options you can specify for an assembly: @@ -40,8 +40,8 @@ assembly. ### Installing JBrowse CLI The JBrowse 2 CLI is designed to set up a configuration file for JBrowse Web, -but since JBrowse Linear Genome View is based on the same code, we can use it -to generate what we need as well. +but since JBrowse Linear Genome View is based on the same code, we can use it to +generate what we need as well. The instructions for installing JBrowse CLI are on the "[Introduction](../01_introduction)" page. After installing, if you run the @@ -65,17 +65,17 @@ get installed. ### Gathering files -Let's use a human GRCh38 assembly as our example. First we need a sequence -file. We'll use this url: +Let's use a human GRCh38 assembly as our example. First we need a sequence file. +We'll use this url: https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz. -We also need to define some reference sequence name aliases so that any files -we want to use that use "chr1" instead of "1" will display correctly. There is -an alias file that we can use at +We also need to define some reference sequence name aliases so that any files we +want to use that use "chr1" instead of "1" will display correctly. There is an +alias file that we can use at http://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/GRCh38.aliases.txt. -This aliases file has on each line a name from the reference sequence and then -a tab-separated list of aliases for that name. +This aliases file has on each line a name from the reference sequence and then a +tab-separated list of aliases for that name. ### Running the `jbrowse` command diff --git a/website/docs/tutorials/embed_linear_genome_view/04_tracks.md b/website/docs/tutorials/embed_linear_genome_view/04_tracks.md index a2a453bbe0..82f913b4df 100644 --- a/website/docs/tutorials/embed_linear_genome_view/04_tracks.md +++ b/website/docs/tutorials/embed_linear_genome_view/04_tracks.md @@ -6,9 +6,9 @@ title: About tracks ## What is a track? A track is the place to display your data files in JBrowse Linear Genome View. -For this tutorial we're going to add a gene track, an [alignments -track](/docs/user_guides/alignment_track), and a [variants -track](/docs/user_guides/variant_track). We're just going to use basic +For this tutorial we're going to add a gene track, an +[alignments track](/docs/user_guides/alignment_track), and a +[variants track](/docs/user_guides/variant_track). We're just going to use basic configuration, but check the links for the track types to see what kinds of things you can configure in them. @@ -45,8 +45,8 @@ jbrowse add-track https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments jbrowse add-track https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz --name "1000 Genomes Variant Calls" --category "1000 Genomes, Variants" --skipCheck ``` -Open "config.json" again and look at the tracks that were generated. You can -see that again, it has guessed index locations for you, which you can change if +Open "config.json" again and look at the tracks that were generated. You can see +that again, it has guessed index locations for you, which you can change if needed. Create a new file called "tracks.js" and copy the tracks array into it and have it be exported, like this: diff --git a/website/docs/tutorials/embed_linear_genome_view/09_conclusion.md b/website/docs/tutorials/embed_linear_genome_view/09_conclusion.md index d6b23e4ef8..016f0ecd55 100644 --- a/website/docs/tutorials/embed_linear_genome_view/09_conclusion.md +++ b/website/docs/tutorials/embed_linear_genome_view/09_conclusion.md @@ -10,12 +10,11 @@ experiment and explore. Some things to try might be: - Add two views to the same web page - Find your own files to add as tracks -- Explore the [configuration guide](../../../config_guide) and learn how to do +- Explore the [configuration guide](/docs/config_guide) and learn how to do things like customize the colors of features in your tracks Let us know how things go. We'd love to hear your feedback or help you in any -way we can. Our contact information can be found -[here](/contact). +way we can. Our contact information can be found [here](/contact). Happy hacking! diff --git a/website/docs/tutorials/no_build_plugin_tutorial.md b/website/docs/tutorials/no_build_plugin_tutorial.md index cbd643e02a..938bc9ec37 100644 --- a/website/docs/tutorials/no_build_plugin_tutorial.md +++ b/website/docs/tutorials/no_build_plugin_tutorial.md @@ -6,13 +6,13 @@ toplevel: true import Figure from '../figure' -The following guide will provide a short tutorial on how to create a single -page no-build plugin for JBrowse 2. +The following guide will provide a short tutorial on how to create a single page +no-build plugin for JBrowse 2. ## Prerequisites -- you can run an instance of JBrowse 2 on the web, see [any of our quickstart - guides](../../quickstart_cli) for details +- you can run an instance of JBrowse 2 on the web, see + [any of our quickstart guides](/docs/quickstart_web) for details - a stable and recent version of [node](https://nodejs.org/en/) - basic familiarity with the command line and navigating the file system @@ -21,18 +21,17 @@ page no-build plugin for JBrowse 2. A "regular" JBrowse plugin often uses our plugin template https://github.com/GMOD/jbrowse-plugin-template which uses `rollup` to compile extra dependencies that your plugin might use. In contrast, "no-build" plugins -have no build step and can be hand edited. This can be useful for adding [extra -jexl config callbacks for making extra config callbacks or similar -modifications](/docs/config_guide/#making-sophisticated-color-callbacks). +have no build step and can be hand edited. This can be useful for adding +[extra jexl config callbacks for making extra config callbacks or similar modifications](/docs/config_guides/customizing_feature_colors/). ## Writing a no-build plugin ### Adding a callback function which you can use in your config -A common method for a no-build plugin might be making a custom function that -you can use to simplify `jexl` callbacks in your config. We will create a file -`myplugin.js`, which will contain a ["UMD"](https://github.com/umdjs/umd) -module providing a single "Plugin" class [1]. +A common method for a no-build plugin might be making a custom function that you +can use to simplify `jexl` callbacks in your config. We will create a file +`myplugin.js`, which will contain a ["UMD"](https://github.com/umdjs/umd) module +providing a single "Plugin" class [1]. `myplugin.js` @@ -104,16 +103,17 @@ you can refer to this plugin and the custom function you added in your config. } ``` -[1] Note that you can also provide an ESM module that has just `export default class` but this is not supported by all browsers, notably firefox, which cannot -import ESM files in webworkers, so for maximum compatibility, we show are using -the UMD format still. Once firefox gains support for ESM modules, we will -update this! +[1] Note that you can also provide an ESM module that has just +`export default class` but this is not supported by all browsers, notably +firefox, which cannot import ESM files in webworkers, so for maximum +compatibility, we show are using the UMD format still. Once firefox gains +support for ESM modules, we will update this! ### Adding a global menu item Another example of a no-build plugin is to add menu items or minor extension -points. Here, we're going to add a menu item using the `configure` method in -the plugin class. +points. Here, we're going to add a menu item using the `configure` method in the +plugin class. `myplugin.js` @@ -137,9 +137,8 @@ the plugin class. Because our plugin is not going to be built with any dependencies, the process for referencing external libraries is a little different. -If a package you need to use is found within the JBrowse core project, a -special function `jbrequire` can provide your plugin access to these packages. -Click +If a package you need to use is found within the JBrowse core project, a special +function `jbrequire` can provide your plugin access to these packages. Click [here](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/ReExports/list.ts) for a full list of packages accessible through `jbrequire`. Using `jbrequire` might look like this: @@ -214,7 +213,7 @@ export default class MyNoBuildPlugin { pluginManager.rootModel.appendToMenu('Citations', { label: 'Cite this JBrowse session', onClick: session => { - // upon clicking on htis menu item, we need to add and show our new widget + // upon clicking on this menu item, we need to add and show our new widget const widget = session.addWidget('CiteWidget', 'citeWidget', { view: self, }) @@ -235,7 +234,7 @@ should look like the following: Congratulations! You built and ran a single file no-build plugin in JBrowse. If you'd like some general development information, checkout the series of -[developer guides](../../developer_guide) available. +[developer guides](/docs/developer_guide) available. Have some questions? [Contact us](/contact) through our various communication channels. diff --git a/website/docs/tutorials/plugin_usage.md b/website/docs/tutorials/plugin_usage.md index e88c7d4ec5..f33fd2403b 100644 --- a/website/docs/tutorials/plugin_usage.md +++ b/website/docs/tutorials/plugin_usage.md @@ -6,31 +6,41 @@ toplevel: true import Figure from '../figure' -The following will provide a short tutorial on how to use some of the [many plugins available](/plugin_store) for JBrowse 2. +The following will provide a short tutorial on how to use some of the +[many plugins available](/plugin_store) for JBrowse 2. -Those plugins featured here are a part of the cancer-related database plugins on the [cancer portal](/cancer). +Those plugins featured here are a part of the cancer-related database plugins on +the [cancer portal](/cancer). ## Prerequisites - JBrowse 2 is [installed on web or desktop](../../quickstart_web) - Familiarity editing JSON -- Optionally, the [JBrowse CLI installed](../../quickstart_cli) +- Optionally, the [JBrowse CLI installed](../../quickstart_web) ## Installing plugins with one click -Some plugins provide all of their available functionality via the JBrowse interface, and thus can be fully accessed after utilizing the one-click install plugin store within the application. +Some plugins provide all of their available functionality via the JBrowse +interface, and thus can be fully accessed after utilizing the one-click install +plugin store within the application.
    ### GDC plugin -The GDC plugin adapts the resources available through [NCI's Genomic Data Commons](https://gdc.cancer.gov/). +The GDC plugin adapts the resources available through +[NCI's Genomic Data Commons](https://gdc.cancer.gov/). -The GDC plugin provides data adapters for the GDC API to retrieve cancer-related mutations and genes and for unique file types available via the GDC data store. The GDC plugin also provides a new internet account type that permits users to enter their GDC token to authenticate against protected data. +The GDC plugin provides data adapters for the GDC API to retrieve cancer-related +mutations and genes and for unique file types available via the GDC data store. +The GDC plugin also provides a new internet account type that permits users to +enter their GDC token to authenticate against protected data. #### Adding the GDC plugin to a JBrowse session -The GDC plugin is fully accessible through the JBrowse interface. Utilize the plugin store's one-click install, or add the plugin to your configuration file, like so: +The GDC plugin is fully accessible through the JBrowse interface. Utilize the +plugin store's one-click install, or add the plugin to your configuration file, +like so: ```json { @@ -72,17 +82,22 @@ Optionally, you can add a GDC Track to your configuration like so: } ``` -However these track types are also available to be added to a session via the GDC data import panel. +However these track types are also available to be added to a session via the +GDC data import panel.
    #### The GDC data import panel -The data import panel provides several options to import data originating from the GDC into JBrowse. +The data import panel provides several options to import data originating from +the GDC into JBrowse. -If you have GDC files downloaded locally, you can drag and drop them into the first Drag and Drop panel to populate your JBrowse session with them. +If you have GDC files downloaded locally, you can drag and drop them into the +first Drag and Drop panel to populate your JBrowse session with them. -You can also utilize an export functionality available via the GDC to bulk-import files if you drag that file into the panel. More detailed instructions are provided via the 'more info' button on the panel. +You can also utilize an export functionality available via the GDC to +bulk-import files if you drag that file into the panel. More detailed +instructions are provided via the 'more info' button on the panel.
    @@ -90,13 +105,16 @@ You can also utilize an export functionality available via the GDC to bulk-impor #### Adding files via the add track menu -Once installed, the track types and adapters provided by the GDC plugin are also available via the typical add track workflow. +Once installed, the track types and adapters provided by the GDC plugin are also +available via the typical add track workflow.
    #### How do I authenticate protected resources -Ensure that you have added the GDC internet account type to your configuration file. Presently, this must be done manually. Open the config file in a text processor and add the following: +Ensure that you have added the GDC internet account type to your configuration +file. Presently, this must be done manually. Open the config file in a text +processor and add the following: ```json { @@ -109,31 +127,46 @@ Ensure that you have added the GDC internet account type to your configuration f } ``` -When you attempt to add a protected resource to your session either via the add track menu or the GDC data import panel, you will be prompted with a modal overlay to add your GDC token to the session. This token will be retained for other resources you add such that you will not have to add your token every time. +When you attempt to add a protected resource to your session either via the add +track menu or the GDC data import panel, you will be prompted with a modal +overlay to add your GDC token to the session. This token will be retained for +other resources you add such that you will not have to add your token every +time. #### Filtering the GDC Explore track -When you have a GDC Explore track added to a session either via the config file or via the data import panel, you will be able to filter the features displayed on the track using the Filter option available through the track menu. +When you have a GDC Explore track added to a session either via the config file +or via the data import panel, you will be able to filter the features displayed +on the track using the Filter option available through the track menu.
    -You can change whether you're seeing mutations or genes using the topmost dropdown menu. +You can change whether you're seeing mutations or genes using the topmost +dropdown menu. -You can browse through the various filters via the tabs, and add new filters by clicking the 'add' button on the interface. +You can browse through the various filters via the tabs, and add new filters by +clicking the 'add' button on the interface. -Changes made through the filter widget will populated automatically on the track it was opened for. +Changes made through the filter widget will populated automatically on the track +it was opened for. -The bottom-most dropdown menu provides coloration options for the track, such that you can change the color in which features are represented based on a certain trait. A legend is provided to guide which color corresponds to which feature. +The bottom-most dropdown menu provides coloration options for the track, such +that you can change the color in which features are represented based on a +certain trait. A legend is provided to guide which color corresponds to which +feature.
    ### ICGC plugin -The ICGC plugin adapts the resources available through the [International Cancer Genome Consortium](https://dcc.icgc.org/). +The ICGC plugin adapts the resources available through the +[International Cancer Genome Consortium](https://dcc.icgc.org/). #### Adding the ICGC plugin to a JBrowse session -The ICGC plugin is fully accessible through the JBrowse interface. Utilize the plugin store's one-click install, or add the plugin to your configuration file, like so: +The ICGC plugin is fully accessible through the JBrowse interface. Utilize the +plugin store's one-click install, or add the plugin to your configuration file, +like so: ```json { @@ -168,23 +201,31 @@ Optionally, you can add an ICGC Track to your configuration like so: }, ``` -However these track types are also available to be added to a session via the ICGC data import panel. +However these track types are also available to be added to a session via the +ICGC data import panel.
    #### Filtering the ICGC track -The instructions for how to use the filtering functionality of the ICGC track are essentially the same as [those for the GDC Explore track](#filtering-the-gdc-explore-track). Please refer to those instructions. +The instructions for how to use the filtering functionality of the ICGC track +are essentially the same as +[those for the GDC Explore track](#filtering-the-gdc-explore-track). Please +refer to those instructions.
    ## Configuring plugins -Some plugins _require_ their tracks to be configured via the config file because they access remote resources and do not otherwise provide a way to add these tracks to a session. After these plugins have been configured, you can use them with the appropriate assembly like any other track. +Some plugins _require_ their tracks to be configured via the config file because +they access remote resources and do not otherwise provide a way to add these +tracks to a session. After these plugins have been configured, you can use them +with the appropriate assembly like any other track. ### UCSC plugin -The UCSC plugin provides access to resources available through the [UCSC API](https://genome.ucsc.edu/goldenPath/help/api.html). +The UCSC plugin provides access to resources available through the +[UCSC API](https://genome.ucsc.edu/goldenPath/help/api.html). You can add the UCSC plugin to your JBrowse config file as follows: @@ -199,7 +240,8 @@ You can add the UCSC plugin to your JBrowse config file as follows: } ``` -Then add the available tracks that are relevant to you under your "tracks" configuration, for example: +Then add the available tracks that are relevant to you under your "tracks" +configuration, for example: ```json { @@ -215,13 +257,17 @@ Then add the available tracks that are relevant to you under your "tracks" confi } ``` -Make sure to reference the many other available tracks in the [UCSC example config](https://github.com/cmdcolin/jbrowse-plugin-ucsc-api/blob/master/config.json) +Make sure to reference the many other available tracks in the +[UCSC example config](https://github.com/cmdcolin/jbrowse-plugin-ucsc-api/blob/master/config.json) -After adding one or more of these tracks to your configuration with the UCSC plugin installed, you will be able to freely enable them on linear genome views opened to the appropriate assembly using the track menu. +After adding one or more of these tracks to your configuration with the UCSC +plugin installed, you will be able to freely enable them on linear genome views +opened to the appropriate assembly using the track menu. ### Biothings plugin -The Biothings plugin provides access to resources such as myvariant.info and mygene.info. +The Biothings plugin provides access to resources such as myvariant.info and +mygene.info. You can add the Biothings plugin to your JBrowse config file as follows: @@ -236,7 +282,8 @@ You can add the Biothings plugin to your JBrowse config file as follows: } ``` -Then add the available tracks that are relevant to you under your "tracks" configuration, for example: +Then add the available tracks that are relevant to you under your "tracks" +configuration, for example: ```json { @@ -253,13 +300,17 @@ Then add the available tracks that are relevant to you under your "tracks" confi } ``` -Make sure to reference the many other available tracks in the [Biothings example config](https://github.com/cmdcolin/jbrowse-plugin-biothings-api/blob/master/config.json) +Make sure to reference the many other available tracks in the +[Biothings example config](https://github.com/cmdcolin/jbrowse-plugin-biothings-api/blob/master/config.json) -After adding one or more of these tracks to your configuration with the UCSC plugin installed, you will be able to freely enable them on linear genome views opened to the appropriate assembly using the track menu. +After adding one or more of these tracks to your configuration with the UCSC +plugin installed, you will be able to freely enable them on linear genome views +opened to the appropriate assembly using the track menu. ### CIVIC plugin -The CIVIC plugin provides access to resources available through the [CIVIC API](https://civicdb.org/welcome). +The CIVIC plugin provides access to resources available through the +[CIVIC API](https://civicdb.org/welcome). You can add the CIVIC plugin to your JBrowse config file as follows: @@ -301,9 +352,12 @@ Then add the relevant track to the "tracks" configuration: } ``` -Make sure to reference the many other available tracks in the [CIVIC example config](https://github.com/cmdcolin/jbrowse-plugin-civic-api/blob/master/config.json). +Make sure to reference the many other available tracks in the +[CIVIC example config](https://github.com/cmdcolin/jbrowse-plugin-civic-api/blob/master/config.json). -After adding one or more of these tracks to your configuration with the UCSC plugin installed, you will be able to freely enable them on linear genome views opened to the appropriate assembly using the track menu. +After adding one or more of these tracks to your configuration with the UCSC +plugin installed, you will be able to freely enable them on linear genome views +opened to the appropriate assembly using the track menu.
    @@ -311,6 +365,10 @@ After adding one or more of these tracks to your configuration with the UCSC plu ## Conclusion -You should now have an understanding of how to add a plugin to a JBrowse session, and, if applicable, configure a track such that the adapter provided by the plugin is utilized. +You should now have an understanding of how to add a plugin to a JBrowse +session, and, if applicable, configure a track such that the adapter provided by +the plugin is utilized. -Plugins such as those highlighted in this tutorial provide essential annotations and datasets to a user's JBrowse session and as demonstrated can be accessed in a variety of ways. +Plugins such as those highlighted in this tutorial provide essential annotations +and datasets to a user's JBrowse session and as demonstrated can be accessed in +a variety of ways. diff --git a/website/docs/tutorials/simple_plugin.md b/website/docs/tutorials/simple_plugin.md index 9678eb8b1f..8f678f4f07 100644 --- a/website/docs/tutorials/simple_plugin.md +++ b/website/docs/tutorials/simple_plugin.md @@ -1,6 +1,6 @@ --- id: simple_plugin -title: Developing a simple jbrowse plugin +title: Developing a simple JBrowse plugin toplevel: true --- @@ -53,9 +53,11 @@ Most fields can be left blank, but **make sure to enter a descriptive name for your plugin** in the first field. :::note Tip -A typical naming convention for JBrowse plugins is **"jbrowse-plugin-"**, or, -if you are going to publish to an NPM organization, we advise + +A typical naming convention for JBrowse plugins is **"jbrowse-plugin-"**, or, if +you are going to publish to an NPM organization, we advise **"@myscope/jbrowse-plugin-"**. + ::: You also need to install the dependencies: @@ -106,18 +108,21 @@ see your running JBrowse instance!
    -:::info Note -At this point, you _must_ be running your plugin on port `9000` to see a -running JBrowse instance, otherwise you will meet a screen asking you to -configure your instance. +:::info + +At this point, you _must_ be running your plugin on port `9000` to see a running +JBrowse instance, otherwise you will meet a screen asking you to configure your +instance. + +If you'd like to change this port, you can edit the "port" fields under "config" +in the `package.json` file. -If you'd like to change this port, you can edit the "port" fields under -"config" in the `package.json` file. ::: We can verify our plugin has been added to our JBrowse session by clicking the -first square on the splash screen "Empty," and then navigating `Add` -> `Hello View` in the menu bar. This is the example pluggable element that is added in -the template plugin project. +first square on the splash screen "Empty," and then navigating `Add` -> +`Hello View` in the menu bar. This is the example pluggable element that is +added in the template plugin project. Next, we're going to add our own pluggable element to the plugin. @@ -131,8 +136,8 @@ However, if you: - want to test your plugin against the most recent developer build You can develop against the latest JBrowse core build by taking a quick detour -to our [developing with JBrowse web and desktop -tutorial](../develop_web_and_desktop_tutorial). +to our +[developing with JBrowse web and desktop tutorial](../develop_web_and_desktop_tutorial). Now that our environment is set up and running, we're going to add our own pluggable element to the project and observe it running in JBrowse. @@ -230,13 +235,12 @@ export function stateModelFactory(pluginManager: PluginManager) { // ... ``` -Within the `.actions` method, we're definining methods for the model. These can -be far more complex than just accessors and mutators (anything you want -really). +Within the `.actions` method, we're defining methods for the model. These can be +far more complex than just accessors and mutators (anything you want really). -If you have a particularly complex model, consider moving your component's -model into a `model.ts`, and then exporting the stateModel from `index.ts` -similar to how the ReactComponent is exported. +If you have a particularly complex model, consider moving your component's model +into a `model.ts`, and then exporting the stateModel from `index.ts` similar to +how the ReactComponent is exported. ### A widget's ReactComponent @@ -258,9 +262,13 @@ const CircularViewChordWidget = observer(({ model }: { model: any }) => { export default CircularViewChordWidget ``` -It's important to note the use of the mobx observer here: when making modifications to the model, you'll see those changes populated in your widget, thanks to the observer. We export the widget such that it can be seen by `CircularViewChordWidget/index.tsx`. +It's important to note the use of the mobx observer here: when making +modifications to the model, you'll see those changes populated in your widget, +thanks to the observer. We export the widget such that it can be seen by +`CircularViewChordWidget/index.tsx`. -We'll make our widget do something basic: display the chord's information and a message we can edit. +We'll make our widget do something basic: display the chord's information and a +message we can edit. @@ -286,7 +294,7 @@ const CircularViewChordWidget = observer(({ model }: { model: any }) => { {/* features will always have a name, start, end, and id; they can have additional information too */} - {/* here we're just demonstrating using a basic property from the + {/* here we're just demonstrating using a basic property from the model and updating it with observer */}

    {widgetByline}

    Care to change the widget byline?

    @@ -304,15 +312,22 @@ const CircularViewChordWidget = observer(({ model }: { model: any }) => { export default CircularViewChordWidget ``` -As noted in the codeblock, @jbrowse/core has some reusable UI components exported. If you see something proprietary in the application you'd like to reuse, investigate whether it's exported by @jbrowse/core, and if not [make a request](https://github.com/GMOD/jbrowse-components/discussions/new) for that component to be exported for use in your plugin. +As noted in the codeblock, @jbrowse/core has some reusable UI components +exported. If you see something proprietary in the application you'd like to +reuse, investigate whether it's exported by @jbrowse/core, and if not +[make a request](https://github.com/GMOD/jbrowse-components/discussions/new) for +that component to be exported for use in your plugin. -Now that we have our component built, we can install it into our plugin and test it out. +Now that we have our component built, we can install it into our plugin and test +it out. ## Install the plugin to JBrowse at runtime -The file `src/index.ts` exports your plugin and installs all the necessary components to JBrowse at runtime such that it runs properly. +The file `src/index.ts` exports your plugin and installs all the necessary +components to JBrowse at runtime such that it runs properly. -Your `src/index.ts` file is going to look something like the following right now: +Your `src/index.ts` file is going to look something like the following right +now: ```ts import Plugin from '@jbrowse/core/Plugin' @@ -352,7 +367,8 @@ export default class SomeNewPluginPlugin extends Plugin { } ``` -You'll notice we're already adding a new view type and configuring the rootModel in the template's project. We can use these patterns to add our widget. +You'll notice we're already adding a new view type and configuring the rootModel +in the template's project. We can use these patterns to add our widget. `src/index.ts` @@ -396,7 +412,7 @@ import { getSession } from '@jbrowse/core/util' /* .jexl.addFunction is the method to add a function the first parameter is the name of your jexl function, and how you'll call it - the second paramter is the supplementary properties the function + the second parameter is the supplementary properties the function needs, here, we need these three properties for the circular view's chord click function */ pluginManager.jexl.addFunction( @@ -428,7 +444,7 @@ import { getSession } from '@jbrowse/core/util' Now that we've configured the jexl function to our JBrowse session, we can use it essentially anywhere. -While we could programatically tell certain displays to use this jexl function +While we could programmatically tell certain displays to use this jexl function when they perform an action, for our use case (clicking a chord on the circular view), we can simply write it into our config file. @@ -487,7 +503,7 @@ Take some time to dissect what's being added here: names of the assembly We're now going to add a track that will make use of our jexl function. As -mentioned previously, you _could_ add your jexl function programatically to all +mentioned previously, you _could_ add your jexl function programmatically to all tracks of this type, but for now we're just adding it to our assembly _for this specific track_. @@ -520,15 +536,15 @@ specific track_. Take some time to dissect what's being added here: -- this is a track that will appear in our track list when we run JBrowse - against this assembly +- this is a track that will appear in our track list when we run JBrowse against + this assembly - it's a VariantTrack called "demo_vcf" - it derives its data from a given UriLocation, the file is a `.vcf` file using the VcfAdapter - it declares its display, the `ChordVariantDisplay`, and specifies its `onChordClick` callback function -- the specified `onChordClick` callback function is that which we defined in - our plugin class, the jexl function +- the specified `onChordClick` callback function is that which we defined in our + plugin class, the jexl function
    @@ -564,12 +580,14 @@ widget byline, and one with our feature data.
    :::info Troubleshooting -If you get to this point and note that nothing happens, open the developer -tools in your browser and investigate the console errors. Also check your -running process in your terminal for any errors. Review the code you added to -ensure you didn't miss any imports or statements. Check over your config file + +Troubleshooting If you get to this point and note that nothing happens, open the +developer tools in your browser and investigate the console errors. Also check +your running process in your terminal for any errors. Review the code you added +to ensure you didn't miss any imports or statements. Check over your config file to ensure that "plugins", "assemblies", and "tracks" are all present for the configuration to work properly. + ::: ## Writing a simple integration test with cypress @@ -578,13 +596,13 @@ For completeness, we might want to write a few tests for our plugin to ensure that future changes we make do not break the application. The `jbrowse-plugin-template` uses cypress to write its integration tests. For -plugins, integration tests are a particularly good way to test functionality, -as a failing test might indicate the plugin needs to be updated for a new -version of JBrowse, or, if interfacing with a third-party API or toolset, that -the plugin might have to be tweaked to suit these changes. +plugins, integration tests are a particularly good way to test functionality, as +a failing test might indicate the plugin needs to be updated for a new version +of JBrowse, or, if interfacing with a third-party API or toolset, that the +plugin might have to be tweaked to suit these changes. -We're going to write a simple integration test suite that executes the action -we tested [above](#run-jbrowse-with-your-new-plugin-and-manually-test). +We're going to write a simple integration test suite that executes the action we +tested [above](#run-jbrowse-with-your-new-plugin-and-manually-test). ### Add a cypress test @@ -595,8 +613,8 @@ brief overview to get you started. Within the directory `cypress`, you'll see a number of folders; you'll likely only need to make use of `fixtures` and `integration`. -- `fixtures`: This directory is where you might place testing files or a - testing config.json file. +- `fixtures`: This directory is where you might place testing files or a testing + config.json file. - `integration`: This directory is where all your integration tests go. You can organize them however you want. Using the template project, there will be two in there already you can use as an example, but we'll write one of our own. @@ -674,9 +692,9 @@ it('can access the widget', () => { // .get can retrieve a given property of an element, data-testid is used for testing with jest and works well cy.get('[data-testid="circular_track_select"]').click() cy.contains('demo_vcf').click() - // if any asyncronous calls are made it might be pertinent to .wait + // if any asynchronous calls are made it might be pertinent to .wait cy.wait(2000) - // we use force: true here to make sure we can click the chord, that's an svg overlayed over many other svg's + // we use force: true here to make sure we can click the chord, that's an svg overlaid over many other svg's cy.get('[data-testid="chord-1591034956-148"]').click({ force: true }) // we can see this text, so we know we've accomplished our goal cy.contains('Care to change the widget byline?') @@ -717,7 +735,7 @@ organization's needs, but you also might want to share it with the greater community. That's where the [plugin store](/plugin_store) shows off its strengths. -As a plugin developer, you can publish your plugin to NPM, and then reqest that +As a plugin developer, you can publish your plugin to NPM, and then request that your plugin be added to the plugin store. After your plugin is successfully whitelisted, you will see it within the JBrowse app's plugin store widget and you and others can freely install the plugin into their JBrowse session. Any @@ -732,12 +750,12 @@ The following will guide you through publishing with [NPM](https://www.npmjs.com/). You'll need an NPM account and token to do this, so please set that up first through the NPM site. -If you'd prefer not to publish to NPM, you can host your plugin files -elsewhere, just ensure the link is accessible publicly. +If you'd prefer not to publish to NPM, you can host your plugin files elsewhere, +just ensure the link is accessible publicly. -When your plugin is in a publishable state and you have NPM credentials, you -can run the following within your plugin's root directory (where `package.json` -is found): +When your plugin is in a publishable state and you have NPM credentials, you can +run the following within your plugin's root directory (where `package.json` is +found): ```bash yarn publish @@ -749,19 +767,20 @@ to the next step. ## Request your plugin be added to the plugin store -To populate your plugin to the plugin store, it must be added to the [plugin -list](https://github.com/GMOD/jbrowse-plugin-list), a whitelist of JBrowse -plugins. +To populate your plugin to the plugin store, it must be added to the +[plugin list](https://github.com/GMOD/jbrowse-plugin-list), a whitelist of +JBrowse plugins. -Navigate to the [plugin list -repository](https://github.com/GMOD/jbrowse-plugin-list) and use the github UI -to **Fork** the repository. +Navigate to the +[plugin list repository](https://github.com/GMOD/jbrowse-plugin-list) and use +the github UI to **Fork** the repository.
    :::info Tip -It's easy enough to edit the files required using the github UI, but feel free to clone and push to the forked repo using your local environment as well. +It's easy enough to edit the files required using the github UI, but feel free +to clone and push to the forked repo using your local environment as well. ::: @@ -811,21 +830,21 @@ Push your changes to the `main` branch of your forked repo when you're done. ### Make a pull request -Now that your plugin's information is accurate, navigate again to the [plugin -list repository](https://github.com/GMOD/jbrowse-plugin-list), and create a new -pull request. +Now that your plugin's information is accurate, navigate again to the +[plugin list repository](https://github.com/GMOD/jbrowse-plugin-list), and +create a new pull request. -In the pull request UI, click "compare across forks" and select your fork as -the head repository to merge into the main of `jbrowse-plugin-list`. Your -changes should show in the editor, and you can create your PR. +In the pull request UI, click "compare across forks" and select your fork as the +head repository to merge into the main of `jbrowse-plugin-list`. Your changes +should show in the editor, and you can create your PR.
    ## Next steps The JBrowse development team will review your plugin to ensure that it is -functional, then when it is merged in the plugin will be available on the -plugin store. +functional, then when it is merged in the plugin will be available on the plugin +store. In this tutorial, we set up a development environment for JBrowse 2 and added a custom pluggable element to a plugin. @@ -834,11 +853,10 @@ We also published the plugin to NPM and requested that it be added to the JBrowse plugin store so others can access our plugin. To learn more about the various pluggable elements available in JBrowse (and -thus more that you can do with plugins!) checkout our [developer guide -documentation](../../../developer_guide/). +thus more that you can do with plugins!) checkout our +[developer guide documentation](/docs/developer_guide/). If you have further questions about plugin development, or development with -JBrowse in general, stop by the JBrowse team [gitter -channel](https://gitter.im/GMOD/jbrowse2), or start a discssion on the -[jbrowse-components discussions -forum](https://github.com/GMOD/jbrowse-components/discussions). +JBrowse in general, stop by the JBrowse team +[gitter channel](https://gitter.im/GMOD/jbrowse2), or start a discssion on the +[jbrowse-components discussions forum](https://github.com/GMOD/jbrowse-components/discussions). diff --git a/website/docs/urlparams.md b/website/docs/urlparams.md index 4d0985d10d..a0df37fabc 100644 --- a/website/docs/urlparams.md +++ b/website/docs/urlparams.md @@ -9,9 +9,9 @@ import Figure from './figure' JBrowse Web features the ability to automatically provide URL parameters to setup a session -Note that the embedded components like @jbrowse/react-linear-genome-view make -no assumptions on how URL params are used, so would have to be implemented by -the consumer of the library +Note that the embedded components like @jbrowse/react-linear-genome-view make no +assumptions on how URL params are used, so would have to be implemented by the +consumer of the library ## Simple API for linear genome view @@ -138,12 +138,13 @@ localStorage entry. #### Shared sessions -If you click the "Share button" in the header bar, it will generate a -"shareable link" that you can give to other users +If you click the "Share button" in the header bar, it will generate a "shareable +link" that you can give to other users https://host/jbrowse2/?session=share-HShsEcnq3i&password=nYzTU -See [this FAQ entry for more info about how shared sessions work](../faq#how-does-the-session-sharing-with-shortened-urls-work-in-jbrowse-web) +See +[this FAQ entry for more info about how shared sessions work](../faq#how-does-the-session-sharing-with-shortened-urls-work-in-jbrowse-web) #### Session spec @@ -179,10 +180,10 @@ Expanded } ``` -As you can see, you can supply an array of views (so you can open multiple -views at once) and can specify the loc, tracks, assembly, and view type, or -other view specific parameters (different view types may accept different -params, e.g. dotplot has two assemblies) +As you can see, you can supply an array of views (so you can open multiple views +at once) and can specify the loc, tracks, assembly, and view type, or other view +specific parameters (different view types may accept different params, e.g. +dotplot has two assemblies) ##### Circular view @@ -306,9 +307,9 @@ Expanded #### JSON sessions -Similar to encoded sessions, but more readable, JSON session let you specify -the input a JSON snapshot of a session session. This is slightly different from -a session spec, which has extra logic that loads the session. JSON sessions are +Similar to encoded sessions, but more readable, JSON session let you specify the +input a JSON snapshot of a session session. This is slightly different from a +session spec, which has extra logic that loads the session. JSON sessions are literal session snapshots, like those that might come from the "Export session..." process @@ -332,5 +333,5 @@ https://jbrowse.org/code/jb2/v1.5.9/?session=encoded-eJyNU2FzmkAQ_SvOfaaNIKDyLbF Note that the "Share" button has a gear icon that let's you select "Long URL" that produces these URLs. The encoded share links can be used without the -central session sharing system in place, as the entire session is encoded in -the URL. +central session sharing system in place, as the entire session is encoded in the +URL. diff --git a/website/docs/user_guide.md b/website/docs/user_guide.md index 8174c6edf4..e25bbf2f35 100644 --- a/website/docs/user_guide.md +++ b/website/docs/user_guide.md @@ -7,5 +7,5 @@ title: Overview import Figure from './figure' This user guide is a comprehensive compilation of all general UI navigation, -tools/features available for some of the different track types, and other -useful features for using JBrowse. +tools/features available for some of the different track types, and other useful +features for using JBrowse. diff --git a/website/docs/user_guides/alignments_track.md b/website/docs/user_guides/alignments_track.md index 778f860e56..482de2b400 100644 --- a/website/docs/user_guides/alignments_track.md +++ b/website/docs/user_guides/alignments_track.md @@ -12,8 +12,8 @@ is a combination of a pileup and a coverage visualization. ### Pileup visualization -The pileup is the lower part of the alignments track and shows each of the -reads as boxes positioned on the genome. +The pileup is the lower part of the alignments track and shows each of the reads +as boxes positioned on the genome. By default the reads are colored red if they aligned to the forward strand of the reference genome, or blue if they aligned to the reverse strand. @@ -22,21 +22,21 @@ the reference genome, or blue if they aligned to the reverse strand. The coverage visualization shows the depth-of-coverage of the reads at each position on the genome, and also draws using colored boxes any occurrence of -mismatches between the read and the reference genome, so if 50% of the reads -had a T instead of the reference A, half the height of the coverage histogram -would contain a 'red' box. +mismatches between the read and the reference genome, so if 50% of the reads had +a T instead of the reference A, half the height of the coverage histogram would +contain a 'red' box.
    ### Show soft clipping If a read contains bases that do not map the the genome properly, they can -either be removed from the alignment (hard clipping) or can be included, and -not shown by default (soft clipping). +either be removed from the alignment (hard clipping) or can be included, and not +shown by default (soft clipping). JBrowse 2 also contains an option to "show the soft clipping" that has occurred. -This can be valuable to show the signal around a region that contains -structural variation or difficult mappability. +This can be valuable to show the signal around a region that contains structural +variation or difficult mappability.
    @@ -46,8 +46,8 @@ structural variation or difficult mappability. The alignments tracks can also be configured to "sort by" a specific attribute for reads that span **the center line**. -By default the center line is not shown, but by showing it (detailed below) then you will obtain a better idea -of what the "sort by" option is doing. +By default the center line is not shown, but by showing it (detailed below) then +you will obtain a better idea of what the "sort by" option is doing. ### Showing the center line @@ -58,9 +58,11 @@ of what the "sort by" option is doing.
    :::info Note -The center line is used by the 'Sort by' function discussed in this section; -the sort is performed using properties of the feature, or even exact base pair + +The center line is used by the 'Sort by' function discussed in this section; the +sort is performed using properties of the feature, or even exact base pair underlying the center line. + ::: ### Sorting by base pair @@ -90,7 +92,7 @@ format, then the alignments track can use these merks to color these modification. It uses two modes: 1. Modifications mode - draws the modifications as they are -2. Methylation mode - draws both unmodified and modifified CpGs (unmodified +2. Methylation mode - draws both unmodified and modified CpGs (unmodified positions are not indicated by the MM tag and this mode considers the sequence context) @@ -104,7 +106,8 @@ JBrowse uses the same color scheme as IGV for coloring by pair orientation. These pair orientations can be used to reveal complex patterns of structural variation. -See [IGV's Interpreting Color by Pair Orientation guide](https://software.broadinstitute.org/software/igv/interpreting_pair_orientations) +See +[IGV's Interpreting Color by Pair Orientation guide](https://software.broadinstitute.org/software/igv/interpreting_pair_orientations) for further details on interpreting these pair orientations.
    @@ -119,9 +122,11 @@ the alignment.
    :::info Note + You can disable these by clicking on the track menu (vertical "..." next to track label, then hovering over SNPCoverage options, and unchecking "Draw arcs"). + ::: ### Insertion and clipping indicators @@ -134,17 +139,56 @@ soft/hard clipped read counts at all positions, and mark significant positions Also, insertions that are larger than 10bp are marked with a larger purple rectangle, seen in the screenshot below. Generally, long reads span larger -insertions better, so this feature is more prominant with large reads. +insertions better, so this feature is more prominent with large reads.
    :::info Note + You can disable these by clicking on the track menu (vertical "..." next to track label, then hovering over SNPCoverage options, and unchecking "Draw insertion/clipping indicators" and "Draw insertion/clipping counts"). + ::: -### Opening a synteny view from a dotplot view +### Using the "Arc display" + +In JBrowse 2.3.0, we introduced the ability to render "Arcs" to show long range +connections between reads. This information is very valuable for revealing +structural variation, misassemblies, etc. + +To enable, use the track menu to launch "Display types"->"Arc display" or +"Replace lower panel with..."->"Arc display" + +
    + +The "Arc display" bezier curves will automatically try to fit into the window +when you click and drag the track height, so you can create a dense display of +arcs using multiple data tracks + +Long range interactions are indicated using vertical lines (connecting to other +chromosomes for example) or larger semi-circular arcs for off-screen +interactions). You can turn off rendering these events using the track menu if +they are not relevant to your interest. + + + +
    + +### Using the "Read cloud display" + +Similar to the "Arc display" we also offer what we call the "Read cloud" +display. It is similar in some ways to the "Arc display" but renders paired-end +or split read features as connected and stratified by the distance between their +connections logarithmically on the "y-position" of the track. Similar to the +"Arc display", clicking and dragging the track height of the "Read cloud +display" will re-pack features into that area. + +
    + +### Compacting the view of alignments tracks + +Users can create a more compact display of alignments using Track menu->Pileup +settings->Set feature height->Compact -You can open a synteny view from a dotplot view by selecting a region on the -dotplot and clicking "Open linear synteny view", shown below: +![](/img/alignments/compact.png) diff --git a/website/docs/user_guides/basic_usage.md b/website/docs/user_guides/basic_usage.md index 11c072f6e5..21195fbff4 100644 --- a/website/docs/user_guides/basic_usage.md +++ b/website/docs/user_guides/basic_usage.md @@ -8,7 +8,8 @@ import Figure from '../figure' ### Linear genome view -To open a linear genome view (LGV), use the menu bar: `Add` -> `Linear genome view` +To open a linear genome view (LGV), use the menu bar: `Add` -> +`Linear genome view` #### Scrolling @@ -21,8 +22,14 @@ in their respective directions. The zoom buttons and the slider bar found in the header of the linear genome view can be used to zoom in and out on the view -You can also hold the `Ctrl` key and use your mousewheel or trackpad to scroll -to zoom in and out. +You can also + +- hold the `Ctrl` key and use your mousewheel or trackpad to scroll to zoom in + and out of the linear genome view +- hold the `Shift` key and click and drag the linear genome view to create a + "rubberband" selection +- hold the `Shift` key without click and drag to just reveal a red vertical + guide bar on the linear genome view #### Re-ordering tracks @@ -31,6 +38,12 @@ six vertical dots) to reorder tracks.
    +#### Re-ordering views + +Re-ordering views doesn't use a drag and drop like re-ordering tracks does, but +instead, you can click the view menu (the "hamburger" menu that is available for +each view) and select "Move up"/"Move down" + #### Using the location search box The location search box is located at the top of the LGV. @@ -47,21 +60,23 @@ You can search a location in several ways when typing in the search box: 5. If configured, searching by gene name or feature keywords, e.g. `BRCA1` To configure name searching, you or the admin of the instance will need to -create a "text index". See the [configuration -guide](/docs/tutorials/config_cli#indexing-feature-names-for-searching) for more -information. +create a "text index". See the +[configuration guide](/docs/tutorials/config_cli#indexing-feature-names-for-searching) +for more information.
    -## Opening tracks +### Opening tracks To open a new track or connection, use the menu bar: `File` -> `Open track..`
    :::info Tip + There is a circular plus (+) icon button inside the "Available tracks" widget that can also be used to access the "Add a track" form. + :::
    @@ -74,25 +89,43 @@ e.g. if you provide a URL for a BAM and the index filename is bamfilename +'.bai' but you may need to manually supply it in some cases (index inference can't be done with files from your local machine) +### File format support + The following file formats are supported in core JBrowse 2: +#### General + - CRAM - BAM -- htsget +- htsget (requires hand-edited config) - VCF (Tabix-indexed) - GFF3 (Tabix-indexed) - BED (Tabix-indexed) - BigBed - BigWig -- JBrowse 1 nested containment lists (NCLists) +- BEDPE +- JBrowse 1 nested containment lists (NCList) +- .hic (Hi-C contact matrix visualization) + +#### SV inspector + - plain text VCF, BED, CSV, TSV, BEDPE, STAR-fusion output (tabular formats) -- PAF (synteny/dotplot) -- Indexed FASTA/BGZip indexed FASTA + +#### Synteny and dotplot + +- PAF (e.g. minimap2) +- .delta (MUMmer) +- .anchors (MCScan python version) +- .out (MashMap) + +#### Sequence adapters + +- Indexed FASTA +- BGZip indexed FASTA - 2bit -- .hic (Hi-C contact matrix visualization) -Additional data formats can be supported via plugins; checkout the [plugin -store](/plugin_store). +Additional data formats can be supported via plugins; checkout the +[plugin store](/plugin_store). For tabix files, TBI or CSI indexes are allowed. CSI or BAI is allowed for BAM. Only CRAI is allowed for CRAM. The index will be inferred for BAI or TBI files @@ -100,9 +133,11 @@ as filename+'.bai' for example, but if it is different than this, make sure to specify the index file explicitly. :::info Note -If you are an administrator, you can add tracks with the [command -line](/docs/tutorials/config_cli/#adding-a-track) or with the [admin -server](/docs/tutorials/config_gui). + +If you are an administrator, you can add tracks with the +[command line](/docs/tutorials/config_cli/#adding-a-track) or with the +[admin server](/docs/tutorials/config_gui). + ::: ### Undo and redo @@ -121,7 +156,9 @@ You **cannot** copy the URL in your address bar and send it to other users, you **must** use the "Share" button to share your session. :::info Note + Sharing sessions is not available for JBrowse Desktop. + :::
    @@ -136,8 +173,8 @@ The session URL will contain the following: pileup - ...and more! -This means you can share links with your custom tracks with other users, -without being a JBrowse admin! +This means you can share links with your custom tracks with other users, without +being a JBrowse admin! ### Track menu @@ -158,19 +195,21 @@ dialog. ### Editing track configs -As a non-admin user, in order to edit a track config, you have to make a copy -of the track. This will copy it to your "session tracks", which you can edit +As a non-admin user, in order to edit a track config, you have to make a copy of +the track. This will copy it to your "session tracks", which you can edit freely.
    -#### Rubberband selection +### Rubberband selection -The scale bars accept a click-and-drag action to select a region. Rubberband selection can be performed on both the main (lower) and overview (upper) scale bars. +The scale bars accept a click-and-drag action to select a region. Rubberband +selection can be performed on both the main (lower) and overview (upper) scale +bars.
    -#### Track label positioning +### Track label positioning Track labels can be positioned on their own row or overlapping the data to save vertical screen space. They can also be hidden. This is done by clicking on the @@ -178,7 +217,7 @@ hamburger menu for a specific view.
    -#### Horizontally flip +### Horizontally flip The view can be horizontally flipped, or reverse complemented, to make the coordinates go from right to left instead of left to right. @@ -189,3 +228,10 @@ bar to help indicate whether the app is horizontally flipped or not. Here is an example of before and after horizontally flipping the view:
    + +### Toggle drawer widget on left or right side of screen + +Using a drop-down menu in the header bar, you can toggle the drawer widget to +the left or right side of the screen. It is on the right side by default + +
    diff --git a/website/docs/user_guides/bookmark_widget.md b/website/docs/user_guides/bookmark_widget.md index fbdb457eec..6b26ddba7a 100644 --- a/website/docs/user_guides/bookmark_widget.md +++ b/website/docs/user_guides/bookmark_widget.md @@ -6,8 +6,8 @@ title: Bookmark widget import Figure from '../figure' -The "bookmark widget" can store lists of interesting regions that you might -like to easily revisit. +The "bookmark widget" can store lists of interesting regions that you might like +to easily revisit.
    @@ -20,8 +20,10 @@ You can also import a list of regions from a BED file.
    :::info Note + You can add "notes" for your list of regions by double clicking on the label field to easily "annotate" your datasets. + :::
    diff --git a/website/docs/user_guides/feature_sequence.md b/website/docs/user_guides/feature_sequence.md index 499db5f13d..6fd4ba00c9 100644 --- a/website/docs/user_guides/feature_sequence.md +++ b/website/docs/user_guides/feature_sequence.md @@ -9,8 +9,8 @@ import Figure from '../figure' ### Gene features If you have a track with gene or transcript level features, then the feature -detail sidebar will automatically stitch together the sequence for that -feature. Options include: +detail sidebar will automatically stitch together the sequence for that feature. +Options include: - CDS - the coding sequences, spliced together - Protein - performs protein translation on the CDS, currently assuming the diff --git a/website/docs/user_guides/hic_track.md b/website/docs/user_guides/hic_track.md index d0c289990a..99b93fa7bb 100644 --- a/website/docs/user_guides/hic_track.md +++ b/website/docs/user_guides/hic_track.md @@ -8,12 +8,12 @@ import Figure from '../figure' ## Hi-C tracks -Visualizing Hi-C data can be performed with .hic files generated by the -Juicebox software suite. It uses the hic-straw module developed by the -juicebox/igv.js team to visualize it in JBrowse. +Visualizing Hi-C data can be performed with .hic files generated by the Juicebox +software suite. It uses the hic-straw module developed by the juicebox/igv.js +team to visualize it in JBrowse. -Currently configuration options are basic for Hi-C tracks, see [the -comprehensive config guide](/docs/config_guide#hictrack-config) for info about +Currently configuration options are basic for Hi-C tracks, see +[the comprehensive config guide](/docs/config_guides/hic_track/) for info about configuring Hi-C tracks.
    diff --git a/website/docs/user_guides/multiquantitative_track.md b/website/docs/user_guides/multiquantitative_track.md index 46435f47b0..915d33667e 100644 --- a/website/docs/user_guides/multiquantitative_track.md +++ b/website/docs/user_guides/multiquantitative_track.md @@ -22,28 +22,27 @@ You can interactively change these settings through the track menu. With the "multi-row" settings (multirowxyplot, multirowline, multidensity) the track colors are not modified. For the overlapping (xyplot, multiline), the -tracks will be autoassigned a color from the palette. You can manually -customize the subtrack colors from the track menu as well. +tracks will be autoassigned a color from the palette. You can manually customize +the subtrack colors from the track menu as well.
    Oftentimes, one of the outliers on one of the subtracks may affect the Y-scalebar too much, so it is often helpful to use the "Autoscale type->Local -+/- 3SD" setting (3 standard deviations are displayed). Manually configuring -the min or max scores is available via the track menu also. ++/- 3SD" setting (3 standard deviations are displayed). Manually configuring the +min or max scores is available via the track menu also. ### Adding multi-quantitative tracks via the UI There are several ways to create multi-quantitative tracks from scratch. -1. Using the add track panel to open up a list of URLs for bigwig files, or - from several local tracks from your machine +1. Using the add track panel to open up a list of URLs for bigwig files, or from + several local tracks from your machine 2. Using the track selector to add multiple tracks to your current selection, and then creating a multi-wiggle track from the tracks in your selection 3. Hardcoding the multiwiggle track in your config file (see - [multi-quantitative track - configuration](/docs/config_guide/#multiquantitativetrack-config) for more - info) + [multi-quantitative track configuration](/docs/config_guides/multiquantitative_track/) + for more info)
    diff --git a/website/docs/user_guides/plugin_store.md b/website/docs/user_guides/plugin_store.md index ce11c32495..e6d52d9759 100644 --- a/website/docs/user_guides/plugin_store.md +++ b/website/docs/user_guides/plugin_store.md @@ -6,19 +6,21 @@ toplevel: true import Figure from '../figure' -Users can add plugins to their session using the in-app plugin store. The -plugin will be added to your "session" which can be shared with the share -button (or if you are an admin running the admin-server, then it will be added -to the config file). +Users can add plugins to their session using the in-app plugin store. The plugin +will be added to your "session" which can be shared with the share button (or if +you are an admin running the admin-server, then it will be added to the config +file). This can add extra functions, tracks, or many other interesting features. For example, if you add the CIVIC plugin, it will automatically add a track that contains the CIVIC cancer gene annotations to hg19. :::info Note + Not all plugins are directly useful from being added, and require hand-editing of the configuration file to be useful. If you would like to use such a plugin and do not have access to the configuration file, contact your administrator. + :::
    diff --git a/website/docs/user_guides/quantitative_track.md b/website/docs/user_guides/quantitative_track.md index 5a80530a92..bdaae5a54e 100644 --- a/website/docs/user_guides/quantitative_track.md +++ b/website/docs/user_guides/quantitative_track.md @@ -25,12 +25,14 @@ coverage visualization: 3sd" allows the autoscaling to avoid outliers 4. Go to the track menu and select "Turn off histogram fill", which then shows only a dot for each point on the graph -5. Go to the track menu and select "Resolution->Finer resolution" a couple - times until resolution looks nice +5. Go to the track menu and select "Resolution->Finer resolution" a couple times + until resolution looks nice :::info Note -All tracks have a drag handle on the bottom, which you can drag down to make -the track taller. + +All tracks have a drag handle on the bottom, which you can drag down to make the +track taller. + :::
    diff --git a/website/docs/user_guides/sv_inspector.md b/website/docs/user_guides/sv_inspector.md index b4965321e7..5adbbfb066 100644 --- a/website/docs/user_guides/sv_inspector.md +++ b/website/docs/user_guides/sv_inspector.md @@ -26,6 +26,25 @@ The following formats are supported:
    +### Sources of data for SV inspector + +The SV inspector currently is designed for viewing `` and breakend type +entries. + +Examples of variant callers that produce a VCF that can be used with the SV +inspector: + +Short read based: + +- Manta +- Delly +- Lumpy + +Long read based + +- pbsv +- Sniffles + ### Example SV inspector workflow We can start the SV inspector workflow by opening up this file containing @@ -59,7 +78,7 @@ By clicking on the features in the circular view, or clicking on the triangle drop-down on the leftmost column of the table, we can dynamically launch a new view of the data that is called the "split view" or the "breakpoint split view" -This allows us to inspect the breakpoints of the structural variant, and -compare each side to the alignments. +This allows us to inspect the breakpoints of the structural variant, and compare +each side to the alignments.
    diff --git a/website/docs/user_guides/variant_track.md b/website/docs/user_guides/variant_track.md index 86116488e8..c648be8a1f 100644 --- a/website/docs/user_guides/variant_track.md +++ b/website/docs/user_guides/variant_track.md @@ -17,7 +17,7 @@ evidence track is a common workflow for validating your results, shown below: The variant features have a specialized widget that contains a table indicating all the calls that were made in a multi-sample VCF. Some VCF files, like the -1000 genomes VCF, can contain thousands of samples in a single file. This -table can display the details. +1000 genomes VCF, can contain thousands of samples in a single file. This table +can display the details.
    diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index b647aada3b..2ff120a2e4 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,7 +9,7 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.1.7" + "currentVersion": "v2.3.2" }, "themeConfig": { "colorMode": { diff --git a/website/out5.csv b/website/out5.csv deleted file mode 100644 index 47adb490d1..0000000000 --- a/website/out5.csv +++ /dev/null @@ -1,11 +0,0 @@ -# created by LinkChecker at 2022-10-26 16:00:43-006 -# Read the documentation at https://linkchecker.github.io/linkchecker/ -# Write comments and bugs to https://github.com/linkchecker/linkchecker/issues -urlname;parentname;base;result;warningstring;infostring;valid;url;line;column;name;dltime;size;checktime;cached;level;modified -localhost:8999/?config=localhost:3000/jbrowse_config.json;http://localhost:3000/jb2/docs/tutorials/simple_plugin_tutorial/03_adding_pluggable_element/;;URL is unrecognized or has invalid syntax;;The URL is outside of the domain filter, checked only syntax.;False;localhost:8999/?config=localhost:3000/jbrowse_config.json;13;127935;localhost:8999/?config=localhost:3000/jbrowse_config.json;-1;-1;0;0;4; -/jb2/docs/developer_guides/devguide_pluggable_elements/#creating-renderers;http://localhost:3000/jb2/docs/developer_guides/whats_in_a_plugin/;;404 Not Found;;;False;http://localhost:3000/jb2/docs/developer_guides/devguide_pluggable_elements/#creating-renderers;52;37;"creating -renderers";-1;-1;3.470278263092041;0;4; -/jb2/docs/pluggable_elements/#adding-track-context-menu-items;http://localhost:3000/jb2/docs/developer_guides/whats_in_a_plugin/;;404 Not Found;;;False;http://localhost:3000/jb2/docs/pluggable_elements/#adding-track-context-menu-items;69;4;"example for adding context menu -items";-1;-1;3.3503594398498535;0;4; -mailto:material@5.0.0;http://localhost:3000/jb2/blog/page/4/;;Invalid top level domain part of mail address `material@5.0.0'.;;The URL is outside of the domain filter, checked only syntax.;False;mailto:material@5.0.0;68;4735;material@5.0.0;-1;-1;0;0;5; -# Stopped checking at 2022-10-26 16:03:43-006 (2 minutes, 59 seconds) diff --git a/website/release_announcement_drafts/v1.0.4.md b/website/release_announcement_drafts/v1.0.4.md deleted file mode 100644 index 44712605d8..0000000000 --- a/website/release_announcement_drafts/v1.0.4.md +++ /dev/null @@ -1,23 +0,0 @@ -This release of JBrowse Web includes a _great_ many small improvements and bug fixes, see the full changelog below. - -Some particularly salient improvements include: - -## Linear view sequence fetching - -Users can now download regions of sequence by selecting a region in the linear genome view and clicking "get sequence". See the demonstration video below: - -A long-requested feature, implemented in [#1588](https://github.com/GMOD/jbrowse-components/pull/1588) by [@teresam856](https://github.com/teresam856)! - -## Enhanced navigation of paired end reads and BND/TRA breakends - -Feature details of paired-end alignment reads and variants now contain links to open new views to help understand the regions or reads that they are related to. - -Aligned reads with information on "supplementary" alignments, such as most paired-end reads, now contain special links in their feature details that open a new linear genome view showing the other read(s) in the group. - -![localhost_3000__config=test_data%2Fconfig_demo json session=local-bHWWb4AhO](https://user-images.githubusercontent.com/6511937/107866463-8f7fcb00-6e2e-11eb-847f-0084939a9bfd.png) - -Similarly, feature details for `BND` and `TRA` breakpoints in variant tracks have links to open new breakpoint split views, allowing users to visualize both sides of the breakend or translocation. - -![localhost_3000__config=test_data%2Fconfig_demo json session=local-mlN3tEAII](https://user-images.githubusercontent.com/6511937/108010771-e4ece100-6fc2-11eb-8fc0-2b04be2891ae.png) - -Implemented by [@cmdcolin](https://github.com/cmdcolin) in [#1701](https://github.com/GMOD/jbrowse-components/pull/1701). diff --git a/website/release_announcement_drafts/v1.1.0.md b/website/release_announcement_drafts/v1.1.0.md deleted file mode 100644 index bd98a22340..0000000000 --- a/website/release_announcement_drafts/v1.1.0.md +++ /dev/null @@ -1,29 +0,0 @@ -We're pleased to announce a new release of JBrowse Web! - -## Changed callbacks language from JavaScript to Jexl - -To allow users to safely and seamlessly share advanced configurations in sessions, we now use [Jexl](https://github.com/TomFrost/Jexl/blob/master/README.md) to express configuration callbacks. Note that this is a breaking change, `function()`-style callbacks will no longer work. - -For details, see the [callbacks section of our configuration guide](../docs/config_guide#configuration-callbacks). - -## Fetch intron and upstream/downstream sequences - -We also have several other improvements including the ability to get intron and -upstream/downstream sequence in the feature details - -![](./img/upstream_downstream_details.png) - -## Interactive documentation using Storybook - -Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View. -The docs contain live examples of how the LGV component can be used, along with source-code examples. -The site can be found [here](https://jbrowse.org/storybook/lgv/v1.1.0). - -## Enhanced navigation to drawer widget stack - -We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web. - -See below for demos of the new navigation UI. - -![Minimize button demo](https://media.giphy.com/media/VkkAJWQevhezVR2jCj/giphy.gif) -widget_navigation diff --git a/website/release_announcement_drafts/v1.2.0.md b/website/release_announcement_drafts/v1.2.0.md deleted file mode 100644 index 4759db62c3..0000000000 --- a/website/release_announcement_drafts/v1.2.0.md +++ /dev/null @@ -1,35 +0,0 @@ -We're excited to announce the v1.2.0 release of JBrowse Web! - -## New plugin store added to website - -One of the core aspects of JBrowse 2 is that it is an extensible -platform for biological visualization that can be extended with -plugins. We are excited to introduce the first version of our -plugin store, where we list the current external plugins that -are available. Check it out [here](https://jbrowse.org/jb2/plugin_store). -In the coming weeks, we will also be bringing this plugin store directly -into the application, allowing plugin installation with the click of a button. -Stay tuned! - -## SVG export - -We're excited to introduce a new feature to JBrowse Web: built-in -SVG export of track visualizations! This feature currently supports -the linear genome view, and will be extended to more views in future -releases. - -![](https://raw.githubusercontent.com/cmdcolin/jb2export/6e5486c1939499923045c011b33cfb96b125faba/img/1.png) - -With the addition of this feature, it is now even easier to create -publication-ready screenshots of JBrowse views. - -## Virtualized track lists - -An important consideration for genomics software is scaling to very large -datasets. We have implemented a virtualization of our hierarchical track -selector, enabling it to support arbitrarily large track lists. - -## Lazy loading - -We have expanded our use of [lazy loading](https://reactjs.org/docs/code-splitting.html#reactlazy), which optimizes app performance and -improves load times. diff --git a/website/release_announcement_drafts/v1.3.0.md b/website/release_announcement_drafts/v1.3.0.md deleted file mode 100644 index 0ced101db4..0000000000 --- a/website/release_announcement_drafts/v1.3.0.md +++ /dev/null @@ -1,32 +0,0 @@ -We're excited to announce the v1.3.0 release of JBrowse Web! Some highlights of -this release include: - -## In-app plugin store - -Building on the plugin store on our website in the last release, we're now -excited to announce that plugins can be installed from within JBrowse Web! -Plugins from our plugin store can now be installed with the click of a button. - -![Screenshot of plugin store with MsaView plugin installed and open](https://user-images.githubusercontent.com/19295181/117894797-f9631180-b271-11eb-9c81-69c5aa6ae497.png) - -## Open local files - -JBrowse Web now has the ability for tracks to use files on your local hard -drive. This is a great option if you want to visualize files you have locally -without uploading them to a server. These files will need to be re-opened each -time the app is opened or refreshed, but more robust handling of local files -will be available when we release JBrowse Desktop. - -![Screenshot of selector in URL and File states](https://user-images.githubusercontent.com/25592344/119404009-6f1ca380-bc9c-11eb-8d77-d8706dfa1d90.png) - -## Color by MM and MP/ML tags in BAM/CRAM - -The MM and MP/ML tags can be used to color alignments tracks by either base -modifications or by methylation. The modifications mode is exciting because it -can show arbitrary DNA/RNA modifications, and the methylation mode uses -specific CpG context to show both modified and unmodified CpGs. - -![Screenshot of alignments tracks colored by methylation and base modification](https://raw.githubusercontent.com/GMOD/jbrowse-components/7f0c725a929bb15a6adfcf3a155bf9dc5f717af7/website/static/img/alignments/modifications1.png) - -In this screenshot, the top alignments track is colored by methylation and the -bottom alignments track is colored by base modification. diff --git a/website/release_announcement_drafts/v1.3.1.md b/website/release_announcement_drafts/v1.3.1.md deleted file mode 100644 index 967a3e90f3..0000000000 --- a/website/release_announcement_drafts/v1.3.1.md +++ /dev/null @@ -1,6 +0,0 @@ -Hello everyone! This release offers a couple important bug fixes. - -For users of `@jbrowse/react-linear-genome-view`, we have fixes that improve -speed, CSS style consistency, and theming. We also have another speed -improvement for users with many scaffolds or contigs. Please see the release -notes below for more details! diff --git a/website/release_announcement_drafts/v1.3.2.md b/website/release_announcement_drafts/v1.3.2.md deleted file mode 100644 index 8c88c99ee3..0000000000 --- a/website/release_announcement_drafts/v1.3.2.md +++ /dev/null @@ -1,4 +0,0 @@ -This is a hotfix release that fixes a bug that prevented the -@jbrowse/react-linear-genome-view component from being used in v1.3.1 - -It also contains a couple other small improvements diff --git a/website/release_announcement_drafts/v1.3.3.md b/website/release_announcement_drafts/v1.3.3.md deleted file mode 100644 index 770eeae8d4..0000000000 --- a/website/release_announcement_drafts/v1.3.3.md +++ /dev/null @@ -1,5 +0,0 @@ -This is a small bugfix release that includes notable fixes for the -methylation/modifications drawing (the negative strand reads displayed the data -incorrectly) and the reference name selector - -Please check the release notes for more details! diff --git a/website/release_announcement_drafts/v1.3.4.md b/website/release_announcement_drafts/v1.3.4.md deleted file mode 100644 index 0ca86e6d81..0000000000 --- a/website/release_announcement_drafts/v1.3.4.md +++ /dev/null @@ -1,36 +0,0 @@ -We're excited to announce the v1.3.4 release of JBrowse! Some highlights of this -release include: - -## New embedding build of `@jbrowse/react-linear-genome-view` - -This release adds a new UMD build of our -[`@jbrowse/react-linear-genome-view`](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) -React component. This build will allow users to use our React Linear Genome View -in a website that doesn't otherwise use React. See a tutorial for how to get -started using this build: - -- https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view/01_introduction - -A preliminary beta version of this build was used in a tutorial at BOSC2020, and -that tutorial was also on our website. If you've used that version, the -interface has changed somewhat, so come check out the new tutorial for the -official released version! - -## Bookmark widget - -A new widget has been added that is accessible from the Linear Genome View view -menu or when you click and drag over a region in the header (a.k.a rubber band -selection). This view keeps a list of bookmarked regions, which you can add -custom labels to, and also which you can use to navigate back to that region. -The bookmarks can also be exported. - -![Bookmark widget in use](https://user-images.githubusercontent.com/19295181/130518189-d8fa8904-d52f-45b0-8403-34f08c23740e.gif) - -## Note to plugin developers - -If your plugin adds menu items or context menu items to a track, or customizes -`renderProps`, there may be some changes that affect how those menu items work, -particularly in [#2226](https://github.com/GMOD/jbrowse-components/pull/2226) -and [#2229](https://github.com/GMOD/jbrowse-components/pull/2229). Also see an -updated example of context menu items -[here](https://jbrowse.org/jb2/docs/developer_guide#adding-track-context-menu-items). diff --git a/website/release_announcement_drafts/v1.3.5.md b/website/release_announcement_drafts/v1.3.5.md deleted file mode 100644 index a11e0bd027..0000000000 --- a/website/release_announcement_drafts/v1.3.5.md +++ /dev/null @@ -1,5 +0,0 @@ -This is a bugfix release to address the UMD build files in -`@jbrowse/react-linear-genome-view` not getting included properly in the -published package. See -[the previous release](https://jbrowse.org/jb2/blog/2021/08/23/%2015:52:32-v1.3.4-release) -for more information on the UMD build. diff --git a/website/release_announcement_drafts/v1.4.0.md b/website/release_announcement_drafts/v1.4.0.md deleted file mode 100644 index 676354f970..0000000000 --- a/website/release_announcement_drafts/v1.4.0.md +++ /dev/null @@ -1,17 +0,0 @@ -We're excited to announce the v1.4.0 release! Some highlights of this release -include: - -## Text searching - -Finally, we have added the ability to search by gene name! - -Users will now be able to create their own text indexes with the `jbrowse text-index` command, which creates an index for searching by gene names, identifiers and descriptions. - -![searching in lgv](https://user-images.githubusercontent.com/45598764/132396329-f3fa9ed4-ace4-40b6-8eff-8289bbd3d2ca.gif) -GIF showing the process of searching via the location search box of the Linear Genome View - -For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this [quick start](/docs/quickstart_cli#indexing-feature-names-for-searching) - -Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases. - -Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page diff --git a/website/release_announcement_drafts/v1.4.1.md b/website/release_announcement_drafts/v1.4.1.md deleted file mode 100644 index 676354f970..0000000000 --- a/website/release_announcement_drafts/v1.4.1.md +++ /dev/null @@ -1,17 +0,0 @@ -We're excited to announce the v1.4.0 release! Some highlights of this release -include: - -## Text searching - -Finally, we have added the ability to search by gene name! - -Users will now be able to create their own text indexes with the `jbrowse text-index` command, which creates an index for searching by gene names, identifiers and descriptions. - -![searching in lgv](https://user-images.githubusercontent.com/45598764/132396329-f3fa9ed4-ace4-40b6-8eff-8289bbd3d2ca.gif) -GIF showing the process of searching via the location search box of the Linear Genome View - -For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this [quick start](/docs/quickstart_cli#indexing-feature-names-for-searching) - -Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases. - -Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page diff --git a/website/release_announcement_drafts/v1.4.2.md b/website/release_announcement_drafts/v1.4.2.md deleted file mode 100644 index 409f071140..0000000000 --- a/website/release_announcement_drafts/v1.4.2.md +++ /dev/null @@ -1,18 +0,0 @@ -We're excited to announce the v1.4.2 release! Some highlights of this release -include: - -## Text searching - -Finally, we have added the ability to search by gene name! - -Users will now be able to create their own text indexes with the `jbrowse text-index` command, which creates an index for searching by gene names, identifiers and descriptions. - -![searching in lgv](https://user-images.githubusercontent.com/45598764/132396329-f3fa9ed4-ace4-40b6-8eff-8289bbd3d2ca.gif) - -GIF showing the process of searching via the location search box of the Linear Genome View - -For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this [quick start](/docs/quickstart_cli#indexing-feature-names-for-searching) - -Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases. - -Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page diff --git a/website/release_announcement_drafts/v1.4.3.md b/website/release_announcement_drafts/v1.4.3.md deleted file mode 100644 index 7d7b85070f..0000000000 --- a/website/release_announcement_drafts/v1.4.3.md +++ /dev/null @@ -1,18 +0,0 @@ -We're excited to announce the v1.4.3 release! Some highlights of this release -include: - -## Text searching - -Finally, we have added the ability to search by gene name! - -Users will now be able to create their own text indexes with the `jbrowse text-index` command, which creates an index for searching by gene names, identifiers and descriptions. - -![searching in lgv](https://user-images.githubusercontent.com/45598764/132396329-f3fa9ed4-ace4-40b6-8eff-8289bbd3d2ca.gif) - -GIF showing the process of searching via the location search box of the Linear Genome View - -For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this [quick start](/docs/quickstart_cli#indexing-feature-names-for-searching) - -Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases. - -Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page diff --git a/website/release_announcement_drafts/v1.4.4.md b/website/release_announcement_drafts/v1.4.4.md deleted file mode 100644 index 9ef0a16f8a..0000000000 --- a/website/release_announcement_drafts/v1.4.4.md +++ /dev/null @@ -1,18 +0,0 @@ -We're excited to announce the v1.4.4 release! Some highlights of this release -include: - -## Text searching - -Finally, we have added the ability to search by gene name! - -Users will now be able to create their own text indexes with the `jbrowse text-index` command, which creates an index for searching by gene names, identifiers and descriptions. - -![searching in lgv](https://user-images.githubusercontent.com/45598764/132396329-f3fa9ed4-ace4-40b6-8eff-8289bbd3d2ca.gif) - -GIF showing the process of searching via the location search box of the Linear Genome View - -For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this [quick start](/docs/quickstart_cli#indexing-feature-names-for-searching) - -Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases. - -Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page diff --git a/website/release_announcement_drafts/v1.5.0.md b/website/release_announcement_drafts/v1.5.0.md deleted file mode 100644 index 886d5ee2d4..0000000000 --- a/website/release_announcement_drafts/v1.5.0.md +++ /dev/null @@ -1,33 +0,0 @@ -We are pleased to present the release of v1.5.0! We have some major new -features to announce with this version! - -## JBrowse Desktop - -JBrowse Desktop is our fully featured desktop application available for Mac, -Windows, and Linux. - -Everything you can do with JBrowse Web, you can do with JBrowse Desktop! In -fact, because it runs as a desktop app, JBrowse Desktop can do things that the -web can't like saving sessions to a file on your computer to revisit later. - -![JBrowse Desktop session](/img/desktop-session.png) - -JBrowse Desktop features a new landing page designed to help you manage your -work. Here's a few things you can do with it: - -- re-visit saved sessions using the recent session panel -- launch new sessions easily from the quick start panel (e.g. hg19 and hg38 are built-in) -- create a new entries in the quick start panel (e.g. quick launch your favorite organism) -- quickly rename or delete sessions from the landing page - -![JBrowse Desktop landing page](/img/desktop-landing.png) - -With JBrowse Desktop, your genome browser and your web browser can finally live -in harmony on your taskbar! :heart: - -## Access authenticated resources - -This release also contains the ability to access authenticated resources. For -JBrowse Desktop, the ability to open files from Google Drive and Dropbox share -links is built in. For JBrowse Web, administrators can add some extra -configuration to set these up. diff --git a/website/release_announcement_drafts/v1.5.1.md b/website/release_announcement_drafts/v1.5.1.md deleted file mode 100644 index f63a861592..0000000000 --- a/website/release_announcement_drafts/v1.5.1.md +++ /dev/null @@ -1,24 +0,0 @@ -This is the release of v1.5.1 with a bunch of small improvements and bugfixes, -including... - -## Cytoband overview - -We can now display the cytoband data for your genome assembly in the linear -genome view overview, and this will now be available for hg19 and hg38 assembly -configs on JBrowse Desktop - -![](/img/cytobands.png) - - - -This can also appear in SVG exports - -![](img/cytobands_svg.png) - -## Plugins can integrate with "Add track" workflow better - -Plugins that register new adapter types can integrate with the "Add track" -workflow by registering themselves for a particular file type or file extension -with the Core-guessAdapterForLocation diff --git a/website/release_announcement_drafts/v1.5.2.md b/website/release_announcement_drafts/v1.5.2.md deleted file mode 100644 index 46e0662f39..0000000000 --- a/website/release_announcement_drafts/v1.5.2.md +++ /dev/null @@ -1,27 +0,0 @@ -We're excited to present some great new features and performance improvements -in v1.5.2! - -## New arc display type - -A new display type has been added for drawing arcs. The color, thickness, -height, label, and caption of the arcs can be customized. - -![Example of new arc track](https://user-images.githubusercontent.com/83305007/146266347-52edde29-b368-454a-8e2f-dc6396789dae.png) - -## New plugin build system - -We've re-worked the system used by developers to build external plugins for more -stability and flexibility. The current plugin build system will continue to -work, but if you want to check out how the new template works, check out the -[JBrowse Plugin Template](https://github.com/GMOD/jbrowse-plugin-template). - -## Storybook docs added for Circular Genome View React component - -Find them linked under `@jbrowse/react-circular-genome-view` [here](https://jbrowse.org/jb2/download/#embedded-components). - -## Performance improvements - -The alignments track now has 25% faster speed on most datasets and particularly -on deep short read sequencing, it can be up to 10x faster. - -Check out the release notes for more! diff --git a/website/release_announcement_drafts/v1.5.3.md b/website/release_announcement_drafts/v1.5.3.md deleted file mode 100644 index 51d178b3ba..0000000000 --- a/website/release_announcement_drafts/v1.5.3.md +++ /dev/null @@ -1,4 +0,0 @@ -This release fixes `@jbrowse/development-tools`, which was broken in `v1.5.2`, -and is otherwise identical to `v1.5.2`. See -[the `v1.5.2` release announcement](https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) -for details about that release. diff --git a/website/release_announcement_drafts/v1.5.4.md b/website/release_announcement_drafts/v1.5.4.md deleted file mode 100644 index c53982753d..0000000000 --- a/website/release_announcement_drafts/v1.5.4.md +++ /dev/null @@ -1,7 +0,0 @@ -This release fixes an important bug for users of -@jbrowse/react-linear-genome-view where some features would not be able to be -clicked in v1.5.3 and v1.5.2. - -It also adds some better layout in the feature details panel, improved -typescript interfaces, and allows users to open multiple genome assemblies from -the start screen in JBrowse Desktop diff --git a/website/release_announcement_drafts/v1.5.5.md b/website/release_announcement_drafts/v1.5.5.md deleted file mode 100644 index c53982753d..0000000000 --- a/website/release_announcement_drafts/v1.5.5.md +++ /dev/null @@ -1,7 +0,0 @@ -This release fixes an important bug for users of -@jbrowse/react-linear-genome-view where some features would not be able to be -clicked in v1.5.3 and v1.5.2. - -It also adds some better layout in the feature details panel, improved -typescript interfaces, and allows users to open multiple genome assemblies from -the start screen in JBrowse Desktop diff --git a/website/release_announcement_drafts/v1.5.6.md b/website/release_announcement_drafts/v1.5.6.md deleted file mode 100644 index 0f62ee352e..0000000000 --- a/website/release_announcement_drafts/v1.5.6.md +++ /dev/null @@ -1,5 +0,0 @@ -Fixes a bug in usage of packages that caused usage of @jbrowse/core to fail due -to a erroneous babel config (affecting v1.5.5 of -@jbrowse/react-linear-genome-view and @jbrowse/react-circular-genome-view) - -Also we now can access the parent feature in jexl callbacks with parent(feature) or get(feature, 'parent') which is often needed when coloring subfeatures like exon/CDS features diff --git a/website/release_announcement_drafts/v1.5.7.md b/website/release_announcement_drafts/v1.5.7.md deleted file mode 100644 index 17db468d9c..0000000000 --- a/website/release_announcement_drafts/v1.5.7.md +++ /dev/null @@ -1 +0,0 @@ -This release includes a small update to help users resize the height of dotplot views. It also republishes v1.5.6 diff --git a/website/release_announcement_drafts/v1.5.8.md b/website/release_announcement_drafts/v1.5.8.md deleted file mode 100644 index 5621620812..0000000000 --- a/website/release_announcement_drafts/v1.5.8.md +++ /dev/null @@ -1 +0,0 @@ -This fixes a broken v1.5.7 release on npm diff --git a/website/release_announcement_drafts/v1.5.9.md b/website/release_announcement_drafts/v1.5.9.md deleted file mode 100644 index ec52664eda..0000000000 --- a/website/release_announcement_drafts/v1.5.9.md +++ /dev/null @@ -1 +0,0 @@ -This fixes a babel misconfiguration in v1.5.8 that prevented embedded packages from working diff --git a/website/release_announcement_drafts/v1.6.0.md b/website/release_announcement_drafts/v1.6.0.md deleted file mode 100644 index 72b50287d4..0000000000 --- a/website/release_announcement_drafts/v1.6.0.md +++ /dev/null @@ -1,18 +0,0 @@ -This release has a couple long awaited features! - -- Ability to load a session from a URL in JBrowse Web, for example, - https://jbrowse.org/code/jb2/v1.6.0/?config=test_data/volvox/config.json&loc=ctgA:2000-40000&assembly=volvox&tracks=gff3tabix_genes,volvox_filtered_vcf,volvox_microarray,volvox_cram - (note: the embedded components do not make any assumptions about the URL, so - do not have this functionality. Just the JBrowse Web package) -- Stats estimation, tracks will try to estimate how much data they have to load - and hide themselves if it is determined to be too much - -There are also some improvements to synteny and dotplot views. The synteny view -can now render curvy lines and "square" the views (so they each have the same -zoom level), and have individual search panels in the synteny view. You can now -also vertically resize the linear synteny view panel allowing for a taller or -shorter view! The rendering has also been sped up in both linear synteny and -dotplot views with certain code paths being up to 40x faster - -![](https://user-images.githubusercontent.com/6511937/151449824-8993a755-cc44-440f-bd98-8d251f144c58.png) -Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.0/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj diff --git a/website/release_announcement_drafts/v1.6.1.md b/website/release_announcement_drafts/v1.6.1.md deleted file mode 100644 index 72b50287d4..0000000000 --- a/website/release_announcement_drafts/v1.6.1.md +++ /dev/null @@ -1,18 +0,0 @@ -This release has a couple long awaited features! - -- Ability to load a session from a URL in JBrowse Web, for example, - https://jbrowse.org/code/jb2/v1.6.0/?config=test_data/volvox/config.json&loc=ctgA:2000-40000&assembly=volvox&tracks=gff3tabix_genes,volvox_filtered_vcf,volvox_microarray,volvox_cram - (note: the embedded components do not make any assumptions about the URL, so - do not have this functionality. Just the JBrowse Web package) -- Stats estimation, tracks will try to estimate how much data they have to load - and hide themselves if it is determined to be too much - -There are also some improvements to synteny and dotplot views. The synteny view -can now render curvy lines and "square" the views (so they each have the same -zoom level), and have individual search panels in the synteny view. You can now -also vertically resize the linear synteny view panel allowing for a taller or -shorter view! The rendering has also been sped up in both linear synteny and -dotplot views with certain code paths being up to 40x faster - -![](https://user-images.githubusercontent.com/6511937/151449824-8993a755-cc44-440f-bd98-8d251f144c58.png) -Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.0/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj diff --git a/website/release_announcement_drafts/v1.6.2.md b/website/release_announcement_drafts/v1.6.2.md deleted file mode 100644 index 72b50287d4..0000000000 --- a/website/release_announcement_drafts/v1.6.2.md +++ /dev/null @@ -1,18 +0,0 @@ -This release has a couple long awaited features! - -- Ability to load a session from a URL in JBrowse Web, for example, - https://jbrowse.org/code/jb2/v1.6.0/?config=test_data/volvox/config.json&loc=ctgA:2000-40000&assembly=volvox&tracks=gff3tabix_genes,volvox_filtered_vcf,volvox_microarray,volvox_cram - (note: the embedded components do not make any assumptions about the URL, so - do not have this functionality. Just the JBrowse Web package) -- Stats estimation, tracks will try to estimate how much data they have to load - and hide themselves if it is determined to be too much - -There are also some improvements to synteny and dotplot views. The synteny view -can now render curvy lines and "square" the views (so they each have the same -zoom level), and have individual search panels in the synteny view. You can now -also vertically resize the linear synteny view panel allowing for a taller or -shorter view! The rendering has also been sped up in both linear synteny and -dotplot views with certain code paths being up to 40x faster - -![](https://user-images.githubusercontent.com/6511937/151449824-8993a755-cc44-440f-bd98-8d251f144c58.png) -Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.0/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj diff --git a/website/release_announcement_drafts/v1.6.3.md b/website/release_announcement_drafts/v1.6.3.md deleted file mode 100644 index 72b50287d4..0000000000 --- a/website/release_announcement_drafts/v1.6.3.md +++ /dev/null @@ -1,18 +0,0 @@ -This release has a couple long awaited features! - -- Ability to load a session from a URL in JBrowse Web, for example, - https://jbrowse.org/code/jb2/v1.6.0/?config=test_data/volvox/config.json&loc=ctgA:2000-40000&assembly=volvox&tracks=gff3tabix_genes,volvox_filtered_vcf,volvox_microarray,volvox_cram - (note: the embedded components do not make any assumptions about the URL, so - do not have this functionality. Just the JBrowse Web package) -- Stats estimation, tracks will try to estimate how much data they have to load - and hide themselves if it is determined to be too much - -There are also some improvements to synteny and dotplot views. The synteny view -can now render curvy lines and "square" the views (so they each have the same -zoom level), and have individual search panels in the synteny view. You can now -also vertically resize the linear synteny view panel allowing for a taller or -shorter view! The rendering has also been sped up in both linear synteny and -dotplot views with certain code paths being up to 40x faster - -![](https://user-images.githubusercontent.com/6511937/151449824-8993a755-cc44-440f-bd98-8d251f144c58.png) -Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.0/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj diff --git a/website/release_announcement_drafts/v1.6.4.md b/website/release_announcement_drafts/v1.6.4.md deleted file mode 100644 index 72b50287d4..0000000000 --- a/website/release_announcement_drafts/v1.6.4.md +++ /dev/null @@ -1,18 +0,0 @@ -This release has a couple long awaited features! - -- Ability to load a session from a URL in JBrowse Web, for example, - https://jbrowse.org/code/jb2/v1.6.0/?config=test_data/volvox/config.json&loc=ctgA:2000-40000&assembly=volvox&tracks=gff3tabix_genes,volvox_filtered_vcf,volvox_microarray,volvox_cram - (note: the embedded components do not make any assumptions about the URL, so - do not have this functionality. Just the JBrowse Web package) -- Stats estimation, tracks will try to estimate how much data they have to load - and hide themselves if it is determined to be too much - -There are also some improvements to synteny and dotplot views. The synteny view -can now render curvy lines and "square" the views (so they each have the same -zoom level), and have individual search panels in the synteny view. You can now -also vertically resize the linear synteny view panel allowing for a taller or -shorter view! The rendering has also been sped up in both linear synteny and -dotplot views with certain code paths being up to 40x faster - -![](https://user-images.githubusercontent.com/6511937/151449824-8993a755-cc44-440f-bd98-8d251f144c58.png) -Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.0/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj diff --git a/website/release_announcement_drafts/v1.6.5.md b/website/release_announcement_drafts/v1.6.5.md deleted file mode 100644 index 449b09418b..0000000000 --- a/website/release_announcement_drafts/v1.6.5.md +++ /dev/null @@ -1,9 +0,0 @@ -We are pleased to announce v1.6.5! - -This features some various bugfixes to the @jbrowse/cli tool, including better -support for large config files with the admin-server, and renaming --out to ---root for the admin-server. - -It also includes two important fixes related to stats estimation in 1.6.4, one -where tracks would display an error on sparse tracks and another where tracks -would fail to perform stats estimation on BAM files due to a type confusion. diff --git a/website/release_announcement_drafts/v1.6.6.md b/website/release_announcement_drafts/v1.6.6.md deleted file mode 100644 index 20b478ff52..0000000000 --- a/website/release_announcement_drafts/v1.6.6.md +++ /dev/null @@ -1,41 +0,0 @@ -We are pleased to release v1.6.6! - -This contains several updated synteny features, including: - -- load .chain files from UCSC -- load .delta files from mummer -- load .anchors and .anchors.simple files from MCScan from the GUI -- ability to "rectangularize" the dotplot view and improved dotplot view overviews (shows total bp of selected regions) - -![](https://user-images.githubusercontent.com/6511937/157131973-1c8962cb-bea2-4bde-a4ee-a5a874d5f370.png) - -Screenshot showing updated import form with ability to load MCScan data - -![](https://user-images.githubusercontent.com/6511937/157134881-732f0e4b-d811-4515-8b41-6b44f0668611.png) - -Screenshot showing multiple tracks open at once, with the .anchors (green, gene -pairs) and .anchors.simple (black, larger synteny blocks) files from MCScan -shown in the dotplot view - -Note: MCScan functionality existed internally but was not easy to use. The -configuration schema for MCScan anchors files changed also to load the .bed -files at startup. See the config guide for details - -We also have an updated configuration editor GUI with collapsible sections - -![](https://user-images.githubusercontent.com/6511937/158277132-760f4c2b-8cfb-4fcf-84b8-3ad27ee76290.png) - -Screenshot showing new collapsible (turquoise) sections in the config editor - -A number of alignments track look and feel improvements were also added. The -scale bar was made to just list the min and max values when the height is -small, clip indicator position when horizontally flipped was fixed, and the -headroom was removed making the snpcoverage take up the full height of the -small area it uses. - -![](https://user-images.githubusercontent.com/6511937/158481635-142063b3-0cba-424e-8e06-de6a89b9ef9f.png) - -There have also been some changes to how internet accounts work. If you use one -of the built-in accounts like Google Drive or Dropbox, there's no need to change -anything. If you've implemented your own internet account, though, see -[#2725](https://github.com/GMOD/jbrowse-components/pull/2725) for more details. diff --git a/website/release_announcement_drafts/v1.6.7.md b/website/release_announcement_drafts/v1.6.7.md deleted file mode 100644 index cdfb4ef647..0000000000 --- a/website/release_announcement_drafts/v1.6.7.md +++ /dev/null @@ -1,6 +0,0 @@ -This release fixes an issue with JBrowse Desktop on v1.6.6 where the first -tracks to be opened would not load. - -It also adds a speed optimization for BAM files (in some cases, 5x speed -improvement seen in deep coverage files), and fixes a scroll issue on wiggle -tracks! diff --git a/website/release_announcement_drafts/v1.6.8.md b/website/release_announcement_drafts/v1.6.8.md deleted file mode 100644 index 887b5ec37b..0000000000 --- a/website/release_announcement_drafts/v1.6.8.md +++ /dev/null @@ -1,20 +0,0 @@ -We are pleased to announce the v1.6.8 release! - -This release includes a change to the default gene style to use boxes instead of "chevron" features, with a directional arrowhead - -Before - -![](https://user-images.githubusercontent.com/6511937/160173804-e73787b2-934f-45c3-8448-48f8e47512c5.png) - -After - -![](https://user-images.githubusercontent.com/6511937/160173798-660c2f84-f783-4d5d-ae5b-29847b9b18f7.png) - -Some additional highlights - -- Draws the correct the proportion of SNPs when displaying the SNPCoverage - height in log scale (thanks @gringer for reporting) -- Adds more optimizations for some alignments tracks -- Adds a per-base drawing mode to alignments tracks - -![](https://user-images.githubusercontent.com/6511937/159740142-706a46c4-a00c-4fa4-a6fb-46270d728b78.png) diff --git a/website/release_announcement_drafts/v1.6.9.md b/website/release_announcement_drafts/v1.6.9.md deleted file mode 100644 index 3d83220dd8..0000000000 --- a/website/release_announcement_drafts/v1.6.9.md +++ /dev/null @@ -1 +0,0 @@ -This is a re-release of 1.6.8 to fix the Mac build of JBrowse Desktop diff --git a/website/release_announcement_drafts/v1.7.0.md b/website/release_announcement_drafts/v1.7.0.md deleted file mode 100644 index 771537880a..0000000000 --- a/website/release_announcement_drafts/v1.7.0.md +++ /dev/null @@ -1,32 +0,0 @@ -We are excited to announce the latest JBrowse release! This has many great -features including - -1. Floating feature labels, so if you are zoomed into the middle of a gene, the - feature label hangs out alongside it on the left side of the screen! The - results may not be pixel perfect in all cases (reverse complement labels can - end up overallping other features for example) but we hope this helps you - see the labels for features that extend off the screen! - - ![](https://user-images.githubusercontent.com/6511937/163470981-cfbd4464-bd5a-4421-8d9c-c8e6bb2d19bc.png) - - Figure showing the feature labels floating alongside gene even when you are - zoomed into the feature - -2. Upgraded build system for jbrowse-web and jbrowse-desktop to webpack 5, and - added examples of using webpack 5 with embedded components. Webpack 5 - results in smaller build sizes for jbrowse-web. For a typical session, - amount of .js downloaded with gzip enabled in v1.6.9 is ~1.4MB, in v1.7.0 - ~900kb (-500kb smaller). Without gzip enabled v1.6.9 4.8MB, v1.7.0 2.5MB - (-2MB smaller). The result is largely due to better webworker bundling. - -3. Optimizations and improved visualization of paired-end reads in the - breakpoint split view - -4. Optimized linear synteny renderings with long CIGAR strings. These - optimizations help viewing large alignments such as the CHM13-T2T-v2.0 - assembly vs hg38 PAF file from https://github.com/marbl/CHM13#downloads - (example here - https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=share-0qD2-d_k4K&password=GF8Sk) - -5. The "Assembly selector" dropdown box now remembers your last selection, so - you can more easily return to your genome of interest diff --git a/website/release_announcement_drafts/v1.7.1.md b/website/release_announcement_drafts/v1.7.1.md deleted file mode 100644 index c46e6be060..0000000000 --- a/website/release_announcement_drafts/v1.7.1.md +++ /dev/null @@ -1,4 +0,0 @@ -This is a small patch release that fixes two bugs that were in v1.7.0 - -- restores typescript typings to our NPM packages -- fixes the @jbrowse/img fetch polyfill diff --git a/website/release_announcement_drafts/v1.7.10.md b/website/release_announcement_drafts/v1.7.10.md deleted file mode 100644 index 7db66d2ebc..0000000000 --- a/website/release_announcement_drafts/v1.7.10.md +++ /dev/null @@ -1,67 +0,0 @@ -We are pleased to present the latest JBrowse 2 release! - -This has some great new features including - -- Feature detail formatters - add callback to add links or other customizations - to the feature details panels (see - https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels - for more info) -- Session URL formats for loading spreadsheet, SV inspector, and linear and - dotplot synteny views (see https://jbrowse.org/jb2/docs/urlparams/ for details) -- You can enter "chr1 100 200" to navigate to "chr1:100-200" as a simple way to - copy from a bed file or similar - -## Feature detail formatter - -Here is an example which adds a link to the "Name" panel in the feature -details. It uses the jexl callback that returns an object with keys for each -field to modify (e.g. the key name is used here). See - -```json -{ - "type": "FeatureTrack", - "trackId": "ncbi_gff_hg19_2", - "name": "NCBI RefSeq", - "formatDetails": { - "feature": "jexl:{name:''+feature.name+''}" - }, - "assemblyNames": ["hg19"], - "adapter": { - "type": "Gff3TabixAdapter", - "gffGzLocation": { - "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz" - }, - "index": { - "location": { - "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi" - } - } - } -} -``` - -Example screenshot - -![](https://user-images.githubusercontent.com/6511937/173461279-1afebb28-5928-47c1-8157-ecd2427a7fb2.png) - -See https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info - -## Clearer configuration panel with explicit "Add item" button with "OK"/"Cancel" to confirm - -![](https://user-images.githubusercontent.com/6511937/172203086-bf99e089-192a-46a6-baf1-96b3f97a36f2.png) - -## Large track menus no longer disappear off the screen - -Before - -![](https://user-images.githubusercontent.com/6511937/172012588-b82cace7-6c0c-4de8-991e-d1bc9ce17a77.png) - -After - -![](https://user-images.githubusercontent.com/6511937/172013123-0117cc8d-7008-408a-978a-72ccb4aec7da.png) - -## Automatically generate clickable links for data files in About track dialog - -![](https://user-images.githubusercontent.com/6511937/172653136-720e48f9-2e9f-494b-8dda-a1708e74d089.png) - -See also the "Copy config" button to download the config diff --git a/website/release_announcement_drafts/v1.7.11.md b/website/release_announcement_drafts/v1.7.11.md deleted file mode 100644 index 1cbd94886c..0000000000 --- a/website/release_announcement_drafts/v1.7.11.md +++ /dev/null @@ -1,7 +0,0 @@ -We are excited to announce v1.7.11! - -This release has some relatively small fixes to the UI, docs, and examples. For -developers, they may notice that we have removed `node-canvas` due to it's need -for having extra system dependencies, and becuase it only really was needed in -niche circumstances. This will improve the ease of installing packages like -`@jbrowse/react-linear-genome-view`. diff --git a/website/release_announcement_drafts/v1.7.2.md b/website/release_announcement_drafts/v1.7.2.md deleted file mode 100644 index 1b702f8d23..0000000000 --- a/website/release_announcement_drafts/v1.7.2.md +++ /dev/null @@ -1 +0,0 @@ -Fixes missing dependency in the @jbrowse/react-linear-genome-view in v1.7.1 diff --git a/website/release_announcement_drafts/v1.7.3.md b/website/release_announcement_drafts/v1.7.3.md deleted file mode 100644 index 5a770517fe..0000000000 --- a/website/release_announcement_drafts/v1.7.3.md +++ /dev/null @@ -1 +0,0 @@ -v1.7.2 was a botched upload to npm diff --git a/website/release_announcement_drafts/v1.7.4.md b/website/release_announcement_drafts/v1.7.4.md deleted file mode 100644 index 24ab929ddb..0000000000 --- a/website/release_announcement_drafts/v1.7.4.md +++ /dev/null @@ -1,2 +0,0 @@ -This is a small patch release that fixes our UMD builds for embedded components -fixes the @babel/runtime dependency in some npm packages diff --git a/website/release_announcement_drafts/v1.7.5.md b/website/release_announcement_drafts/v1.7.5.md deleted file mode 100644 index bb548eda5b..0000000000 --- a/website/release_announcement_drafts/v1.7.5.md +++ /dev/null @@ -1,29 +0,0 @@ -We are pleased to present the release of v1.7.5 - -This release includes two major improvements - -- Ability to index tracks for searching by gene names in JBrowse Desktop. This - let's users choose per-track indexes in the add track widget interactively, - or index them after-the-fact using the track menu. -- Removed serialization of BAM/CRAM features for pileup tracks which brings - large performance benefits for jbrowse-web and jbrowse-desktop. The main - thread has to manually request any data it needs from the worker after - rendering (e.g. when we click a feature), and not assume the feature data is - available on the main thread - -![](https://user-images.githubusercontent.com/6511937/165193301-fc573cac-2e5f-41f9-a91d-5ff5f9b94fcd.png) - -Figure showing the "Index track" option in the track menu of JBrowse Desktop - -![](https://user-images.githubusercontent.com/6511937/165193294-8905d757-0941-4f5c-85d6-61a831c9ad54.png) - -Figure showing the "Index track" option in the add track widget of JBrowse -Desktop - -![](https://user-images.githubusercontent.com/6511937/165193655-3d5482f3-2dec-423d-aab4-c7d54a180d11.png) - -Figure showing performance improvement of the noserialize improvement compared -with v1.7.4, which brings the webworker performance in line with the embedded -app (which does no serialzation) - -This release also fixes a bug with using trix indexes created by `jbrowse text-index` in v1.7.0-v1.7.4 (with the adjustable prefix size) diff --git a/website/release_announcement_drafts/v1.7.6.md b/website/release_announcement_drafts/v1.7.6.md deleted file mode 100644 index cb4faf92c7..0000000000 --- a/website/release_announcement_drafts/v1.7.6.md +++ /dev/null @@ -1,2 +0,0 @@ -This fixes a bug that affected v1.7.0-v1.7.6 where CRAM, TwoBit, and other file -types would not load on jbrowse-desktop after the upgrade to webpack 5. diff --git a/website/release_announcement_drafts/v1.7.7.md b/website/release_announcement_drafts/v1.7.7.md deleted file mode 100644 index 30b41b3719..0000000000 --- a/website/release_announcement_drafts/v1.7.7.md +++ /dev/null @@ -1,2 +0,0 @@ -This is a small bugfix release, where in v1.7.5-1.7.6 the read vs ref and -sequence panels in the feature details failed to load diff --git a/website/release_announcement_drafts/v1.7.8.md b/website/release_announcement_drafts/v1.7.8.md deleted file mode 100644 index f5b9700765..0000000000 --- a/website/release_announcement_drafts/v1.7.8.md +++ /dev/null @@ -1,12 +0,0 @@ -We are happy to announce v1.7.8 - -Some highlights include - -- ~20% speed improvement for CRAM data -- bugfix for filter-by being broken on alignments tracks in v1.7.0-v1.7.7 -- bugfix for certain methylation/modifications being drawn incorrectly on alignments tracks -- bugfix for the "Open" button not navigating to the correct location on the LGV import form -- improved visualization of indels in methylation/modifications mode on alignments tracks -- skip text index query if the input is a loc string, resulting in quicker navigation - -See the release notes for details diff --git a/website/release_announcement_drafts/v1.7.9.md b/website/release_announcement_drafts/v1.7.9.md deleted file mode 100644 index b7f1613a5f..0000000000 --- a/website/release_announcement_drafts/v1.7.9.md +++ /dev/null @@ -1,15 +0,0 @@ -We are pleased to present v1.7.9! - -This release features several bugfixes and improvements submitted by community -members, including a CLI fix when specifying --indexFile with CSI files, and a -new feature to get FASTA metadata from an external file. - -Additionally, we have switched to canvas2svg for SVG exports, which can now -handle more sophisticated operations like bezierCurves (used for sashimi-style -arc in RNA-seq data), and circles (used by jbrowse-plugin-gwas) - -Before (note bad intron and lack of arcs rendered on bottom track) -![](https://user-images.githubusercontent.com/6511937/171530567-8401e44d-4ae9-4d84-b918-3b7dec4fc3ee.png) - -After (fixed intron rendering and arcs) -![](https://user-images.githubusercontent.com/6511937/171530346-8466465f-fbae-49bd-a099-1acb2baddf1d.png) diff --git a/website/release_announcement_drafts/v2.0.0.md b/website/release_announcement_drafts/v2.0.0.md deleted file mode 100644 index 7fd8c5f492..0000000000 --- a/website/release_announcement_drafts/v2.0.0.md +++ /dev/null @@ -1,19 +0,0 @@ -We are pleased to release v2.0.0! This is a major version milestone, but it -does not have a huge number of changes. Instead, the major change that resulted -in becoming v2.0.0 was the upgrade of many of our dependencies including - -- material-ui v4 -> v5 -- mobx-state-tree v3.14.1 -> v5 -- mobx-react v6 -> v7 -- mobx v5 -> v6 - -Therefore, to help users that may have been relying on library versions like -this, it is safer to make the version a major bump. If you run into any issues -with this upgrade, let us know and we can help - -Some notable improvements: - -- This release improves bundle sizes for users of embedded components, by - adding ESM builds to NPM. This can reduce the initial load of a webpage using - e.g. @jbrowse/react-linear-genome-view by about 55% (1.4MB gzipped js->770kb - gzipped js) diff --git a/website/release_announcement_drafts/v2.0.1.md b/website/release_announcement_drafts/v2.0.1.md deleted file mode 100644 index bec73f0321..0000000000 --- a/website/release_announcement_drafts/v2.0.1.md +++ /dev/null @@ -1,8 +0,0 @@ -We are pleased to announce 2.0.1 - -This release features the ability to mouseover and click synteny alignments on -the linear synteny view - -![](https://user-images.githubusercontent.com/6511937/178566572-6fb7600b-172f-4317-8a6d-1318310d2baf.png) - -It also has some other small fixes and improvements, see release notes! diff --git a/website/release_announcement_drafts/v2.1.0.md b/website/release_announcement_drafts/v2.1.0.md deleted file mode 100644 index 5777c9c93f..0000000000 --- a/website/release_announcement_drafts/v2.1.0.md +++ /dev/null @@ -1,33 +0,0 @@ -We are pleased to present 2.1.0! This release adds some significant new -features including: - -- Multi-wiggle tracks - This allows, for example, multiple bigwig files to be - displayed in a single track with synchronized scalebar settings. See - [multi-wiggle docs](/jb2/docs/user_guide/#multi-quantitative-tracks) for more - info. -- Undo and redo functionality, let's you undo an operation in the UI e.g. - closing a view, closing a track can be recovered -- An alert when the dotplot view renders features that go beyond the bounds of - the selected region. This is often an indication that the wrong assembly is - being used or the query and target are backwards - -![](https://user-images.githubusercontent.com/6511937/181639088-9159d60d-a49d-4601-bfb8-6201a26dc185.png) - -Multi-row plot showing 21 ENCODE bigWig tracks - -![](https://user-images.githubusercontent.com/6511937/181639797-69294456-cbe6-403a-9131-98af27c849f3.png) - -Overlapping "xyplot" rendering multiwiggle rendering mode with "emphasised" -points showing tumor vs normal coverage - -![](https://user-images.githubusercontent.com/6511937/181640836-76257585-bfde-4568-8f44-dbf2590131cb.png) - -Dotplot view showing warnings from rendering dotplot, generally due to the -wrong assemblies being compared. Screenshot also shows the dropdown menu to -choose whether mouse click-and-drag pans the view or selects a region - -![](https://user-images.githubusercontent.com/6511937/181638930-730a522d-b58e-4505-a83a-7eb5ff1fe34d.png) - -Undo and redo buttons in the Tools menu, also accessible from keyboard -shortcuts ctrl+z/ctrl+y and cmd+z/cmd+shift+z. The Undo/Redo function is -available in jbrowse-web and jbrowse-desktop currently diff --git a/website/release_announcement_drafts/v2.1.1.md b/website/release_announcement_drafts/v2.1.1.md deleted file mode 100644 index a7fc115e98..0000000000 --- a/website/release_announcement_drafts/v2.1.1.md +++ /dev/null @@ -1,18 +0,0 @@ -Hello all, we are pleased to announce v2.1.1! - -This release includes a number of small bugfixes to the multi-wiggle track -type, and a new feature for performing small sequence searches/motifs in the -visible region. - -![](https://user-images.githubusercontent.com/6511937/186729490-40cbc638-c64a-4eef-a3f9-b80da4b6fdb6.png) -![](https://user-images.githubusercontent.com/6511937/186729296-2a0dda34-d298-4e7f-8b2b-f938ce89fb76.png) - -Screenshot of the sequence search feature. It is available from the "view menu" -on the linear genome view - -Also, we just recently published the pre-print for our JBrowse 2 paper on -bioRxiv! https://www.biorxiv.org/content/10.1101/2022.07.28.501447v1 - -This is a tour de force describing the basic ideas behind JBrowse 2 as an app. -We are really pleased with how users and developers have helped to contribute -to JBrowse 2 thus far, and look forward to many more years! diff --git a/website/release_announcement_drafts/v2.1.2.md b/website/release_announcement_drafts/v2.1.2.md deleted file mode 100644 index f46b9f9ab1..0000000000 --- a/website/release_announcement_drafts/v2.1.2.md +++ /dev/null @@ -1 +0,0 @@ -Bugfix release after 2.1.1 diff --git a/website/release_announcement_drafts/v2.1.3.md b/website/release_announcement_drafts/v2.1.3.md deleted file mode 100644 index 234a7bfdb2..0000000000 --- a/website/release_announcement_drafts/v2.1.3.md +++ /dev/null @@ -1,13 +0,0 @@ -This release includes a quality-of-life improvement for users plotting synteny -with CIGAR strings. Before this version, the x-axis in the dotplot was assumed -to be target sequence (and similarly, the top row in the linear synteny view -was assumed to be the target sequence). But now, target can be either x- or -y-axis in dotplot, and top or bottom in linear synteny views, removing the need -for the user to care as much about query-vs-target ordering. - -This release also includes several fixes for the the behavior of text searching -in the linear genome view, a new button to open a .jbrowse file directly from -the start screen on jbrowse-desktop, and an important bugfix to plotting -inverted alignments on dotplots that affected versions v2.1.0-v2.1.2. - -Enjoy! diff --git a/website/release_announcement_drafts/v2.1.4.md b/website/release_announcement_drafts/v2.1.4.md deleted file mode 100644 index 14df335138..0000000000 --- a/website/release_announcement_drafts/v2.1.4.md +++ /dev/null @@ -1 +0,0 @@ -This release fixes the UMD builds for the react components which failed to upload to npm in 2.1.3 diff --git a/website/release_announcement_drafts/v2.1.5.md b/website/release_announcement_drafts/v2.1.5.md deleted file mode 100644 index adb38de695..0000000000 --- a/website/release_announcement_drafts/v2.1.5.md +++ /dev/null @@ -1,6 +0,0 @@ -We are happy to present v2.1.5! This release adds the ability for the embedded -linear genome view component to have session tracks, and we added a new UI for -alerts/errors on tracks. See the changelog for details. - -Other issues with the circular genome view, authentication on jbrowse-desktop, -and the trackhub registry were also fixed. Enjoy! diff --git a/website/release_announcement_drafts/v2.1.6.md b/website/release_announcement_drafts/v2.1.6.md deleted file mode 100644 index 77c6320979..0000000000 --- a/website/release_announcement_drafts/v2.1.6.md +++ /dev/null @@ -1,36 +0,0 @@ -We are happy to release v2.1.6 - -This has several important fixes and improvements - -- Tracks no longer hang in "Loading..." state under Safari and Webkit based - browsers, a bug with starting the webworker was fixed -- There is now an option to use the WebWorkerRpc on the - @jbrowse/react-linear-genome-view. This is a great improvement because the - WebWorkerRpc dramatically reduces the "stalling" of the main thread when - large datasets like BAM/CRAM are being loaded. See - https://jbrowse.org/storybook/lgv/main/?path=/story/using-webworker-rpc--page - for more info! -- All feature types, not just gene features, can obtain the underlying feature - sequence with upstream/downstream options -- The ability to refer to plugins in a path relative to your data directory - has been fixed, so you can easily refer to plugins in your config file with - e.g. `"plugins":[{"name":"MyPlugin","umdLoc":{"uri":"myplugin.js"}}]` - (`umdLoc` resolves the uri relative to the config.json file that it is in - use). There is also `umdUrl` which can be used in place of `umdLoc` which can - be used like this `"plugins":[{"name":"MyPlugin","umdUrl":"myplugin.js"}]` - and this will resolve relative to the jbrowse root directory e.g. where the - index.html is. We recommend using UMD for now, as ESM modules do not have - full browser support e.g. in firefox yet, but this will likely be changing - soon and we will update tutorials when this occurs! - -See our volvox example for a simple no-build plugin -https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/umd_plugin.js -along with it's config -https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/config.json -and see our no-build plugin tutorial! -https://jbrowse.org/jb2/docs/tutorials/no_build_plugin_tutorial/ - -![](https://user-images.githubusercontent.com/6511937/196806717-5b94a8cd-38fa-4861-9692-393158a5b2b0.png) - -Screenshot of the feature sequence panel showing on a SNP, allowing you to get -upstream and downstream sequence of the SNP diff --git a/website/release_announcement_drafts/v2.1.7.md b/website/release_announcement_drafts/v2.1.7.md deleted file mode 100644 index bb0600d690..0000000000 --- a/website/release_announcement_drafts/v2.1.7.md +++ /dev/null @@ -1 +0,0 @@ -This release fixes the build of @jbrowse/react-linear-genome-view under webpack 4, which had trouble due to the web worker support added in v2.1.6 diff --git a/website/release_announcement_drafts/v2.3.0.md b/website/release_announcement_drafts/v2.3.0.md new file mode 100644 index 0000000000..9998c5facd --- /dev/null +++ b/website/release_announcement_drafts/v2.3.0.md @@ -0,0 +1,58 @@ +Hello all! This release adds some great new features! + +- New "arc" and "read cloud" alignments track modes which render long range + connections between read pairs/split reads. These views have a big impact on + being able to visualize structural variants. + +- We now automatically optimize the "prefix size" for our trix indexes created + by `jbrowse text-index` which should help solve issues with slow text + searching. + +- We now refer to many pluggable elements by a "display name" instead of the + coded class name so we have instead of "LinearGCContentDisplay" -> "GC content + display". + +### New alignments track displays + +We created a new display mode that changes the "pileup" of reads into "arcs" +which connects both paired-end reads and split-long read alignments. + +![](https://user-images.githubusercontent.com/6511937/205725535-6b058cc6-7dba-41e9-ac2a-eba4ee881d89.png) + +New track menu showing the ability to replace the "lower panel" with arc display +or read cloud display + +![](https://user-images.githubusercontent.com/6511937/205730944-07347472-a9e6-44b9-8c8c-ca4380a3c75a.png) + +The arc view and read cloud view rendering across discontinuous displayedRegions + +![](https://user-images.githubusercontent.com/6511937/207134568-577cdcb3-4458-4e71-8063-aa493a21593c.png) + +A zoomed in view of long-reads (top) and paired-end reads (bottom) at the +breakpoint of a large deletion + +## Easily toggleable "compact" view of alignments + +![](https://user-images.githubusercontent.com/6511937/207207662-50778dfe-ffa8-4ca1-93fe-febcda3fdcb7.png) + +We now have an easily toggleable compact setting on alignments tracks +(previously had to manually change feature height) + +## Optimized prefix size for text search indexing + +Previously, if indexing long gene IDs with `jbrowse text-index` it would often +be slow because the "trix" format is generally optimized for short gene symbols. +We added the --prefixSize parameter in previous jbrowse versions to allow +optimizing for specific gene lengths, but this was sort of a magic number. Now, +`jbrowse text-index` will automatically calculate the --prefixSize if none is +provided, which tries to get an even ~64kb bin size. Let us know how it goes for +your data! + +Re-install the CLI tools with e.g. `npm install -g @jbrowse/cli` to get the +latest version with this feature. + +## Moved "Track Hub Registry" plugin to plugin store + +We removed the "Track Hub Registry" plugin, which was previously a "core +plugin", to the plugin store. This will allow us to update the plugin over time +and respond better to issues when they change their remote API. diff --git a/website/release_announcement_drafts/v2.3.1.md b/website/release_announcement_drafts/v2.3.1.md new file mode 100644 index 0000000000..fc33b53fda --- /dev/null +++ b/website/release_announcement_drafts/v2.3.1.md @@ -0,0 +1 @@ +This fixes the release of the desktop builds after electron-notarize upgrade diff --git a/website/release_announcement_drafts/v2.3.2.md b/website/release_announcement_drafts/v2.3.2.md new file mode 100644 index 0000000000..213b351017 --- /dev/null +++ b/website/release_announcement_drafts/v2.3.2.md @@ -0,0 +1,13 @@ +This release contains important fixes for drawing base-level synteny based on +CIGAR strings, especially in inverted regions. We also fixed refName renaming +(e.g. your BAM file has 'chr1' but the FASTA has '1') on the new arc display +(see v2.3.1). + +Additionally, it offers the ability to reverse/complement the sequence in the +"Get sequence" dialog. + +![](https://user-images.githubusercontent.com/6511937/208767035-90f1fb23-0fa4-468a-8095-14dc597014b2.png) + +Screenshot showing how insertions from relative to one assembly exactly match up +at a "deletion" relative to another, using the LGV synteny display and curved +arcs. Previous versions had bugs but will now match exactly. diff --git a/website/sidebars.json b/website/sidebars.json index dcff2447aa..f065c15fbc 100644 --- a/website/sidebars.json +++ b/website/sidebars.json @@ -4,13 +4,7 @@ { "type": "category", "label": "Quickstart guides", - "items": [ - "quickstart_desktop", - "quickstart_web", - "quickstart_cli", - "tutorials/config_cli", - "tutorials/config_gui" - ] + "items": ["quickstart_desktop", "quickstart_web", "tutorials/config_gui"] }, { "type": "category", diff --git a/website/src/pages/contact.md b/website/src/pages/contact.md index 8330aee96a..26470ec473 100644 --- a/website/src/pages/contact.md +++ b/website/src/pages/contact.md @@ -4,7 +4,8 @@ id: contact # Contact us -We **really** love talking to our users. Please reach out with any thoughts you have on what we are building! +We **really** love talking to our users. Please reach out with any thoughts you +have on what we are building! - Ask a question on our discussion board at https://github.com/GMOD/jbrowse-components/discussions diff --git a/website/src/pages/demos.mdx b/website/src/pages/demos.mdx index faf586a3b7..63c4a9908f 100644 --- a/website/src/pages/demos.mdx +++ b/website/src/pages/demos.mdx @@ -12,10 +12,10 @@ export const Link = ({ extra, children }) => { # JBrowse 2 demos -These demos contain examples of new workflows and views in JBrowse 2, with -links to live sessions on the web in order for you to be able to experience the -app yourself. The link above will always direct to the most recent demo that -has been released. +These demos contain examples of new workflows and views in JBrowse 2, with links +to live sessions on the web in order for you to be able to experience the app +yourself. The link above will always direct to the most recent demo that has +been released. Note: everything demonstrated here on the web can also be done in JBrowse desktop. @@ -57,8 +57,7 @@ desktop. [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.07.28.501447v1) preprint for more info) - [2022 Plant and Animal Genomes](https://jbrowse.org/demos/pag2022/) (see also - [workshop video tutorial - here](/docs/tutorials/archive/pag2022_synteny_tutorial)) + [workshop video tutorial here](/docs/archive/pag2022_synteny_tutorial)) - [2021 Biology of Genomes](https://jbrowse.org/demos/bog2021/) - [2020 Cancer SVs demo](https://jbrowse.org/demos/cancer-demo-2020/) - guided demo of structural variant visualization diff --git a/website/src/pages/download.mdx b/website/src/pages/download.mdx index c86c0a57c6..8190c41e54 100644 --- a/website/src/pages/download.mdx +++ b/website/src/pages/download.mdx @@ -156,9 +156,9 @@ export const DownloadCardContainer = () => { # Download JBrowse 2 -JBrowse 2 is a new browser for today's increasingly complex data. We -make several different products for use in different scenarios, choose -the one below that best fits your needs. +JBrowse 2 is a new browser for today's increasingly complex data. We make +several different products for use in different scenarios, choose the one below +that best fits your needs. ## JBrowse Desktop @@ -169,16 +169,18 @@ sources. Download JBrowse Desktop on the platform of your choice: ## JBrowse Web -Run a full-featured genome browser with many types of built-in views on your -own website. +Run a full-featured genome browser with many types of built-in views on your own +website. -Consider installing the JBrowse CLI tools (below), which can be used to create and manage JBrowse Web instances from the command line. +Consider installing the JBrowse CLI tools (below), which can be used to create +and manage JBrowse Web instances from the command line. ## JBrowse CLI tools -The JBrowse CLI helps administrators add genome assemblies, tracks, and more to their config files. +The JBrowse CLI helps administrators add genome assemblies, tracks, and more to +their config files. To install: @@ -186,9 +188,8 @@ To install: npm install -g @jbrowse/cli ``` -After installing the CLI tools, check out our [super-quick start -guide](/docs/superquickstart_web) or the slightly longer [quick-start -guide](/docs/quickstart_web). +After installing the CLI tools, check out our +[quick-start guide](/docs/quickstart_web). ## Static image generator @@ -198,15 +199,20 @@ guide](/docs/quickstart_web). ## Embedded components - [@jbrowse/react-linear-genome-view](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) - linear genome browser view React component on NPM. Also see our + linear genome browser view React component on NPM + - See code examples here in the linear genome view - [@jbrowse/react-circular-genome-view](https://www.npmjs.com/package/@jbrowse/react-circular-genome-view) - circular genome browser view React component on NPM. Also see our + circular genome browser view React component on NPM + - See code examples here in the circular genome view -More info here [embedded docs](../docs/embedded_components) +More info here [embedded docs](../docs/embedded_components) including examples +of including the app with various build systems (create-react-app, vite, +next.js, vanillajs, etc.) ## Jupyter Notebooks Extension -- [Documentation](https://gmod.github.io/jbrowse-jupyter/docs/html/index.html) [Source code (GitHub)](https://github.com/GMOD/jbrowse-jupyter) +- [Documentation](https://gmod.github.io/jbrowse-jupyter/docs/html/index.html) +- [Source code](https://github.com/GMOD/jbrowse-jupyter) ## Dash - Python diff --git a/website/src/pages/features.md b/website/src/pages/features.md index db5202ec28..0121734614 100644 --- a/website/src/pages/features.md +++ b/website/src/pages/features.md @@ -11,9 +11,9 @@ The view types available by default with JBrowse 2 web include translocations. The VCF breakend `` and `` type features can be rendered as arcs across the view -- Breakpoint split view - Our breakpoint split view shows the connection - between long split alignments or paired end reads across multiple chromosomes - using stacked linear genome views +- Breakpoint split view - Our breakpoint split view shows the connection between + long split alignments or paired end reads across multiple chromosomes using + stacked linear genome views - Dotplot view - Zoomable comparison of whole genome alignments or synteny datasets @@ -21,8 +21,8 @@ The view types available by default with JBrowse 2 web include - Linear synteny view - Another option for exploration of syntenic alignments using stacked linear genome views -- Tabular view - Open formats like BED, VCF, CSV, TSV, or even bespoke - formats like STAR-fusion in the tabular view +- Tabular view - Open formats like BED, VCF, CSV, TSV, or even bespoke formats + like STAR-fusion in the tabular view ## Feature comparison @@ -46,9 +46,11 @@ The view types available by default with JBrowse 2 web include | Ability to search by gene name/ID (added in 1.4.0) | :heavy_check_mark: | :heavy_check_mark: | | URL query API e.g. specifying ?loc=chr1:1-100 in URL bar (added in 1.6.4) | :heavy_check_mark: | :heavy_check_mark: | -[^1] If using with JBrowse 2 web, requires that trackhub server be configured to allow [CORS](https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS) +[^1] If using with JBrowse 2 web, requires that trackhub server be configured to +allow [CORS](https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS) -[^2] See [`@jbrowse/react-linear-genome-view` on npm](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) +[^2] See +[`@jbrowse/react-linear-genome-view` on npm](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) ## Supported data formats @@ -72,18 +74,23 @@ available for additional data formats. ## Integration and embedding -The JBrowse 2 platform and plugins are designed from the ground up to be -modular and reusable. For example, individual JBrowse 2 views (e.g. linear, -circular, tabular, etc) can be packaged to be embeddable in other web -applications (as demonstrated by the +The JBrowse 2 platform and plugins are designed from the ground up to be modular +and reusable. For example, individual JBrowse 2 views (e.g. linear, circular, +tabular, etc) can be packaged to be embeddable in other web applications (as +demonstrated by the [@jbrowse/react-linear-genome-view](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) package). -See the full list of our embedded components [here](https://jbrowse.org/jb2/docs/embedded_components/). +See the full list of our embedded components +[here](https://jbrowse.org/jb2/docs/embedded_components/). ### Embedded views versus full JBrowse app -Embedded views are intended to facilitate genome browsing within the context of an existing webpage, however if it makes sense for a given use case, one might decide to run an instance of JBrowse on one's hosting website instead. Detailed below are the core differences between embedded components and the full JBrowse app: +Embedded views are intended to facilitate genome browsing within the context of +an existing webpage, however if it makes sense for a given use case, one might +decide to run an instance of JBrowse on one's hosting website instead. Detailed +below are the core differences between embedded components and the full JBrowse +app: | Embedded components [^3] | JBrowse Web | | ------------------------------------------------------- | -------------------------------------------------------------------------------------- | @@ -97,8 +104,13 @@ Embedded views are intended to facilitate genome browsing within the context of - enable/disable tracks through the Track interface - change the track's assembly based on what is available in the configuration -- manipulate the views with zoom, horizontal flip, view all regions, track label positioning, etc. +- manipulate the views with zoom, horizontal flip, view all regions, track label + positioning, etc. - change track display options - export the view as an SVG -[^3] Note that though the embedded components lack certain functionality, they are designed for web developers to build a custom system around, so though some of these options are not available by default, the ability to design mechanics such as sessions and custom track manipulation is present for a developer seeking to do these things. +[^3] Note that though the embedded components lack certain functionality, they +are designed for web developers to build a custom system around, so though some +of these options are not available by default, the ability to design mechanics +such as sessions and custom track manipulation is present for a developer +seeking to do these things. diff --git a/website/src/pages/gallery.md b/website/src/pages/gallery.md index b390416889..df94f9b3d4 100644 --- a/website/src/pages/gallery.md +++ b/website/src/pages/gallery.md @@ -1,33 +1,39 @@ # JBrowse 2 visualizations gallery -Below are some examples of the visualizations JBrowse 2 has to offer. For live demos, have a look at the [demos page](../demos). +Below are some examples of the visualizations JBrowse 2 has to offer. For live +demos, have a look at the [demos page](../demos). --- ![](/img/dotplot.png) + A genome vs genome dotplot displayed in the DotplotView. This displays grape vs peach genomes via PAF file --- ![](/img/linear_synteny.png) + A linear synteny display for grape vs peach displayed in the LinearSyntenyView via MCScan anchors file results --- ![](/img/alignments_sort_by_base.png) + Shows sorting the alignments pileup by the base-pair-at-the-given-position in the AlignmentsTrack --- ![](/img/hic_track.png) + Shows rendering of a .hic file type in the HicTrack --- ![](/img/sv_inspector_importform_loaded.png) + Screenshot of the SV inspector displaying inter-chromosomal translocations in the SKBR3 cell line. The SV inspector is a tabular view plus whole-genome circular overview of the SVs @@ -35,34 +41,39 @@ circular overview of the SVs --- ![](/img/horizontally_flip.png) + Shows the ability to horizontally flip the current view. This allows the anti-sense strand to be read left to right --- ![](/img/linear_longread.png) + Using the synteny view to render a long-read vs the reference genome. This is -available simply by clicking an alignments feature and selecting "Linear read -vs ref" +available simply by clicking an alignments feature and selecting "Linear read vs +ref" --- ![](/img/dotplot_longread.png) + Using the dotplot view to render a long-read vs the reference genome. This is -available by right-clicking an alignments feature and selecting "Dotplot read -vs ref" +available by right-clicking an alignments feature and selecting "Dotplot read vs +ref" --- ![](/img/cnv.png) -This is a whole-genome overview of CNV data using a BigWig file of -read-coverage depth. This uses the XYPlot, with fill turned off. The BigWig -data is binned at this resolution, and the blue shades represent the min, mean, -and max value in each bin + +This is a whole-genome overview of CNV data using a BigWig file of read-coverage +depth. This uses the XYPlot, with fill turned off. The BigWig data is binned at +this resolution, and the blue shades represent the min, mean, and max value in +each bin --- ![](/img/breakpoint_split_view.png) + Image of the "breakpoint split view" which examines the breakpoints of a structural variant, e.g. an interchromosomal translocation, and connects supporting reads (black splines) and the variant call itself (green thicker @@ -71,12 +82,14 @@ line, with feet indicating directionality) --- ![](/img/color_by_tag.png) + Image of coloring and sorting by the HP (haplotype) tag, which can be done for BAM and CRAM. Users can color, sort, and filter by tags --- ![](/img/insertion_indicators.png) + The browser has a variety of ways to help show insertions including "large insertion indicators" (a feature also seen in IGV) and upside down histogram of insertion/clipping counts @@ -84,12 +97,14 @@ insertion/clipping counts --- ![](/img/read_vs_ref_insertion.png) + The read vs reference visualization can show the "sequence track" on the "read" -to see which bases are inserted. Users can also use the "Get sequence" click -and drag to get the sequence of the contents of the insertions or unaligned -portions of the read (e.g. softclipped parts) +to see which bases are inserted. Users can also use the "Get sequence" click and +drag to get the sequence of the contents of the insertions or unaligned portions +of the read (e.g. softclipped parts) --- ![](/img/alignments/modifications2.png) + A hypo-methylated CpG island shown using the MM tag with nanopore reads diff --git a/website/static/img/alignments/arc_display.png b/website/static/img/alignments/arc_display.png new file mode 100644 index 0000000000..8876149084 Binary files /dev/null and b/website/static/img/alignments/arc_display.png differ diff --git a/website/static/img/alignments/arc_selector.png b/website/static/img/alignments/arc_selector.png new file mode 100644 index 0000000000..e968ec0eb9 Binary files /dev/null and b/website/static/img/alignments/arc_selector.png differ diff --git a/website/static/img/alignments/compact.png b/website/static/img/alignments/compact.png new file mode 100644 index 0000000000..f5b10714ea Binary files /dev/null and b/website/static/img/alignments/compact.png differ diff --git a/website/static/img/alignments/read_cloud.png b/website/static/img/alignments/read_cloud.png new file mode 100644 index 0000000000..3107577991 Binary files /dev/null and b/website/static/img/alignments/read_cloud.png differ diff --git a/website/static/img/alignments/select_arc_display.png b/website/static/img/alignments/select_arc_display.png new file mode 100644 index 0000000000..2c6418d741 Binary files /dev/null and b/website/static/img/alignments/select_arc_display.png differ diff --git a/website/static/img/drawer_widget_toggle.png b/website/static/img/drawer_widget_toggle.png new file mode 100644 index 0000000000..49fa4ea953 Binary files /dev/null and b/website/static/img/drawer_widget_toggle.png differ diff --git a/website/static/img/plugin_store.png b/website/static/img/plugin_store.png index a33d86f7fb..85118eca56 100644 Binary files a/website/static/img/plugin_store.png and b/website/static/img/plugin_store.png differ diff --git a/website/yarn.lock b/website/yarn.lock index 85a6210b7c..d71a97138a 100644 --- a/website/yarn.lock +++ b/website/yarn.lock @@ -9,14 +9,21 @@ dependencies: "@algolia/autocomplete-shared" "1.7.2" +"@algolia/autocomplete-core@1.7.3": + version "1.7.3" + resolved "https://registry.yarnpkg.com/@algolia/autocomplete-core/-/autocomplete-core-1.7.3.tgz#a26caf9b09dd4546c173da532096a2a8e56c15e7" + integrity sha512-RFv3xndlhfnFYhRqbPAEgXhHp2mJV3ht1nFf5dNM6eXdJGLdBKQGt0ygKDXMSBpSYTUoX0US04xRTArMOMSYJw== + dependencies: + "@algolia/autocomplete-shared" "1.7.3" + "@algolia/autocomplete-js@^1.5.1": - 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"@babel/plugin-syntax-import-assertions" "^7.18.6" + "@babel/plugin-syntax-import-assertions" "^7.20.0" "@babel/plugin-syntax-json-strings" "^7.8.3" "@babel/plugin-syntax-logical-assignment-operators" "^7.10.4" "@babel/plugin-syntax-nullish-coalescing-operator" "^7.8.3" @@ -1073,10 +1092,10 @@ "@babel/plugin-transform-arrow-functions" "^7.18.6" "@babel/plugin-transform-async-to-generator" "^7.18.6" "@babel/plugin-transform-block-scoped-functions" "^7.18.6" - "@babel/plugin-transform-block-scoping" "^7.19.4" - "@babel/plugin-transform-classes" "^7.19.0" + "@babel/plugin-transform-block-scoping" "^7.20.2" + "@babel/plugin-transform-classes" "^7.20.2" "@babel/plugin-transform-computed-properties" "^7.18.9" - "@babel/plugin-transform-destructuring" "^7.19.4" + "@babel/plugin-transform-destructuring" "^7.20.2" "@babel/plugin-transform-dotall-regex" "^7.18.6" "@babel/plugin-transform-duplicate-keys" "^7.18.9" "@babel/plugin-transform-exponentiation-operator" "^7.18.6" @@ -1084,14 +1103,14 @@ "@babel/plugin-transform-function-name" "^7.18.9" "@babel/plugin-transform-literals" "^7.18.9" "@babel/plugin-transform-member-expression-literals" "^7.18.6" - 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integrity sha512-EXpLCrk55f+cYqmHsSR+yD/0gAIMxxA9QK9lnQWzhMCvt+YmoBN7Zx94s++Kv0+unHk39vxNO8t+CMA2WSS3wA== +"@babel/runtime@^7.1.2", "@babel/runtime@^7.10.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.18.3", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.6", "@babel/runtime@^7.5.5", "@babel/runtime@^7.8.4", "@babel/runtime@^7.8.7": + version "7.20.6" + resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.20.6.tgz#facf4879bfed9b5326326273a64220f099b0fce3" + integrity sha512-Q+8MqP7TiHMWzSfwiJwXCjyf4GYA4Dgw3emg/7xmwsdLJOZUp+nMqcOwOzzYheuM1rhDu8FSj2l0aoMygEuXuA== dependencies: - regenerator-runtime "^0.13.4" + regenerator-runtime "^0.13.11" "@babel/template@^7.12.7", "@babel/template@^7.18.10": version "7.18.10" @@ -1166,26 +1185,26 @@ "@babel/parser" "^7.18.10" "@babel/types" "^7.18.10" -"@babel/traverse@^7.12.9", "@babel/traverse@^7.18.8", "@babel/traverse@^7.19.0", "@babel/traverse@^7.19.1", "@babel/traverse@^7.19.4", "@babel/traverse@^7.19.6": - 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caniuse-lite "^1.0.30001407" + caniuse-lite "^1.0.30001426" fraction.js "^4.2.0" normalize-range "^0.1.2" picocolors "^1.0.0" @@ -2758,9 +2777,9 @@ axios@^0.25.0: follow-redirects "^1.14.7" babel-loader@^8.2.5: - version "8.2.5" - resolved "https://registry.yarnpkg.com/babel-loader/-/babel-loader-8.2.5.tgz#d45f585e654d5a5d90f5350a779d7647c5ed512e" - integrity sha512-OSiFfH89LrEMiWd4pLNqGz4CwJDtbs2ZVc+iGu2HrkRfPxId9F2anQj38IxWpmRfsUY0aBZYi1EFcd3mhtRMLQ== + version "8.3.0" + resolved "https://registry.yarnpkg.com/babel-loader/-/babel-loader-8.3.0.tgz#124936e841ba4fe8176786d6ff28add1f134d6a8" + integrity sha512-H8SvsMF+m9t15HNLMipppzkC+Y2Yq+v3SonZyU70RBL/h1gxPkH08Ot8pEE9Z4Kd+czyWJClmFS8qzIP9OZ04Q== dependencies: find-cache-dir "^3.3.1" loader-utils "^2.0.0" @@ -2928,7 +2947,7 @@ braces@^3.0.2, braces@~3.0.2: dependencies: fill-range "^7.0.1" -browserslist@^4.0.0, browserslist@^4.14.5, browserslist@^4.16.6, browserslist@^4.18.1, browserslist@^4.20.3, browserslist@^4.21.3, browserslist@^4.21.4: +browserslist@^4.0.0, browserslist@^4.14.5, browserslist@^4.16.6, browserslist@^4.18.1, browserslist@^4.21.3, browserslist@^4.21.4: version "4.21.4" resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.21.4.tgz#e7496bbc67b9e39dd0f98565feccdcb0d4ff6987" integrity sha512-CBHJJdDmgjl3daYjN5Cp5kbTf1mUhZoS+beLklHIvkOWscs83YAhLlF3Wsh/lciQYAcbBJgTOD44VtG31ZM4Hw== @@ -3007,10 +3026,10 @@ caniuse-api@^3.0.0: lodash.memoize "^4.1.2" lodash.uniq "^4.5.0" -caniuse-lite@^1.0.0, caniuse-lite@^1.0.30001400, caniuse-lite@^1.0.30001407: - 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version "3.3.2" - resolved "https://registry.yarnpkg.com/copy-to-clipboard/-/copy-to-clipboard-3.3.2.tgz#5b263ec2366224b100181dded7ce0579b340c107" - integrity sha512-Vme1Z6RUDzrb6xAI7EZlVZ5uvOk2F//GaxKUxajDqm9LhOVM1inxNAD2vy+UZDYsd0uyA9s7b3/FVZPSxqrCfg== + version "3.3.3" + resolved "https://registry.yarnpkg.com/copy-to-clipboard/-/copy-to-clipboard-3.3.3.tgz#55ac43a1db8ae639a4bd99511c148cdd1b83a1b0" + integrity sha512-2KV8NhB5JqC3ky0r9PMCAZKbUHSwtEo4CwCs0KXgruG43gX5PMqDEBbVU4OUzw2MuAWUfsuFmWvEKG5QRfSnJA== dependencies: toggle-selection "^1.0.6" @@ -3334,21 +3353,21 @@ copy-webpack-plugin@^11.0.0: serialize-javascript "^6.0.0" core-js-compat@^3.25.1: - version "3.26.0" - resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.26.0.tgz#94e2cf8ba3e63800c4956ea298a6473bc9d62b44" - integrity sha512-piOX9Go+Z4f9ZiBFLnZ5VrOpBl0h7IGCkiFUN11QTe6LjAvOT3ifL/5TdoizMh99hcGy5SoLyWbapIY/PIb/3A== + version "3.26.1" + resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.26.1.tgz#0e710b09ebf689d719545ac36e49041850f943df" + integrity sha512-622/KzTudvXCDLRw70iHW4KKs1aGpcRcowGWyYJr2DEBfRrd6hNJybxSWJFuZYD4ma86xhrwDDHxmDaIq4EA8A== dependencies: browserslist "^4.21.4" core-js-pure@^3.25.1: - 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browserslist "^4.20.3" + browserslist "^4.21.4" postcss-value-parser "^4.2.0" postcss-discard-comments@^5.1.2: @@ -5864,13 +5876,13 @@ postcss-discard-unused@^5.1.0: postcss-selector-parser "^6.0.5" postcss-loader@^7.0.0: - version "7.0.1" - resolved "https://registry.yarnpkg.com/postcss-loader/-/postcss-loader-7.0.1.tgz#4c883cc0a1b2bfe2074377b7a74c1cd805684395" - integrity sha512-VRviFEyYlLjctSM93gAZtcJJ/iSkPZ79zWbN/1fSH+NisBByEiVLqpdVDrPLVSi8DX0oJo12kL/GppTBdKVXiQ== + version "7.0.2" + resolved "https://registry.yarnpkg.com/postcss-loader/-/postcss-loader-7.0.2.tgz#b53ff44a26fba3688eee92a048c7f2d4802e23bb" + integrity sha512-fUJzV/QH7NXUAqV8dWJ9Lg4aTkDCezpTS5HgJ2DvqznexTbSTxgi/dTECvTZ15BwKTtk8G/bqI/QTu2HPd3ZCg== dependencies: cosmiconfig "^7.0.0" klona "^2.0.5" - semver "^7.3.7" + semver "^7.3.8" postcss-merge-idents@^5.1.1: version "5.1.1" @@ -5880,20 +5892,20 @@ postcss-merge-idents@^5.1.1: cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" -postcss-merge-longhand@^5.1.6: - version "5.1.6" - 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browserslist "^4.16.6" + browserslist "^4.21.4" caniuse-api "^3.0.0" cssnano-utils "^3.1.0" postcss-selector-parser "^6.0.5" @@ -5914,12 +5926,12 @@ postcss-minify-gradients@^5.1.1: cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" -postcss-minify-params@^5.1.3: - version "5.1.3" - resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.3.tgz#ac41a6465be2db735099bbd1798d85079a6dc1f9" - integrity sha512-bkzpWcjykkqIujNL+EVEPOlLYi/eZ050oImVtHU7b4lFS82jPnsCb44gvC6pxaNt38Els3jWYDHTjHKf0koTgg== +postcss-minify-params@^5.1.4: + version "5.1.4" + resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.4.tgz#c06a6c787128b3208b38c9364cfc40c8aa5d7352" + integrity sha512-+mePA3MgdmVmv6g+30rn57USjOGSAyuxUmkfiWpzalZ8aiBkdPYjXWtHuwJGm1v5Ojy0Z0LaSYhHaLJQB0P8Jw== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" @@ -5998,12 +6010,12 @@ postcss-normalize-timing-functions@^5.1.0: dependencies: postcss-value-parser "^4.2.0" -postcss-normalize-unicode@^5.1.0: - 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browserslist "^4.16.6" + browserslist "^4.21.4" caniuse-api "^3.0.0" postcss-reduce-transforms@^5.1.0: @@ -6052,9 +6064,9 @@ postcss-reduce-transforms@^5.1.0: postcss-value-parser "^4.2.0" postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4, postcss-selector-parser@^6.0.5, postcss-selector-parser@^6.0.9: - version "6.0.10" - resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-6.0.10.tgz#79b61e2c0d1bfc2602d549e11d0876256f8df88d" - integrity sha512-IQ7TZdoaqbT+LCpShg46jnZVlhWD2w6iQYAcYXfHARZ7X1t/UGhhceQDs5X0cGqKvYlHNOuv7Oa1xmb0oQuA3w== + version "6.0.11" + resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-6.0.11.tgz#2e41dc39b7ad74046e1615185185cd0b17d0c8dc" + integrity sha512-zbARubNdogI9j7WY4nQJBiNqQf3sLS3wCP4WfOidu+p28LofJqDH1tcXypGrcmMHhDk2t9wGhCsYe/+szLTy1g== dependencies: cssesc "^3.0.0" util-deprecate "^1.0.2" @@ -6091,19 +6103,19 @@ postcss-zindex@^5.1.0: resolved "https://registry.yarnpkg.com/postcss-zindex/-/postcss-zindex-5.1.0.tgz#4a5c7e5ff1050bd4c01d95b1847dfdcc58a496ff" integrity sha512-fgFMf0OtVSBR1va1JNHYgMxYk73yhn/qb4uQDq1DLGYolz8gHCyr/sesEuGUaYs58E3ZJRcpoGuPVoB7Meiq9A== -postcss@^8.3.11, postcss@^8.4.14, postcss@^8.4.17, postcss@^8.4.7: - 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integrity sha512-z9MzKh/UcOqB3i20H6rtrlaE/CgjLOvheWK/9ILrbhROGTweAi1BaFsTT9FbwZi5Trr1qNRs+MXkhmR06awzQA== + version "7.8.0" + resolved "https://registry.yarnpkg.com/rxjs/-/rxjs-7.8.0.tgz#90a938862a82888ff4c7359811a595e14e1e09a4" + integrity sha512-F2+gxDshqmIub1KdvZkaEfGDwLNpPvk9Fs6LD/MyQxNgMds/WH9OdDDXOmxUZpME+iSK3rQCctkL0DYyytUqMg== dependencies: tslib "^2.1.0" @@ -6812,7 +6824,7 @@ semver@^6.0.0, semver@^6.1.1, semver@^6.1.2, semver@^6.2.0, semver@^6.3.0: resolved "https://registry.yarnpkg.com/semver/-/semver-6.3.0.tgz#ee0a64c8af5e8ceea67687b133761e1becbd1d3d" integrity sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw== -semver@^7.3.2, semver@^7.3.4, semver@^7.3.5, semver@^7.3.7: +semver@^7.3.2, semver@^7.3.4, semver@^7.3.7, semver@^7.3.8: version "7.3.8" resolved "https://registry.yarnpkg.com/semver/-/semver-7.3.8.tgz#07a78feafb3f7b32347d725e33de7e2a2df67798" integrity sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A== @@ -6846,15 +6858,15 @@ serialize-javascript@^6.0.0: randombytes "^2.1.0" serve-handler@^6.1.3: - 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version "2.0.0" - resolved "https://registry.yarnpkg.com/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.0.0.tgz#1a01aa57247c14c568b89775a54938788189a714" - integrity sha512-7Yhkc0Ye+t4PNYzOGKedDhXbYIBe1XEQYQxOPyhcXNMJ0WCABqqj6ckydd6pWRZTHV4GuCPKdBAUiMc60tsKVw== +unicode-match-property-value-ecmascript@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.1.0.tgz#cb5fffdcd16a05124f5a4b0bf7c3770208acbbe0" + integrity sha512-qxkjQt6qjg/mYscYMC0XKRn3Rh0wFPlfxB0xkt9CfyTvpX1Ra0+rAmdX2QyAobptSEvuy4RtpPRui6XkV+8wjA== unicode-property-aliases-ecmascript@^2.0.0: version "2.1.0" @@ -7722,9 +7734,9 @@ webpack-sources@^3.2.2, webpack-sources@^3.2.3: integrity sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w== webpack@^5.73.0: - version "5.74.0" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.74.0.tgz#02a5dac19a17e0bb47093f2be67c695102a55980" - integrity sha512-A2InDwnhhGN4LYctJj6M1JEaGL7Luj6LOmyBHjcI8529cm5p6VXiTIW2sn6ffvEAKmveLzvu4jrihwXtPojlAA== + version "5.75.0" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.75.0.tgz#1e440468647b2505860e94c9ff3e44d5b582c152" + integrity sha512-piaIaoVJlqMsPtX/+3KTTO6jfvrSYgauFVdt8cr9LTHKmcq/AMd4mhzsiP7ZF/PGRNPGA8336jldh9l2Kt2ogQ== dependencies: "@types/eslint-scope" "^3.7.3" "@types/estree" "^0.0.51" @@ -7855,9 +7867,9 @@ ws@^7.3.1: integrity sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q== ws@^8.4.2: - version "8.10.0" - resolved "https://registry.yarnpkg.com/ws/-/ws-8.10.0.tgz#00a28c09dfb76eae4eb45c3b565f771d6951aa51" - integrity sha512-+s49uSmZpvtAsd2h37vIPy1RBusaLawVe8of+GyEPsaJTCMpj/2v8NpeK1SHXjBlQ95lQTmQofOJnFiLoaN3yw== + version "8.11.0" + resolved "https://registry.yarnpkg.com/ws/-/ws-8.11.0.tgz#6a0d36b8edfd9f96d8b25683db2f8d7de6e8e143" + integrity sha512-HPG3wQd9sNQoT9xHyNCXoDUa+Xw/VevmY9FoHyQ+g+rrMn4j6FB4np7Z0OhdTgjx6MgQLK7jwSy1YecU1+4Asg== xdg-basedir@^4.0.0: version "4.0.0" diff --git a/yarn.lock b/yarn.lock index 07f190973e..e5ee65bd67 100644 --- a/yarn.lock +++ b/yarn.lock @@ -52,10 +52,10 @@ dependencies: "@babel/highlight" "^7.18.6" -"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.18.8", "@babel/compat-data@^7.19.3": - 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jest-message-util "^28.1.3" - jest-util "^28.1.3" - jest-worker "^28.1.3" + jest-message-util "^29.3.1" + jest-util "^29.3.1" + jest-worker "^29.3.1" slash "^3.0.0" string-length "^4.0.1" strip-ansi "^6.0.0" - terminal-link "^2.0.0" v8-to-istanbul "^9.0.1" "@jest/schemas@^28.1.3": @@ -1983,12 +1988,12 @@ graceful-fs "^4.2.9" source-map "^0.6.0" -"@jest/source-map@^28.1.2": - version "28.1.2" - resolved "https://registry.yarnpkg.com/@jest/source-map/-/source-map-28.1.2.tgz#7fe832b172b497d6663cdff6c13b0a920e139e24" - integrity sha512-cV8Lx3BeStJb8ipPHnqVw/IM2VCMWO3crWZzYodSIkxXnRcXJipCdx1JCK0K5MsJJouZQTH73mzf4vgxRaH9ww== +"@jest/source-map@^29.2.0": + version "29.2.0" + resolved "https://registry.yarnpkg.com/@jest/source-map/-/source-map-29.2.0.tgz#ab3420c46d42508dcc3dc1c6deee0b613c235744" + integrity sha512-1NX9/7zzI0nqa6+kgpSdKPK+WU1p+SJk3TloWZf5MzPbxri9UEeXX5bWZAPCzbQcyuAzubcdUHA7hcNznmRqWQ== dependencies: - "@jridgewell/trace-mapping" "^0.3.13" + "@jridgewell/trace-mapping" "^0.3.15" callsites "^3.0.0" graceful-fs "^4.2.9" @@ -2012,6 +2017,16 @@ "@types/istanbul-lib-coverage" "^2.0.0" collect-v8-coverage "^1.0.0" +"@jest/test-result@^29.3.1": + version "29.3.1" + resolved "https://registry.yarnpkg.com/@jest/test-result/-/test-result-29.3.1.tgz#92cd5099aa94be947560a24610aa76606de78f50" + integrity sha512-qeLa6qc0ddB0kuOZyZIhfN5q0e2htngokyTWsGriedsDhItisW7SDYZ7ceOe57Ii03sL988/03wAcBh3TChMGw== + dependencies: + "@jest/console" "^29.3.1" + "@jest/types" "^29.3.1" + "@types/istanbul-lib-coverage" "^2.0.0" + collect-v8-coverage "^1.0.0" + "@jest/test-sequencer@^27.5.1": version "27.5.1" resolved "https://registry.yarnpkg.com/@jest/test-sequencer/-/test-sequencer-27.5.1.tgz#4057e0e9cea4439e544c6353c6affe58d095745b" @@ -2022,14 +2037,14 @@ jest-haste-map "^27.5.1" jest-runtime "^27.5.1" -"@jest/test-sequencer@^28.1.3": - version "28.1.3" - resolved "https://registry.yarnpkg.com/@jest/test-sequencer/-/test-sequencer-28.1.3.tgz#9d0c283d906ac599c74bde464bc0d7e6a82886c3" - integrity sha512-NIMPEqqa59MWnDi1kvXXpYbqsfQmSJsIbnd85mdVGkiDfQ9WQQTXOLsvISUfonmnBT+w85WEgneCigEEdHDFxw== +"@jest/test-sequencer@^29.3.1": + version "29.3.1" + resolved "https://registry.yarnpkg.com/@jest/test-sequencer/-/test-sequencer-29.3.1.tgz#fa24b3b050f7a59d48f7ef9e0b782ab65123090d" + integrity sha512-IqYvLbieTv20ArgKoAMyhLHNrVHJfzO6ARZAbQRlY4UGWfdDnLlZEF0BvKOMd77uIiIjSZRwq3Jb3Fa3I8+2UA== dependencies: - "@jest/test-result" "^28.1.3" + "@jest/test-result" "^29.3.1" graceful-fs "^4.2.9" - jest-haste-map "^28.1.3" + jest-haste-map "^29.3.1" slash "^3.0.0" "@jest/transform@^26.6.2": @@ -2074,37 +2089,27 @@ source-map "^0.6.1" write-file-atomic "^3.0.0" -"@jest/transform@^28.1.3": - version "28.1.3" - resolved "https://registry.yarnpkg.com/@jest/transform/-/transform-28.1.3.tgz#59d8098e50ab07950e0f2fc0fc7ec462371281b0" - integrity sha512-u5dT5di+oFI6hfcLOHGTAfmUxFRrjK+vnaP0kkVow9Md/M7V/MxqQMOz/VV25UZO8pzeA9PjfTpOu6BDuwSPQA== +"@jest/transform@^29.3.1": + version "29.3.1" + resolved "https://registry.yarnpkg.com/@jest/transform/-/transform-29.3.1.tgz#1e6bd3da4af50b5c82a539b7b1f3770568d6e36d" + integrity sha512-8wmCFBTVGYqFNLWfcOWoVuMuKYPUBTnTMDkdvFtAYELwDOl9RGwOsvQWGPFxDJ8AWY9xM/8xCXdqmPK3+Q5Lug== dependencies: "@babel/core" "^7.11.6" - 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version "8.11.0" - resolved "https://registry.yarnpkg.com/ajv/-/ajv-8.11.0.tgz#977e91dd96ca669f54a11e23e378e33b884a565f" - integrity sha512-wGgprdCvMalC0BztXvitD2hC04YffAvtsUn93JbGXYLAtCUO4xd17mCCZQxUOItiBwZvJScWo8NIvQMQ71rdpg== + version "8.11.2" + resolved "https://registry.yarnpkg.com/ajv/-/ajv-8.11.2.tgz#aecb20b50607acf2569b6382167b65a96008bb78" + integrity sha512-E4bfmKAhGiSTvMfL1Myyycaub+cUEU2/IvpylXkUu7CHBkBj1f/ikdzbD7YQ6FKUbixDxeYvB/xY4fvyroDlQg== dependencies: fast-deep-equal "^3.1.1" json-schema-traverse "^1.0.0" @@ -6131,7 +6172,7 @@ ansi-regex@^2.0.0: resolved "https://registry.yarnpkg.com/ansi-regex/-/ansi-regex-2.1.1.tgz#c3b33ab5ee360d86e0e628f0468ae7ef27d654df" integrity sha512-TIGnTpdo+E3+pCyAluZvtED5p5wCqLdezCyhPZzKPcxvFplEt4i+W7OONCKgeZFT3+y5NZZfOOS/Bdcanm1MYA== -ansi-regex@^5.0.0, ansi-regex@^5.0.1: +ansi-regex@^5.0.1: version "5.0.1" resolved "https://registry.yarnpkg.com/ansi-regex/-/ansi-regex-5.0.1.tgz#082cb2c89c9fe8659a311a53bd6a4dc5301db304" integrity sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ== @@ -6141,11 +6182,6 @@ ansi-regex@^6.0.1: resolved "https://registry.yarnpkg.com/ansi-regex/-/ansi-regex-6.0.1.tgz#3183e38fae9a65d7cb5e53945cd5897d0260a06a" integrity sha512-n5M855fKb2SsfMIiFFoVrABHJC8QtHwVx+mHWP3QcEqBHYienj5dHSgjbxtC0WEZXYt4wcD6zrQElDPhFuZgfA== -ansi-styles@^2.2.1: - version "2.2.1" - resolved "https://registry.yarnpkg.com/ansi-styles/-/ansi-styles-2.2.1.tgz#b432dd3358b634cf75e1e4664368240533c1ddbe" - integrity sha512-kmCevFghRiWM7HB5zTPULl4r9bVFSWjz62MhqizDGUrq2NWuNMQyuv4tHHoKJHs69M/MF64lEcHdYIocrdWQYA== - ansi-styles@^3.2.1: version "3.2.1" resolved "https://registry.yarnpkg.com/ansi-styles/-/ansi-styles-3.2.1.tgz#41fbb20243e50b12be0f04b8dedbf07520ce841d" @@ -6191,9 +6227,9 @@ anymatch@^2.0.0: normalize-path "^2.1.1" anymatch@^3.0.0, anymatch@^3.0.3, anymatch@~3.1.2: - version "3.1.2" - resolved "https://registry.yarnpkg.com/anymatch/-/anymatch-3.1.2.tgz#c0557c096af32f106198f4f4e2a383537e378716" - integrity sha512-P43ePfOAIupkguHUycrc4qJ9kz8ZiuOUijaETwX7THt0Y/GNK7v0aa8rY816xWjZ7rJdA5XdMcpVFTKMq+RvWg== + version "3.1.3" + resolved "https://registry.yarnpkg.com/anymatch/-/anymatch-3.1.3.tgz#790c58b19ba1720a84205b57c618d5ad8524973e" + integrity sha512-KMReFUr0B4t+D+OBkjR3KYqvocp2XaSzO55UcB6mgQMd3KbcE+mWTyvVV7D/zsdEbNnV6acZUutkiHQXvTr1Rw== dependencies: normalize-path "^3.0.0" picomatch "^2.0.4" @@ -6203,10 +6239,10 @@ app-builder-bin@4.0.0: resolved "https://registry.yarnpkg.com/app-builder-bin/-/app-builder-bin-4.0.0.tgz#1df8e654bd1395e4a319d82545c98667d7eed2f0" integrity sha512-xwdG0FJPQMe0M0UA4Tz0zEB8rBJTRA5a476ZawAqiBkMv16GRK5xpXThOjMaEOFnZ6zabejjG4J3da0SXG63KA== -app-builder-lib@23.3.3: - 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qs "6.10.3" + qs "6.11.0" raw-body "2.5.1" type-is "~1.6.18" unpipe "1.0.0" @@ -7003,7 +7062,7 @@ boxen@^4.2.0: type-fest "^0.8.1" widest-line "^3.1.0" -boxen@^5.0.0, boxen@^5.1.2: +boxen@^5.1.2: version "5.1.2" resolved "https://registry.yarnpkg.com/boxen/-/boxen-5.1.2.tgz#788cb686fc83c1f486dfa8a40c68fc2b831d2b50" integrity sha512-9gYgQKXx+1nP8mP7CzFyaUARhg7D3n1dF/FnErWmu9l6JvGpNUN278h0aSb+QjoiKSWG+iZ3uHrcqk0qrY9RQQ== @@ -7138,7 +7197,7 @@ browserify-zlib@^0.2.0: dependencies: pako "~1.0.5" -browserslist@^4.0.0, browserslist@^4.12.0, browserslist@^4.14.5, browserslist@^4.16.6, browserslist@^4.18.1, browserslist@^4.20.3, browserslist@^4.21.3, browserslist@^4.21.4: +browserslist@^4.0.0, browserslist@^4.12.0, browserslist@^4.14.5, browserslist@^4.16.6, browserslist@^4.18.1, browserslist@^4.21.3, browserslist@^4.21.4: version "4.21.4" resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.21.4.tgz#e7496bbc67b9e39dd0f98565feccdcb0d4ff6987" integrity sha512-CBHJJdDmgjl3daYjN5Cp5kbTf1mUhZoS+beLklHIvkOWscs83YAhLlF3Wsh/lciQYAcbBJgTOD44VtG31ZM4Hw== @@ -7228,25 +7287,25 @@ buffers@~0.1.1: resolved "https://registry.yarnpkg.com/buffers/-/buffers-0.1.1.tgz#b24579c3bed4d6d396aeee6d9a8ae7f5482ab7bb" integrity sha512-9q/rDEGSb/Qsvv2qvzIzdluL5k7AaJOTrw23z9reQthrbF7is4CtlT0DXyO1oei2DCp4uojjzQ7igaSHp1kAEQ== -builder-util-runtime@9.0.3: - 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nan "^2.15.0" + nan "^2.17.0" simple-get "^3.0.3" capture-exit@^2.0.0: @@ -7539,13 +7603,13 @@ ccount@^1.0.0: integrity sha512-vlNK021QdI7PNeiUh/lKkC/mNHHfV0m/Ad5JoI0TYtlBnJAslM/JIkm/tGC88bkLIwO6OQ5uV6ztS6kVAtCDlg== chai@^4.3.4: - version "4.3.6" - resolved "https://registry.yarnpkg.com/chai/-/chai-4.3.6.tgz#ffe4ba2d9fa9d6680cc0b370adae709ec9011e9c" - integrity sha512-bbcp3YfHCUzMOvKqsztczerVgBKSsEijCySNlHHbX3VG1nskvqjz5Rfso1gGwD6w6oOV3eI60pKuMOV5MV7p3Q== + version "4.3.7" + resolved "https://registry.yarnpkg.com/chai/-/chai-4.3.7.tgz#ec63f6df01829088e8bf55fca839bcd464a8ec51" + integrity sha512-HLnAzZ2iupm25PlN0xFreAlBA5zaBSv3og0DdeGA4Ar6h6rJ3A0rolRUKJhSF2V10GZKDgWF/VmAEsNWjCRB+A== dependencies: assertion-error "^1.1.0" check-error "^1.0.2" - deep-eql "^3.0.1" + deep-eql "^4.1.2" get-func-name "^2.0.0" loupe "^2.3.1" pathval "^1.1.1" @@ -7566,17 +7630,6 @@ chalk@4.1.0: ansi-styles "^4.1.0" supports-color "^7.1.0" -chalk@^1.1.3: - version "1.1.3" - resolved "https://registry.yarnpkg.com/chalk/-/chalk-1.1.3.tgz#a8115c55e4a702fe4d150abd3872822a7e09fc98" - 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version "6.7.1" - resolved "https://registry.yarnpkg.com/css-loader/-/css-loader-6.7.1.tgz#e98106f154f6e1baf3fc3bc455cb9981c1d5fd2e" - integrity sha512-yB5CNFa14MbPJcomwNh3wLThtkZgcNyI2bNMRt8iE5Z8Vwl7f8vQXFAzn2HDOJvtDq2NTZBUGMSUNNyrv3/+cw== + version "6.7.3" + resolved "https://registry.yarnpkg.com/css-loader/-/css-loader-6.7.3.tgz#1e8799f3ccc5874fdd55461af51137fcc5befbcd" + integrity sha512-qhOH1KlBMnZP8FzRO6YCH9UHXQhVMcEGLyNdb7Hv2cpcmJbW0YrddO+tG1ab5nT41KpHIYGsbeHqxB9xPu1pKQ== dependencies: icss-utils "^5.1.0" - postcss "^8.4.7" + postcss "^8.4.19" postcss-modules-extract-imports "^3.0.0" postcss-modules-local-by-default "^4.0.0" postcss-modules-scope "^3.0.0" postcss-modules-values "^4.0.0" postcss-value-parser "^4.2.0" - semver "^7.3.5" + semver "^7.3.8" css-minimizer-webpack-plugin@^3.2.0: version "3.4.1" @@ -8689,35 +8723,35 @@ css.escape@^1.5.1: resolved "https://registry.yarnpkg.com/css.escape/-/css.escape-1.5.1.tgz#42e27d4fa04ae32f931a4b4d4191fa9cddee97cb" integrity sha512-YUifsXXuknHlUsmlgyY0PKzgPOr7/FjCePfHNt0jxm83wHZi44VDMQ7/fGNkjY3/jV1MC+1CmZbaHzugyeRtpg== -cssdb@^7.0.1: - 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css-declaration-sorter "^6.3.0" + css-declaration-sorter "^6.3.1" cssnano-utils "^3.1.0" postcss-calc "^8.2.3" postcss-colormin "^5.3.0" - postcss-convert-values "^5.1.2" + postcss-convert-values "^5.1.3" postcss-discard-comments "^5.1.2" postcss-discard-duplicates "^5.1.0" postcss-discard-empty "^5.1.1" postcss-discard-overridden "^5.1.0" - postcss-merge-longhand "^5.1.6" - postcss-merge-rules "^5.1.2" + postcss-merge-longhand "^5.1.7" + postcss-merge-rules "^5.1.3" postcss-minify-font-values "^5.1.0" postcss-minify-gradients "^5.1.1" - postcss-minify-params "^5.1.3" + postcss-minify-params "^5.1.4" postcss-minify-selectors "^5.2.1" postcss-normalize-charset "^5.1.0" postcss-normalize-display-values "^5.1.0" @@ -8725,11 +8759,11 @@ cssnano-preset-default@^5.2.12: postcss-normalize-repeat-style "^5.1.1" postcss-normalize-string "^5.1.0" postcss-normalize-timing-functions "^5.1.0" - postcss-normalize-unicode "^5.1.0" + postcss-normalize-unicode "^5.1.1" postcss-normalize-url "^5.1.0" postcss-normalize-whitespace "^5.1.1" postcss-ordered-values "^5.1.3" - postcss-reduce-initial "^5.1.0" + postcss-reduce-initial "^5.1.1" postcss-reduce-transforms "^5.1.0" postcss-svgo "^5.1.0" postcss-unique-selectors "^5.1.1" @@ -8740,11 +8774,11 @@ cssnano-utils@^3.1.0: integrity sha512-JQNR19/YZhz4psLX/rQ9M83e3z2Wf/HdJbryzte4a3NSuafyp9w/I4U+hx5C2S9g41qlstH7DEWnZaaj83OuEA== cssnano@^5.0.6: - version "5.1.13" - resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-5.1.13.tgz#83d0926e72955332dc4802a7070296e6258efc0a" - integrity sha512-S2SL2ekdEz6w6a2epXn4CmMKU4K3KpcyXLKfAYc9UQQqJRkD/2eLUG0vJ3Db/9OvO5GuAdgXw3pFbR6abqghDQ== + version "5.1.14" + resolved "https://registry.yarnpkg.com/cssnano/-/cssnano-5.1.14.tgz#07b0af6da73641276fe5a6d45757702ebae2eb05" + integrity sha512-Oou7ihiTocbKqi0J1bB+TRJIQX5RMR3JghA8hcWSw9mjBLQ5Y3RWqEDoYG3sRNlAbCIXpqMoZGbq5KDR3vdzgw== dependencies: - cssnano-preset-default "^5.2.12" + cssnano-preset-default "^5.2.13" lilconfig "^2.0.3" yaml "^1.10.2" @@ -8881,7 +8915,7 @@ data-urls@^2.0.0: whatwg-mimetype "^2.3.0" whatwg-url "^8.0.0" -data-urls@^3.0.1: +data-urls@^3.0.2: version "3.0.2" resolved "https://registry.yarnpkg.com/data-urls/-/data-urls-3.0.2.tgz#9cf24a477ae22bcef5cd5f6f0bfbc1d2d3be9143" integrity sha512-Jy/tj3ldjZJo63sVAvg6LHt2mHvl4V6AgRAmNDtLdm7faqtsx+aJG42rsyCo9JCoRVKwPFzKlIPx3DIibwSIaQ== @@ -8890,11 +8924,6 @@ data-urls@^3.0.1: whatwg-mimetype "^3.0.0" whatwg-url "^11.0.0" -date-fns@^2.29.1: - 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"@electron/get" "^1.14.1" + "@electron/get" "^2.0.0" "@types/node" "^16.11.26" extract-zip "^2.0.1" @@ -9654,6 +9676,11 @@ emittery@^0.10.2: resolved "https://registry.yarnpkg.com/emittery/-/emittery-0.10.2.tgz#902eec8aedb8c41938c46e9385e9db7e03182933" integrity sha512-aITqOwnLanpHLNXZJENbOgjUBeHocD+xsSJmNrjovKBW5HbSpW3d1pEls7GFQPUWXiwG9+0P4GtHfEqC/4M0Iw== +emittery@^0.13.1: + version "0.13.1" + resolved "https://registry.yarnpkg.com/emittery/-/emittery-0.13.1.tgz#c04b8c3457490e0847ae51fced3af52d338e3dad" + integrity sha512-DeWwawk6r5yR9jFgnDKYt4sLS0LmHJJi3ZOnb5/JdbYwj3nW+FxQnHIjhBKz8YLC7oRNPVM9NQ47I3CVx34eqQ== + emittery@^0.8.1: version "0.8.1" resolved "https://registry.yarnpkg.com/emittery/-/emittery-0.8.1.tgz#bb23cc86d03b30aa75a7f734819dee2e1ba70860" @@ -9674,7 +9701,7 @@ emojis-list@^3.0.0: resolved "https://registry.yarnpkg.com/emojis-list/-/emojis-list-3.0.0.tgz#5570662046ad29e2e916e71aae260abdff4f6a78" integrity sha512-/kyM18EfinwXZbno9FyUGeFh87KC8HRQBQGildHZbEuRyWFOmv1U10o9BBp8XVZDVNNuQKyIGIu5ZYAAXJ0V2Q== -encodeurl@^1.0.2, encodeurl@~1.0.2: +encodeurl@~1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/encodeurl/-/encodeurl-1.0.2.tgz#ad3ff4c86ec2d029322f5a02c3a9a606c95b3f59" integrity sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w== @@ -9712,9 +9739,9 @@ enhanced-resolve@^4.5.0: tapable "^1.0.0" enhanced-resolve@^5.0.0, enhanced-resolve@^5.10.0: - version "5.10.0" - resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.10.0.tgz#0dc579c3bb2a1032e357ac45b8f3a6f3ad4fb1e6" - integrity sha512-T0yTFjdpldGY8PmuXXR0PyQ1ufZpEGiHVrp7zHKB7jdR4qlmZHhONVM5AQOAWXuF/w3dnHbEQVrNptJgt7F+cQ== + version "5.12.0" + resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.12.0.tgz#300e1c90228f5b570c4d35babf263f6da7155634" + integrity sha512-QHTXI/sZQmko1cbDoNAa3mJ5qhWUUNAq3vR0/YiD379fWQrcfuoX1+HW2S0MTt7XmoPLapdaDKUtelUSPic7hQ== dependencies: graceful-fs "^4.2.4" tapable "^2.2.0" @@ -9731,6 +9758,11 @@ entities@^2.0.0: resolved "https://registry.yarnpkg.com/entities/-/entities-2.2.0.tgz#098dc90ebb83d8dffa089d55256b351d34c4da55" integrity sha512-p92if5Nz619I0w+akJrLZH0MX0Pb5DX39XOwQTtXSdQQOaYH03S1uIQp4mhOZtAXrxq4ViO67YTiLBo2638o9A== +entities@^4.4.0: + version "4.4.0" + resolved "https://registry.yarnpkg.com/entities/-/entities-4.4.0.tgz#97bdaba170339446495e653cfd2db78962900174" + integrity sha512-oYp7156SP8LkeGD0GF85ad1X9Ai79WtRsZ2gxJqtBuzH+98YUV6jkHEKlZkMbcrjJjIVJNIDP/3WL9wQkoPbWA== + env-paths@^2.2.0: version "2.2.1" resolved "https://registry.yarnpkg.com/env-paths/-/env-paths-2.2.1.tgz#420399d416ce1fbe9bc0a07c62fa68d67fd0f8f2" @@ -9767,10 +9799,10 @@ error-stack-parser@^2.0.6: dependencies: stackframe "^1.3.4" -es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19.2, es-abstract@^1.19.5, es-abstract@^1.20.0, es-abstract@^1.20.1: - version "1.20.3" - resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.3.tgz#90b143ff7aedc8b3d189bcfac7f1e3e3f81e9da1" - integrity sha512-AyrnaKVpMzljIdwjzrj+LxGmj8ik2LckwXacHqrJJ/jxz6dDDBcZ7I7nlHM0FvEW8MfbWJwOd+yT2XzYW49Frw== +es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.20.4: + version "1.20.5" + resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.20.5.tgz#e6dc99177be37cacda5988e692c3fa8b218e95d2" + integrity sha512-7h8MM2EQhsCA7pU/Nv78qOXFpD8Rhqd12gYiSJVkrH9+e8VuA8JlPJK/hQjjlLv6pJvx/z1iRFKzYb0XT/RuAQ== dependencies: call-bind "^1.0.2" es-to-primitive "^1.2.1" @@ -9778,11 +9810,12 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 function.prototype.name "^1.1.5" get-intrinsic "^1.1.3" get-symbol-description "^1.0.0" + gopd "^1.0.1" has "^1.0.3" has-property-descriptors "^1.0.0" has-symbols "^1.0.3" internal-slot "^1.0.3" - is-callable "^1.2.6" + is-callable "^1.2.7" is-negative-zero "^2.0.2" is-regex "^1.1.4" is-shared-array-buffer "^1.0.2" @@ -9793,8 +9826,8 @@ es-abstract@^1.17.2, es-abstract@^1.19.0, es-abstract@^1.19.1, es-abstract@^1.19 object.assign "^4.1.4" regexp.prototype.flags "^1.4.3" safe-regex-test "^1.0.0" - string.prototype.trimend "^1.0.5" - string.prototype.trimstart "^1.0.5" + string.prototype.trimend "^1.0.6" + string.prototype.trimstart "^1.0.6" unbox-primitive "^1.0.2" es-array-method-boxes-properly@^1.0.0: @@ -9802,7 +9835,7 @@ es-array-method-boxes-properly@^1.0.0: resolved "https://registry.yarnpkg.com/es-array-method-boxes-properly/-/es-array-method-boxes-properly-1.0.0.tgz#873f3e84418de4ee19c5be752990b2e44718d09e" integrity sha512-wd6JXUmyHmt8T5a2xreUwKcGPq6f1f+WwIJkijUqiGcJz1qqnZgP6XIK+QyIWU5lT7imeNxUll48bziG+TSYcA== -es-get-iterator@^1.0.2: +es-get-iterator@^1.0.2, es-get-iterator@^1.1.2: version "1.1.2" resolved "https://registry.yarnpkg.com/es-get-iterator/-/es-get-iterator-1.1.2.tgz#9234c54aba713486d7ebde0220864af5e2b283f7" integrity sha512-+DTO8GYwbMCwbywjimwZMHp8AuYXOS2JZFWoi2AlPOS3ebnII9w/NLpNZtA7A0YLaVDw+O7KFCeoIV7OPvM7hQ== @@ -9852,7 +9885,7 @@ es6-object-assign@^1.1.0: resolved "https://registry.yarnpkg.com/es6-object-assign/-/es6-object-assign-1.1.0.tgz#c2c3582656247c39ea107cb1e6652b6f9f24523c" integrity sha512-MEl9uirslVwqQU369iHNWZXsI8yaZYGg/D65aOgZkeyFJwHYSxilf7rQzXKI7DdDuBPrBXbfk3sl9hJhmd5AUw== -es6-promisify@^6.0.1, es6-promisify@^6.1.1: +es6-promisify@^6.1.1: version "6.1.1" resolved "https://registry.yarnpkg.com/es6-promisify/-/es6-promisify-6.1.1.tgz#46837651b7b06bf6fff893d03f29393668d01621" integrity sha512-HBL8I3mIki5C1Cc9QjKUenHtnG0A5/xA8Q/AllRcfiwl2CZFXGK7ddBiCoRwAix4i2KxcQfjtIVcrVbB3vbmwg== @@ -9872,11 +9905,6 @@ escalade@^3.1.1: resolved "https://registry.yarnpkg.com/escalade/-/escalade-3.1.1.tgz#d8cfdc7000965c5a0174b4a82eaa5c0552742e40" integrity sha512-k0er2gUkLf8O0zKJiAhmkTnJlTvINGv7ygDNPbeIsX/TJjGJZHuh9B2UxbsaEkmlEo9MfhrSzmhIlhRlI2GXnw== -escape-goat@^2.0.0: - version "2.1.1" - resolved "https://registry.yarnpkg.com/escape-goat/-/escape-goat-2.1.1.tgz#1b2dc77003676c457ec760b2dc68edb648188675" - integrity sha512-8/uIhbG12Csjy2JEW7D9pHbreaVaS/OpN3ycnyvElTdwM5n6GY6W6e2IPemfvGZeUMqZ9A/3GqIZMgKnBhAw/Q== - escape-html@^1.0.3, escape-html@~1.0.3: version "1.0.3" resolved "https://registry.yarnpkg.com/escape-html/-/escape-html-1.0.3.tgz#0258eae4d3d0c0974de1c169188ef0051d1d1988" @@ -9887,7 +9915,7 @@ escape-string-regexp@4.0.0, escape-string-regexp@^4.0.0: resolved "https://registry.yarnpkg.com/escape-string-regexp/-/escape-string-regexp-4.0.0.tgz#14ba83a5d373e3d311e5afca29cf5bfad965bf34" integrity sha512-TtpcNJ3XAzx3Gq8sWRzJaVajRs0uVxA2YAkdb1jm2YkPz4G6egUFAyA3n5vtEIZefPk5Wa4UXbKuS5fKkJWdgA== -escape-string-regexp@^1.0.2, escape-string-regexp@^1.0.5: +escape-string-regexp@^1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/escape-string-regexp/-/escape-string-regexp-1.0.5.tgz#1b61c0562190a8dff6ae3bb2cf0200ca130b86d4" integrity sha512-vbRorB5FUQWvla16U8R/qgaFIya2qGzwDrNmCZuYKrbdSUMG6I1ZCGQRefkRVhuOkIGVne7BQ35DSfo1qvJqFg== @@ -10047,29 +10075,30 @@ eslint-plugin-react-hooks@^4.3.0: integrity sha512-oFc7Itz9Qxh2x4gNHStv3BqJq54ExXmfC+a1NjAta66IAN87Wu0R/QArgIS9qKzX3dXKPI9H5crl9QchNMY9+g== eslint-plugin-react@^7.27.1: - version "7.31.8" - resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.8.tgz#3a4f80c10be1bcbc8197be9e8b641b2a3ef219bf" - integrity sha512-5lBTZmgQmARLLSYiwI71tiGVTLUuqXantZM6vlSY39OaDSV0M7+32K5DnLkmFrwTe+Ksz0ffuLUC91RUviVZfw== + version "7.31.11" + resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.31.11.tgz#011521d2b16dcf95795df688a4770b4eaab364c8" + integrity sha512-TTvq5JsT5v56wPa9OYHzsrOlHzKZKjV+aLgS+55NJP/cuzdiQPC7PfYoUjMoxlffKtvijpk7vA/jmuqRb9nohw== dependencies: - array-includes "^3.1.5" - array.prototype.flatmap "^1.3.0" + array-includes "^3.1.6" + array.prototype.flatmap "^1.3.1" + array.prototype.tosorted "^1.1.1" doctrine "^2.1.0" estraverse "^5.3.0" jsx-ast-utils "^2.4.1 || ^3.0.0" minimatch "^3.1.2" - object.entries "^1.1.5" - object.fromentries "^2.0.5" - object.hasown "^1.1.1" - object.values "^1.1.5" + object.entries "^1.1.6" + object.fromentries "^2.0.6" + object.hasown "^1.1.2" + object.values "^1.1.6" prop-types "^15.8.1" resolve "^2.0.0-next.3" semver "^6.3.0" - string.prototype.matchall "^4.0.7" + string.prototype.matchall "^4.0.8" eslint-plugin-testing-library@^5.0.1: - version "5.7.0" - resolved "https://registry.yarnpkg.com/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.7.0.tgz#08046bce93c63c0d4bf01ec62550130237bb1575" - integrity sha512-pI8LKtFiAflBpN4h14vTtfhKqLwtIW40TNhWyw0ckqHm0W/J0VmYtThoxpTAdHrvEWnkALSG1Z8ABBkIncMIHA== + version "5.9.1" + resolved "https://registry.yarnpkg.com/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.9.1.tgz#12e4bd34c48683ee98af4df2e3318ec9f51dcf8a" + integrity sha512-6BQp3tmb79jLLasPHJmy8DnxREe+2Pgf7L+7o09TSWPfdqqtQfRZmZNetr5mOs3yqZk/MRNxpN3RUpJe0wB4LQ== dependencies: "@typescript-eslint/utils" "^5.13.0" @@ -10133,15 +10162,15 @@ eslint-webpack-plugin@^3.1.1: normalize-path "^3.0.0" schema-utils "^4.0.0" -eslint@^8.3.0: - version "8.24.0" - resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.24.0.tgz#489516c927a5da11b3979dbfb2679394523383c8" - integrity sha512-dWFaPhGhTAiPcCgm3f6LI2MBWbogMnTJzFBbhXVRQDJPkr9pGZvVjlVfXd+vyDcWPA2Ic9L2AXPIQM0+vk/cSQ== +eslint@^8.0.0, eslint@^8.3.0: + version "8.30.0" + resolved "https://registry.yarnpkg.com/eslint/-/eslint-8.30.0.tgz#83a506125d089eef7c5b5910eeea824273a33f50" + integrity sha512-MGADB39QqYuzEGov+F/qb18r4i7DohCDOfatHaxI2iGlPuC65bwG2gxgO+7DkyL38dRFaRH7RaRAgU6JKL9rMQ== dependencies: - "@eslint/eslintrc" "^1.3.2" - "@humanwhocodes/config-array" "^0.10.5" - "@humanwhocodes/gitignore-to-minimatch" "^1.0.2" + "@eslint/eslintrc" "^1.4.0" + "@humanwhocodes/config-array" "^0.11.8" "@humanwhocodes/module-importer" "^1.0.1" + "@nodelib/fs.walk" "^1.2.8" ajv "^6.10.0" chalk "^4.0.0" cross-spawn "^7.0.2" @@ -10157,14 +10186,14 @@ eslint@^8.3.0: fast-deep-equal "^3.1.3" file-entry-cache "^6.0.1" find-up "^5.0.0" - glob-parent "^6.0.1" - globals "^13.15.0" - globby "^11.1.0" + glob-parent "^6.0.2" + globals "^13.19.0" grapheme-splitter "^1.0.4" ignore "^5.2.0" import-fresh "^3.0.0" imurmurhash "^0.1.4" is-glob "^4.0.0" + is-path-inside "^3.0.3" js-sdsl "^4.1.4" js-yaml "^4.1.0" json-stable-stringify-without-jsonify "^1.0.1" @@ -10179,9 +10208,9 @@ eslint@^8.3.0: text-table "^0.2.0" espree@^9.4.0: - version "9.4.0" - resolved "https://registry.yarnpkg.com/espree/-/espree-9.4.0.tgz#cd4bc3d6e9336c433265fc0aa016fc1aaf182f8a" - integrity sha512-DQmnRpLj7f6TgN/NYb0MTzJXL+vJF9h3pHy4JhCIs3zwcgez8xmGg3sXHcEO97BrmO2OSvCwMdfdlyl+E9KjOw== + version "9.4.1" + resolved "https://registry.yarnpkg.com/espree/-/espree-9.4.1.tgz#51d6092615567a2c2cff7833445e37c28c0065bd" + integrity sha512-XwctdmTO6SIvCzd9810yyNzIrOrqNYV9Koizx4C/mRhf9uq0o4yHoCEU/670pOxOL/MSraektvSAji79kX90Vg== dependencies: acorn "^8.8.0" acorn-jsx "^5.3.2" @@ -10192,7 +10221,7 @@ esprima@^4.0.0, esprima@^4.0.1, esprima@~4.0.0: resolved "https://registry.yarnpkg.com/esprima/-/esprima-4.0.1.tgz#13b04cdb3e6c5d19df91ab6987a8695619b0aa71" integrity sha512-eGuFFw7Upda+g4p+QHvnW0RyTX/SVeJBDM/gCtMARO0cLuT2HcEKnTPvhjV6aGeqrCB/sbNop0Kszm0jsaWU4A== -esquery@^1.4.0: +esquery@^1.0.1, esquery@^1.4.0: version "1.4.0" resolved "https://registry.yarnpkg.com/esquery/-/esquery-1.4.0.tgz#2148ffc38b82e8c7057dfed48425b3e61f0f24a5" integrity sha512-cCDispWt5vHHtwMY2YrAQ4ibFkAL8RbH5YGBnZBc90MolvvfkkQcJro/aZiAQUlQ3qgrYS6D6v8Gc5G5CQsc9w== @@ -10240,6 +10269,11 @@ etag@~1.8.1: resolved "https://registry.yarnpkg.com/etag/-/etag-1.8.1.tgz#41ae2eeb65efa62268aebfea83ac7d79299b0887" integrity sha512-aIL5Fx7mawVa300al2BnEE4iNvo1qETxLrPI/o05L7z6go7fCw1J6EQmbK4FmJ2AS7kgVF/KEZWufBfdClMcPg== +event-target-shim@^5.0.0: + version "5.0.1" + resolved "https://registry.yarnpkg.com/event-target-shim/-/event-target-shim-5.0.1.tgz#5d4d3ebdf9583d63a5333ce2deb7480ab2b05789" + integrity sha512-i/2XbnSz/uxRCU6+NdVJgKWDTM427+MqYbkQzD321DuCQJUqOuJKIA0IM2+W2xtYHdKOmZ4dR6fExsd4SXL+WQ== + eventemitter3@^4.0.0, eventemitter3@^4.0.4: version "4.0.7" resolved "https://registry.yarnpkg.com/eventemitter3/-/eventemitter3-4.0.7.tgz#2de9b68f6528d5644ef5c59526a1b4a07306169f" @@ -10332,36 +10366,25 @@ expect@^27.5.1: jest-matcher-utils "^27.5.1" jest-message-util "^27.5.1" -expect@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/expect/-/expect-28.1.3.tgz#90a7c1a124f1824133dd4533cce2d2bdcb6603ec" - integrity sha512-eEh0xn8HlsuOBxFgIss+2mX85VAS4Qy3OSkjV7rlBWljtA4oWH37glVGyOZSZvErDT/yBywZdPGwCXuTvSG85g== - dependencies: - "@jest/expect-utils" "^28.1.3" - jest-get-type "^28.0.2" - jest-matcher-utils "^28.1.3" - jest-message-util "^28.1.3" - jest-util "^28.1.3" - -expect@^29.0.0: - version "29.1.2" - resolved "https://registry.yarnpkg.com/expect/-/expect-29.1.2.tgz#82f8f28d7d408c7c68da3a386a490ee683e1eced" - integrity sha512-AuAGn1uxva5YBbBlXb+2JPxJRuemZsmlGcapPXWNSBNsQtAULfjioREGBWuI0EOvYUKjDnrCy8PW5Zlr1md5mw== +expect@^29.0.0, expect@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/expect/-/expect-29.3.1.tgz#92877aad3f7deefc2e3f6430dd195b92295554a6" + integrity sha512-gGb1yTgU30Q0O/tQq+z30KBWv24ApkMgFUpvKBkyLUBL68Wv8dHdJxTBZFl/iT8K/bqDHvUYRH6IIN3rToopPA== dependencies: - "@jest/expect-utils" "^29.1.2" - jest-get-type "^29.0.0" - jest-matcher-utils "^29.1.2" - jest-message-util "^29.1.2" - jest-util "^29.1.2" + "@jest/expect-utils" "^29.3.1" + jest-get-type "^29.2.0" + jest-matcher-utils "^29.3.1" + jest-message-util "^29.3.1" + jest-util "^29.3.1" express@^4.17.1, express@^4.17.3: - version "4.18.1" - resolved "https://registry.yarnpkg.com/express/-/express-4.18.1.tgz#7797de8b9c72c857b9cd0e14a5eea80666267caf" - integrity sha512-zZBcOX9TfehHQhtupq57OF8lFZ3UZi08Y97dwFCkD8p9d/d2Y3M+ykKcwaMDEL+4qyUolgBDX6AblpR3fL212Q== + version "4.18.2" + resolved "https://registry.yarnpkg.com/express/-/express-4.18.2.tgz#3fabe08296e930c796c19e3c516979386ba9fd59" + integrity sha512-5/PsL6iGPdfQ/lKM1UuielYgv3BUoJfz1aUwU9vHZ+J7gyvwdQXFEBIEIaxeGf0GIcreATNyBExtalisDbuMqQ== dependencies: accepts "~1.3.8" array-flatten "1.1.1" - body-parser "1.20.0" + body-parser "1.20.1" content-disposition "0.5.4" content-type "~1.0.4" cookie "0.5.0" @@ -10380,7 +10403,7 @@ express@^4.17.1, express@^4.17.3: parseurl "~1.3.3" path-to-regexp "0.1.7" proxy-addr "~2.0.7" - qs "6.10.3" + qs "6.11.0" range-parser "~1.2.1" safe-buffer "5.2.1" send "0.18.0" @@ -10420,7 +10443,7 @@ external-editor@^3.0.3: iconv-lite "^0.4.24" tmp "^0.0.33" -external-sorting@^1.2.1: +external-sorting@^1.3.1: version "1.3.1" resolved "https://registry.yarnpkg.com/external-sorting/-/external-sorting-1.3.1.tgz#caec567906bd8d936cc94165c7daf657cd4e3163" integrity sha512-eqI/TxUu4U5RW90ml7bRyvk/0Qh/Lf3JecZQKeLmC0eVRzPQ2UG3ZR7k66EDO1UnTJat0D8bn129K+gnZYMJuw== @@ -10509,7 +10532,7 @@ fast-glob@^2.2.6: merge2 "^1.2.3" micromatch "^3.1.10" -fast-glob@^3.0.3, fast-glob@^3.2.11, fast-glob@^3.2.9: +fast-glob@^3.0.3, fast-glob@^3.2.12, fast-glob@^3.2.9: version "3.2.12" resolved "https://registry.yarnpkg.com/fast-glob/-/fast-glob-3.2.12.tgz#7f39ec99c2e6ab030337142da9e0c18f37afae80" integrity sha512-DVj4CQIYYow0BlaelwK1pHl5n5cRSJfM60UA0zK891sVInoPri2Ekj7+e1CT3/3qxXenpI+nBBmQAcJPJgaj4w== @@ -10546,9 +10569,9 @@ fastest-levenshtein@^1.0.12: integrity sha512-eRnCtTTtGZFpQCwhJiUOuxPQWRXVKYDn0b2PeHfXL6/Zi53SLAzAHfVhVWK2AryC/WH05kGfxhFIPvTF0SXQzg== fastq@^1.6.0: - version "1.13.0" - resolved "https://registry.yarnpkg.com/fastq/-/fastq-1.13.0.tgz#616760f88a7526bdfc596b7cab8c18938c36b98c" - integrity sha512-YpkpUnK8od0o1hmeSc7UUs/eB/vIPWJYjKck2QKIzAf71Vm1AAQ3EbuZB3g2JIy+pg+ERD0vqI79KyZiB2e2Nw== + version "1.14.0" + resolved "https://registry.yarnpkg.com/fastq/-/fastq-1.14.0.tgz#107f69d7295b11e0fccc264e1fc6389f623731ce" + integrity sha512-eR2D+V9/ExcbF9ls441yIuN6TI2ED1Y2ZcA5BmMtJsOkWOFRJQ0Jt0g1UwqXJJVAb+V+umH5Dfr8oh4EVP7VVg== dependencies: reusify "^1.0.4" @@ -10691,7 +10714,7 @@ find-cache-dir@^2.0.0, find-cache-dir@^2.1.0: make-dir "^2.0.0" pkg-dir "^3.0.0" -find-cache-dir@^3.3.1: +find-cache-dir@^3.3.1, find-cache-dir@^3.3.2: version "3.3.2" resolved "https://registry.yarnpkg.com/find-cache-dir/-/find-cache-dir-3.3.2.tgz#b30c5b6eff0730731aea9bbd9dbecbd80256d64b" integrity sha512-wXZV5emFEjrridIgED11OoUKLxiYjAcqot/NJdAkOhlJ+vGzwhOAfcG5OX1jP+S0PcjEn8bdMJv+g2jwQ3Onig== @@ -10768,11 +10791,6 @@ flatted@^3.1.0: resolved "https://registry.yarnpkg.com/flatted/-/flatted-3.2.7.tgz#609f39207cb614b89d0765b477cb2d437fbf9787" integrity sha512-5nqDSxl8nn5BSNxyR3n4I6eDmbolI6WT+QqR547RwxQapgjQBmtktdP+HTBb/a/zLsbzERTONyUB5pefh5TtjQ== -flatten@^1.0.2: - version "1.0.3" - resolved "https://registry.yarnpkg.com/flatten/-/flatten-1.0.3.tgz#c1283ac9f27b368abc1e36d1ff7b04501a30356b" - integrity sha512-dVsPA/UwQ8+2uoFe5GHtiBMu48dWLTdsuEd7CKGlZlD78r1TTWBvDuFaFGKCo/ZfEr95Uk56vZoX86OsHkUeIg== - flush-write-stream@^1.0.0: version "1.1.1" resolved "https://registry.yarnpkg.com/flush-write-stream/-/flush-write-stream-1.1.1.tgz#8dd7d873a1babc207d94ead0c2e0e44276ebf2e8" @@ -10781,7 +10799,7 @@ flush-write-stream@^1.0.0: inherits "^2.0.3" readable-stream "^2.3.6" -follow-redirects@^1.0.0, follow-redirects@^1.14.7: +follow-redirects@^1.0.0, follow-redirects@^1.14.7, follow-redirects@^1.15.0: version "1.15.2" resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.15.2.tgz#b460864144ba63f2681096f274c4e57026da2c13" integrity sha512-VQLG33o04KaQ8uYi2tVNbdrWp1QWxNNea+nmIB4EVM28v0hmP17z7aG1+wAkNzVq4KeXTq3221ye5qTJP91JwA== @@ -11041,9 +11059,9 @@ gauge@^4.0.3: wide-align "^1.1.5" generic-filehandle@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.0.0.tgz#10d5ddc4adf105de616224dba58370f3dcc3877c" - integrity sha512-THrFJ1fq7wjwMmSN7sdp0JnQKZDVE7aooVwHTWREKHrCGVJGKKiD5BSaboNHiFU84RIzJ+oBOqQsN//ISWj1ZQ== + version "3.0.1" + resolved "https://registry.yarnpkg.com/generic-filehandle/-/generic-filehandle-3.0.1.tgz#9bea8ad8f572bb07c16097df6fccc05a87ec77ff" + integrity sha512-E0eVkls2Ni7fUQ47VxYJN45/ow821pITHcgyaMZXBUt1czZUionT6HSqE0t+bcAozt5MYeJCxVxIrlTxoASXuQ== dependencies: es6-promisify "^6.1.1" @@ -11119,7 +11137,7 @@ get-stream@^3.0.0: resolved "https://registry.yarnpkg.com/get-stream/-/get-stream-3.0.0.tgz#8e943d1358dc37555054ecbe2edb05aa174ede14" integrity sha512-GlhdIUuVakc8SJ6kK0zAFbiGzRFzNnY4jUuEbV9UROo4Y+0Ny4fjvcZFVTeDA4odpFyOQzaw6hXukJSq/f28sQ== -get-stream@^4.0.0, get-stream@^4.1.0: +get-stream@^4.0.0: version "4.1.0" resolved "https://registry.yarnpkg.com/get-stream/-/get-stream-4.1.0.tgz#c1b255575f3dc21d59bfc79cd3d2b46b1c3a54b5" integrity sha512-GMat4EJ5161kIy2HevLlr4luNjBgvmj413KaQA7jt4V8B4RDsfpHk7WQ9GVqfYyyx8OS/L66Kox+rJRNklLK7w== @@ -11170,15 +11188,6 @@ get-value@^3.0.1: dependencies: isobject "^3.0.1" -get-yarn-workspaces@^1.0.2: - version "1.0.2" - resolved "https://registry.yarnpkg.com/get-yarn-workspaces/-/get-yarn-workspaces-1.0.2.tgz#81591bdb392f1c6bac09cdc8491a6d275781aa44" - integrity sha512-Auel048Uclfgr74oNXKZWH30UgKDZXQdfUfgD9iWXdoUGJpeWg9lSuX/FZkQ6RB3KnBfAaf70xQXfwOjiE9rPw== - dependencies: - find-root "^1.1.0" - flatten "^1.0.2" - glob "^7.1.2" - git-raw-commits@^2.0.8: version "2.0.11" resolved "https://registry.yarnpkg.com/git-raw-commits/-/git-raw-commits-2.0.11.tgz#bc3576638071d18655e1cc60d7f524920008d723" @@ -11229,9 +11238,9 @@ gitconfiglocal@^1.0.0: ini "^1.3.2" github-slugger@^1.0.0, github-slugger@^1.2.1: - version "1.4.0" - resolved "https://registry.yarnpkg.com/github-slugger/-/github-slugger-1.4.0.tgz#206eb96cdb22ee56fdc53a28d5a302338463444e" - integrity sha512-w0dzqw/nt51xMVmlaV1+JRzN+oCa1KfcgGEWhxUG16wbdA+Xnt/yoFO8Z8x/V82ZcZ0wy6ln9QDup5avbhiDhQ== + version "1.5.0" + resolved "https://registry.yarnpkg.com/github-slugger/-/github-slugger-1.5.0.tgz#17891bbc73232051474d68bd867a34625c955f7d" + integrity sha512-wIh+gKBI9Nshz2o46B0B3f5k/W+WI9ZAv6y5Dn5WJ5SK1t0TnDimB4WE5rmTD05ZAIn8HALCZVmCsvj0w0v0lw== glob-parent@^3.1.0: version "3.1.0" @@ -11248,7 +11257,7 @@ glob-parent@^5.1.1, glob-parent@^5.1.2, glob-parent@~5.1.2: dependencies: is-glob "^4.0.1" -glob-parent@^6.0.1, glob-parent@^6.0.2: +glob-parent@^6.0.2: version "6.0.2" resolved "https://registry.yarnpkg.com/glob-parent/-/glob-parent-6.0.2.tgz#6d237d99083950c79290f24c7642a3de9a28f9e3" integrity sha512-XxwI8EOhVQgWp6iDL+3b0r86f4d6AX6zSU55HfB4ydCEuXLXc5FcYeOu+nnGftS4TEju/11rt4KJPTMgbfmv4A== @@ -11319,13 +11328,6 @@ global-agent@^3.0.0: semver "^7.3.2" serialize-error "^7.0.1" -global-dirs@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/global-dirs/-/global-dirs-3.0.0.tgz#70a76fe84ea315ab37b1f5576cbde7d48ef72686" - integrity sha512-v8ho2DS5RiCjftj1nD9NmnfaOzTdud7RRnVd9kFNOjqZbISlx5DQ+OrTkywgd0dIt7oFCvKetZSHoHcP3sDdiA== - dependencies: - ini "2.0.0" - global-modules@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/global-modules/-/global-modules-2.0.0.tgz#997605ad2345f27f51539bea26574421215c7780" @@ -11342,16 +11344,6 @@ global-prefix@^3.0.0: kind-of "^6.0.2" which "^1.3.1" -global-tunnel-ng@^2.7.1: - version "2.7.1" - resolved "https://registry.yarnpkg.com/global-tunnel-ng/-/global-tunnel-ng-2.7.1.tgz#d03b5102dfde3a69914f5ee7d86761ca35d57d8f" - integrity sha512-4s+DyciWBV0eK148wqXxcmVAbFVPqtc3sEtUE/GTQfuU80rySLcMhUmHKSHI7/LDj8q0gDYI1lIhRRB7ieRAqg== - dependencies: - encodeurl "^1.0.2" - lodash "^4.17.10" - npm-conf "^1.1.3" - tunnel "^0.0.6" - global@^4.4.0: version "4.4.0" resolved "https://registry.yarnpkg.com/global/-/global-4.4.0.tgz#3e7b105179006a323ed71aafca3e9c57a5cc6406" @@ -11365,10 +11357,10 @@ globals@^11.1.0, globals@^11.12.0: resolved "https://registry.yarnpkg.com/globals/-/globals-11.12.0.tgz#ab8795338868a0babd8525758018c2a7eb95c42e" integrity sha512-WOBp/EEGUiIsJSp7wcv/y6MO+lV9UoncWqxuFfm8eBwzWNgyfBd6Gz+IeKQ9jCmyhoH99g15M3T+QaVHFjizVA== -globals@^13.15.0: - version "13.17.0" - resolved "https://registry.yarnpkg.com/globals/-/globals-13.17.0.tgz#902eb1e680a41da93945adbdcb5a9f361ba69bd4" - integrity sha512-1C+6nQRb1GwGMKm2dH/E7enFAMxGTmGI7/dEdhy/DNelv85w9B72t3uc5frtMNXIbzrarJJ/lTCjcaZwbLJmyw== +globals@^13.19.0: + version "13.19.0" + resolved "https://registry.yarnpkg.com/globals/-/globals-13.19.0.tgz#7a42de8e6ad4f7242fbcca27ea5b23aca367b5c8" + integrity sha512-dkQ957uSRWHw7CFXLUtUHQI3g3aWApYhfNR2O6jn/907riyTYKVBmxYVROkBcY614FSSeSJh7Xm7SrUWCxvJMQ== dependencies: type-fest "^0.20.2" @@ -11436,22 +11428,29 @@ glur@^1.1.2: resolved "https://registry.yarnpkg.com/glur/-/glur-1.1.2.tgz#f20ea36db103bfc292343921f1f91e83c3467689" integrity sha512-l+8esYHTKOx2G/Aao4lEQ0bnHWg4fWtJbVoZZT9Knxi01pB8C80BR85nONLFwkkQoFRCmXY+BUcGZN3yZ2QsRA== -got@^9.6.0: - version "9.6.0" - resolved "https://registry.yarnpkg.com/got/-/got-9.6.0.tgz#edf45e7d67f99545705de1f7bbeeeb121765ed85" - integrity sha512-R7eWptXuGYxwijs0eV+v3o6+XH1IqVK8dJOEecQfTmkncw9AV4dcw/Dhxi8MdlqPthxxpZyizMzyg8RTmEsG+Q== - dependencies: - "@sindresorhus/is" "^0.14.0" - "@szmarczak/http-timer" "^1.1.2" - cacheable-request "^6.0.0" - decompress-response "^3.3.0" - duplexer3 "^0.1.4" - get-stream "^4.1.0" - lowercase-keys "^1.0.1" - mimic-response "^1.0.1" - p-cancelable "^1.0.0" - to-readable-stream "^1.0.0" - url-parse-lax "^3.0.0" +gopd@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/gopd/-/gopd-1.0.1.tgz#29ff76de69dac7489b7c0918a5788e56477c332c" + integrity sha512-d65bNlIadxvpb/A2abVdlqKqV563juRnZ1Wtk6s1sIR8uNsXR70xqIzVqxVf1eTqDunwT2MkczEeaezCKTZhwA== + dependencies: + get-intrinsic "^1.1.3" + +got@^11.8.5: + version "11.8.6" + resolved "https://registry.yarnpkg.com/got/-/got-11.8.6.tgz#276e827ead8772eddbcfc97170590b841823233a" + integrity sha512-6tfZ91bOr7bOXnK7PRDCGBLa1H4U080YHNaAQ2KsMGlLEzRbk44nsZF2E1IeRc3vtJHPVbKCYgdFbaGO2ljd8g== + dependencies: + "@sindresorhus/is" "^4.0.0" + "@szmarczak/http-timer" "^4.0.5" + "@types/cacheable-request" "^6.0.1" + "@types/responselike" "^1.0.0" + cacheable-lookup "^5.0.3" + cacheable-request "^7.0.2" + decompress-response "^6.0.0" + http2-wrapper "^1.0.0-beta.5.2" + lowercase-keys "^2.0.0" + p-cancelable "^2.0.0" + responselike "^2.0.0" graceful-fs@^4.1.11, graceful-fs@^4.1.15, graceful-fs@^4.1.2, graceful-fs@^4.1.6, graceful-fs@^4.2.0, graceful-fs@^4.2.2, graceful-fs@^4.2.4, graceful-fs@^4.2.6, graceful-fs@^4.2.9: version "4.2.10" @@ -11502,13 +11501,6 @@ harmony-reflect@^1.4.6: resolved "https://registry.yarnpkg.com/harmony-reflect/-/harmony-reflect-1.6.2.tgz#31ecbd32e648a34d030d86adb67d4d47547fe710" integrity sha512-HIp/n38R9kQjDEziXyDTuW3vvoxxyxjxFzXLrBr18uB47GnSt+G9D29fqrpM5ZkspMcPICud3XsBJQ4Y2URg8g== -has-ansi@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/has-ansi/-/has-ansi-2.0.0.tgz#34f5049ce1ecdf2b0649af3ef24e45ed35416d91" - integrity sha512-C8vBJ8DwUCx19vhm7urhTuUsr4/IyP6l4VzNQDv+ryHQObW3TTTp9yB68WpYgRe2bbaGuZ/se74IqFeVnMnLZg== - dependencies: - ansi-regex "^2.0.0" - has-bigints@^1.0.1, has-bigints@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/has-bigints/-/has-bigints-1.0.2.tgz#0871bd3e3d51626f6ca0966668ba35d5602d6eaa" @@ -11586,11 +11578,6 @@ has-values@^1.0.0: is-number "^3.0.0" kind-of "^4.0.0" -has-yarn@^2.1.0: - version "2.1.0" - resolved "https://registry.yarnpkg.com/has-yarn/-/has-yarn-2.1.0.tgz#137e11354a7b5bf11aa5cb649cf0c6f3ff2b2e77" - integrity sha512-UqBRqi4ju7T+TqGNdqAO0PaSVGsDGJUBQvk9eUWNGRY1CFGDzYhLWoM7JQEemnlvVcv/YEmc2wNW8BC24EnUsw== - has@^1.0.3: version "1.0.3" resolved "https://registry.yarnpkg.com/has/-/has-1.0.3.tgz#722d7cbfc1f6aa8241f16dd814e011e1f41e8796" @@ -11739,9 +11726,9 @@ hosted-git-info@^4.0.0, hosted-git-info@^4.0.1, hosted-git-info@^4.1.0: lru-cache "^6.0.0" hosted-git-info@^5.0.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/hosted-git-info/-/hosted-git-info-5.1.0.tgz#9786123f92ef3627f24abc3f15c20d98ec4a6594" - integrity sha512-Ek+QmMEqZF8XrbFdwoDjSbm7rT23pCgEMOJmz6GPk/s4yH//RQfNPArhIxbguNxROq/+5lNBwCDHMhA903Kx1Q== + version "5.2.1" + resolved "https://registry.yarnpkg.com/hosted-git-info/-/hosted-git-info-5.2.1.tgz#0ba1c97178ef91f3ab30842ae63d6a272341156f" + integrity sha512-xIcQYMnhcx2Nr4JTjsFmwwnr9vldugPy9uVm0o87bjqqWMv9GaqsTeT+i99wTl0mk1uLxJtHxLb8kymqTENQsw== dependencies: lru-cache "^7.5.1" @@ -11948,12 +11935,20 @@ http-range-fetcher@^1.4.0: quick-lru "^2.0.0" window-or-global "^1.0.1" +http2-wrapper@^1.0.0-beta.5.2: + version "1.0.3" + resolved "https://registry.yarnpkg.com/http2-wrapper/-/http2-wrapper-1.0.3.tgz#b8f55e0c1f25d4ebd08b3b0c2c079f9590800b3d" + integrity sha512-V+23sDMr12Wnz7iTcDeJr3O6AIxlnvT/bmaAAAP/Xda35C90p9599p0F1eHR/N1KILWSoWVAiOMFjBBXaXSMxg== + dependencies: + quick-lru "^5.1.1" + resolve-alpn "^1.0.0" + https-browserify@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/https-browserify/-/https-browserify-1.0.0.tgz#ec06c10e0a34c0f2faf199f7fd7fc78fffd03c73" integrity sha512-J+FkSdyD+0mA0N+81tMotaRMfSL9SGi+xpD3T6YApKsc3bGSXJlfXri3VyFOeYkfLRQisDk1W+jIFFKBeUBbBg== -https-proxy-agent@5, https-proxy-agent@^5.0.0: +https-proxy-agent@5, https-proxy-agent@^5.0.0, https-proxy-agent@^5.0.1: version "5.0.1" resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-5.0.1.tgz#c59ef224a04fe8b754f3db0063a25ea30d0005d6" integrity sha512-dFcAjpTQFgoLMzC2VwU+C/CbS7uRL0lWmxDITmqm7C+7F0Odmj6s9l6alZc6AELXhrnggM2CeWSXHGOdX2YtwA== @@ -11974,9 +11969,9 @@ humanize-ms@^1.2.1: ms "^2.0.0" husky@^8.0.0: - version "8.0.1" - resolved "https://registry.yarnpkg.com/husky/-/husky-8.0.1.tgz#511cb3e57de3e3190514ae49ed50f6bc3f50b3e9" - integrity sha512-xs7/chUH/CKdOCs7Zy0Aev9e/dKOMZf3K1Az1nar3tzlv0jfqnYtu235bstsWTmXOR0EfINrPa97yy4Lz6RiKw== + version "8.0.2" + resolved "https://registry.yarnpkg.com/husky/-/husky-8.0.2.tgz#5816a60db02650f1f22c8b69b928fd6bcd77a236" + integrity sha512-Tkv80jtvbnkK3mYWxPZePGFpQ/tT3HNSs/sasF9P2YfkMezDl3ON37YN6jUUI4eTg5LcyVynlb6r4eyvOmspvg== hyperlinker@^1.0.0: version "1.0.0" @@ -12018,9 +12013,9 @@ icss-utils@^5.0.0, icss-utils@^5.1.0: integrity sha512-soFhflCVWLfRNOPU3iv5Z9VUdT44xFRbzjLsEzSr5AQmgqPMTHdU3PMT1Cf1ssx8fLNJDA1juftYl+PUcv3MqA== idb@^7.0.1: - version "7.1.0" - resolved "https://registry.yarnpkg.com/idb/-/idb-7.1.0.tgz#2cc886be57738419e57f9aab58f647e5e2160270" - integrity sha512-Wsk07aAxDsntgYJY4h0knZJuTxM73eQ4reRAO+Z1liOh8eMCJ/MoDS8fCui1vGT9mnjtl1sOu3I2i/W1swPYZg== + version "7.1.1" + resolved "https://registry.yarnpkg.com/idb/-/idb-7.1.1.tgz#d910ded866d32c7ced9befc5bfdf36f572ced72b" + integrity sha512-gchesWBzyvGHRO9W8tzUWFDycow5gwjvFKfyV9FF32Y7F50yZMp7mP+T2mJIWFx49zicqyC4uefHM17o6xKIVQ== identity-obj-proxy@^3.0.0: version "3.0.0" @@ -12057,14 +12052,14 @@ ignore@^4.0.3: integrity sha512-cyFDKrqc/YdcWFniJhzI42+AzS+gNwmUzOSFcRCQYwySuBBBy/KjuxWLZ/FHEH6Moq1NizMOBWyTcv8O4OZIMg== ignore@^5.0.4, ignore@^5.1.1, ignore@^5.2.0: - version "5.2.0" - resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.2.0.tgz#6d3bac8fa7fe0d45d9f9be7bac2fc279577e345a" - integrity sha512-CmxgYGiEPCLhfLnpPp1MoRmifwEIOgjcHXxOBjv7mY96c+eWScsOP9c112ZyLdWHi0FxHjI+4uVhKYp/gcdRmQ== + version "5.2.1" + resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.2.1.tgz#c2b1f76cb999ede1502f3a226a9310fdfe88d46c" + integrity sha512-d2qQLzTJ9WxQftPAuEQpSPmKqzxePjzVbpAVv62AQ64NTL+wR4JkrVqR/LqFsFEUsHDAiId52mJteHDFuDkElA== immer@^9.0.7: - version "9.0.15" - resolved "https://registry.yarnpkg.com/immer/-/immer-9.0.15.tgz#0b9169e5b1d22137aba7d43f8a81a495dd1b62dc" - integrity sha512-2eB/sswms9AEUSkOm4SbV5Y7Vmt/bKRwByd52jfLkW4OLYeaTP3EEiJ9agqU0O/tq6Dk62Zfj+TJSqfm1rLVGQ== + version "9.0.16" + resolved "https://registry.yarnpkg.com/immer/-/immer-9.0.16.tgz#8e7caab80118c2b54b37ad43e05758cdefad0198" + integrity sha512-qenGE7CstVm1NrHQbMh8YaSzTZTFNP3zPqr3YU0S0UY441j4bJTg4A2Hh5KAhwgaiU6ZZ1Ar6y/2f4TblnMReQ== import-fresh@^3.0.0, import-fresh@^3.1.0, import-fresh@^3.2.1: version "3.3.0" @@ -12074,11 +12069,6 @@ import-fresh@^3.0.0, import-fresh@^3.1.0, import-fresh@^3.2.1: parent-module "^1.0.0" resolve-from "^4.0.0" -import-lazy@^2.1.0: - version "2.1.0" - resolved "https://registry.yarnpkg.com/import-lazy/-/import-lazy-2.1.0.tgz#05698e3d45c88e8d7e9d92cb0584e77f096f3e43" - integrity sha512-m7ZEHgtw69qOGw+jwxXkHlrlIPdTGkyh66zXZ1ajZbxkDBNjSY/LGbmjc7h0s2ELsUDTAhFr55TrPSSqJGPG0A== - import-local@^3.0.2: version "3.1.0" resolved "https://registry.yarnpkg.com/import-local/-/import-local-3.1.0.tgz#b4479df8a5fd44f6cdce24070675676063c95cb4" @@ -12132,12 +12122,7 @@ inherits@2.0.3: resolved "https://registry.yarnpkg.com/inherits/-/inherits-2.0.3.tgz#633c2c83e3da42a502f52466022480f4208261de" integrity sha512-x00IRNXNy63jwGkJmzPigoySHbaqpNuzKbBOmzK+g2OdZpQ9w+sxCN+VSB3ja7IAge2OP2qpfxTjeNcyjmW1uw== -ini@2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/ini/-/ini-2.0.0.tgz#e5fd556ecdd5726be978fa1001862eacb0a94bc5" - integrity sha512-7PnF4oN3CvZF23ADhA5wRaYEQpJ8qygSkbtTXWBeXWXmEVRXK+1ITciHWwHhsjv1TmW0MgacIv6hEi5pX5NQdA== - -ini@^1.3.2, ini@^1.3.4, ini@^1.3.5, ini@~1.3.0: +ini@^1.3.2, ini@^1.3.4, ini@^1.3.5: version "1.3.8" resolved "https://registry.yarnpkg.com/ini/-/ini-1.3.8.tgz#a29da425b48806f34767a4efce397269af28432c" integrity sha512-JV/yugV2uzW5iMRSiZAyDtQd+nxtUnjeLt0acNdw98kKLrvuRVyB80tsREOE7yvGVgalhZ6RNXCmEHkUKBKxew== @@ -12161,9 +12146,9 @@ inline-style-parser@0.1.1: integrity sha512-7NXolsK4CAS5+xvdj5OMMbI962hU/wvwoxk+LWR9Ek9bVtyuuYScDN6eS0rUm6TxApFpw7CX1o4uJzcd4AyD3Q== inquirer@^8.2.4: - version "8.2.4" - resolved "https://registry.yarnpkg.com/inquirer/-/inquirer-8.2.4.tgz#ddbfe86ca2f67649a67daa6f1051c128f684f0b4" - integrity sha512-nn4F01dxU8VeKfq192IjLsxu0/OmMZ4Lg3xKAns148rCaXP6ntAoEkVYZThWjwON8AlzdZZi6oqnhNbxUG9hVg== + version "8.2.5" + resolved "https://registry.yarnpkg.com/inquirer/-/inquirer-8.2.5.tgz#d8654a7542c35a9b9e069d27e2df4858784d54f8" + integrity sha512-QAgPDQMEgrDssk1XiwwHoOGYF9BAbUcc1+j+FhEvaOt8/cKRqyLn0U5qA6F74fGhTMGxf92pOvPBeh29jQJDTQ== dependencies: ansi-escapes "^4.2.1" chalk "^4.1.1" @@ -12182,11 +12167,11 @@ inquirer@^8.2.4: wrap-ansi "^7.0.0" internal-slot@^1.0.3: - version "1.0.3" - resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.3.tgz#7347e307deeea2faac2ac6205d4bc7d34967f59c" - integrity sha512-O0DB1JC/sPyZl7cIo78n5dR7eUSwwpYPiXRhTzNxZVAMUuB8vlnRFyLxdrVToks6XPLVnFfbzaVd5WLjhgg+vA== + version "1.0.4" + resolved "https://registry.yarnpkg.com/internal-slot/-/internal-slot-1.0.4.tgz#8551e7baf74a7a6ba5f749cfb16aa60722f0d6f3" + integrity sha512-tA8URYccNzMo94s5MQZgH8NB/XTa6HsOo0MLfXTKKEnHVVdegzaQoFZ7Jp44bdvLvY2waT5dc+j5ICEswhi7UQ== dependencies: - get-intrinsic "^1.1.0" + get-intrinsic "^1.1.3" has "^1.0.3" side-channel "^1.0.4" @@ -12200,6 +12185,11 @@ interpret@^2.2.0: resolved "https://registry.yarnpkg.com/interpret/-/interpret-2.2.0.tgz#1a78a0b5965c40a5416d007ad6f50ad27c417df9" integrity sha512-Ju0Bz/cEia55xDwUWEa8+olFpCiQoypjnQySseKtmjNrnps3P+xfpUmGr90T7yjlVJmOtybRvPXhKMbHr+fWnw== +interpret@^3.1.1: + version "3.1.1" + resolved "https://registry.yarnpkg.com/interpret/-/interpret-3.1.1.tgz#5be0ceed67ca79c6c4bc5cf0d7ee843dcea110c4" + integrity sha512-6xwYfHbajpoF0xLW+iwLkhwgvLoZDfjYfoFNu8ftMoXINzwuymNLd9u/KmwtdT2GbR+/Cz66otEGEVVUHX9QLQ== + ip@^1.1.5: version "1.1.8" resolved "https://registry.yarnpkg.com/ip/-/ip-1.1.8.tgz#ae05948f6b075435ed3307acce04629da8cdbf48" @@ -12252,7 +12242,7 @@ is-alphanumerical@^1.0.0: is-alphabetical "^1.0.0" is-decimal "^1.0.0" -is-arguments@^1.0.4, is-arguments@^1.1.0: +is-arguments@^1.0.4, is-arguments@^1.1.0, is-arguments@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== @@ -12309,7 +12299,7 @@ is-buffer@^2.0.0: resolved "https://registry.yarnpkg.com/is-buffer/-/is-buffer-2.0.5.tgz#ebc252e400d22ff8d77fa09888821a24a658c191" integrity sha512-i2R6zNFDwgEHJyQUtJEk0XFi1i0dPFn/oqjK3/vPCcDeJvW5NQ83V8QbicfF1SupOaB0h8ntgBC2YiE7dfyctQ== -is-callable@^1.1.3, is-callable@^1.1.4, is-callable@^1.2.6: +is-callable@^1.1.3, is-callable@^1.1.4, is-callable@^1.2.7: version "1.2.7" resolved "https://registry.yarnpkg.com/is-callable/-/is-callable-1.2.7.tgz#3bc2a85ea742d9e36205dcacdd72ca1fdc51b055" integrity sha512-1BC0BVFhS/p0qtw6enp8e+8OD0UrK0oFLztSjNzhcKA3WDuJxxAPXzPuPtKkjEY9UUoEWlX/8fgKeu2S8i9JTA== @@ -12329,9 +12319,9 @@ is-ci@^3.0.0: ci-info "^3.2.0" is-core-module@^2.1.0, is-core-module@^2.5.0, is-core-module@^2.8.1, is-core-module@^2.9.0: - version "2.10.0" - resolved "https://registry.yarnpkg.com/is-core-module/-/is-core-module-2.10.0.tgz#9012ede0a91c69587e647514e1d5277019e728ed" - integrity sha512-Erxj2n/LDAZ7H8WNJXd9tw38GYM3dv8rk8Zcs+jJuxYTW7sozH+SS8NtrSjVL1/vpLvWi1hxy96IzjJ3EHTJJg== + version "2.11.0" + resolved "https://registry.yarnpkg.com/is-core-module/-/is-core-module-2.11.0.tgz#ad4cb3e3863e814523c96f3f58d26cc570ff0144" + integrity sha512-RRjxlvLDkD1YJwDbroBHMb+cukurkDWNyHx7D3oNB5x9rb5ogcksMC5wHCadcXoo67gVr/+3GFySh3134zi6rw== dependencies: has "^1.0.3" @@ -12349,7 +12339,7 @@ is-data-descriptor@^1.0.0: dependencies: kind-of "^6.0.0" -is-date-object@^1.0.1: +is-date-object@^1.0.1, is-date-object@^1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/is-date-object/-/is-date-object-1.0.5.tgz#0841d5536e724c25597bf6ea62e1bd38298df31f" integrity sha512-9YQaSxsAiSwcvS33MBk3wTCVnWK+HhF8VZR2jRxehM16QcVOdHqPn4VPHmRK4lSr38n9JriurInLcP90xsYNfQ== @@ -12455,14 +12445,6 @@ is-hexadecimal@^1.0.0: resolved "https://registry.yarnpkg.com/is-hexadecimal/-/is-hexadecimal-1.0.4.tgz#cc35c97588da4bd49a8eedd6bc4082d44dcb23a7" integrity sha512-gyPJuv83bHMpocVYoqof5VDiZveEoGoFL8m3BXNb2VW8Xs+rz9kqO8LOQ5DH6EsuvilT1ApazU0pyl+ytbPtlw== -is-installed-globally@^0.4.0: - version "0.4.0" - resolved "https://registry.yarnpkg.com/is-installed-globally/-/is-installed-globally-0.4.0.tgz#9a0fd407949c30f86eb6959ef1b7994ed0b7b520" - integrity sha512-iwGqO3J21aaSkC7jWnHP/difazwS7SFeIqxv6wEtLU8Y5KlzFTjyqcSIT0d8s4+dDhKytsk9PJZ2BkS5eZwQRQ== - dependencies: - global-dirs "^3.0.0" - is-path-inside "^3.0.2" - is-interactive@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-interactive/-/is-interactive-1.0.0.tgz#cea6e6ae5c870a7b0a0004070b7b587e0252912e" @@ -12473,7 +12455,7 @@ is-lambda@^1.0.1: resolved "https://registry.yarnpkg.com/is-lambda/-/is-lambda-1.0.1.tgz#3d9877899e6a53efc0160504cde15f82e6f061d5" integrity sha512-z7CMFGNrENq5iFB9Bqo64Xk6Y9sg+epq1myIcdHaGnbMTYOxvzsEtdYqQUylB7LxfkvgrrjP32T6Ywciio9UIQ== -is-map@^2.0.2: +is-map@^2.0.1, is-map@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/is-map/-/is-map-2.0.2.tgz#00922db8c9bf73e81b7a335827bc2a43f2b91127" integrity sha512-cOZFQQozTha1f4MxLFzlgKYPTyj26picdZTx82hbc/Xf4K/tZOOXSCkMvU4pKioRXGDLJRn0GM7Upe7kR721yg== @@ -12496,11 +12478,6 @@ is-negative-zero@^2.0.2: resolved "https://registry.yarnpkg.com/is-negative-zero/-/is-negative-zero-2.0.2.tgz#7bf6f03a28003b8b3965de3ac26f664d765f3150" integrity sha512-dqJvarLawXsFbNDeJW7zAz8ItJ9cd28YufuuFzh0G8pNHjJMnY08Dv7sYX2uF5UpQOwieAeOExEYAWWfu7ZZUA== -is-npm@^5.0.0: - version "5.0.0" - resolved "https://registry.yarnpkg.com/is-npm/-/is-npm-5.0.0.tgz#43e8d65cc56e1b67f8d47262cf667099193f45a8" - integrity sha512-WW/rQLOazUq+ST/bCAVBp/2oMERWLsR7OrKyt052dNDk4DHcDE0/7QSXITlmi+VBcV13DfIbysG3tZJm5RfdBA== - is-number-object@^1.0.4: version "1.0.7" resolved "https://registry.yarnpkg.com/is-number-object/-/is-number-object-1.0.7.tgz#59d50ada4c45251784e9904f5246c742f07a42fc" @@ -12540,7 +12517,7 @@ is-path-cwd@^2.2.0: resolved "https://registry.yarnpkg.com/is-path-cwd/-/is-path-cwd-2.2.0.tgz#67d43b82664a7b5191fd9119127eb300048a9fdb" integrity sha512-w942bTcih8fdJPJmQHFzkS76NEP8Kzzvmw92cXsazb8intwLqPibPPdXf4ANdKV3rYMuuQYGIWtvz9JilB3NFQ== -is-path-inside@^3.0.2: +is-path-inside@^3.0.2, is-path-inside@^3.0.3: version "3.0.3" resolved "https://registry.yarnpkg.com/is-path-inside/-/is-path-inside-3.0.3.tgz#d231362e53a07ff2b0e0ea7fed049161ffd16283" integrity sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ== @@ -12605,7 +12582,7 @@ is-root@^2.1.0: resolved "https://registry.yarnpkg.com/is-root/-/is-root-2.1.0.tgz#809e18129cf1129644302a4f8544035d51984a9c" integrity sha512-AGOriNp96vNBd3HtU+RzFEc75FfR5ymiYv8E553I71SCeXBiMsVDUtdio1OEFvrPyLIQ9tVR5RxXIFe5PUFjMg== -is-set@^2.0.2: +is-set@^2.0.1, is-set@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/is-set/-/is-set-2.0.2.tgz#90755fa4c2562dc1c5d4024760d6119b94ca18ec" integrity sha512-+2cnTEZeY5z/iXGbLhPrOAaK/Mau5k5eXq9j14CpRTftq0pAJu2MwVRSZhyZWBzx3o6X795Lz6Bpb6R0GKf37g== @@ -12655,15 +12632,15 @@ is-text-path@^1.0.1: dependencies: text-extensions "^1.0.0" -is-typed-array@^1.1.3, is-typed-array@^1.1.9: - version "1.1.9" - resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.9.tgz#246d77d2871e7d9f5aeb1d54b9f52c71329ece67" - integrity sha512-kfrlnTTn8pZkfpJMUgYD7YZ3qzeJgWUn8XfVYBARc4wnmNOmLbmuuaAs3q5fvB0UJOn6yHAKaGTPM7d6ezoD/A== +is-typed-array@^1.1.10, is-typed-array@^1.1.3: + version "1.1.10" + resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.10.tgz#36a5b5cb4189b575d1a3e4b08536bfb485801e3f" + integrity sha512-PJqgEHiWZvMpaFZ3uTc8kHPM4+4ADTlDniuQL7cU/UDA0Ql7F70yGfHph3cLNe+c9toaigv+DFzTJKhc2CtO6A== dependencies: available-typed-arrays "^1.0.5" call-bind "^1.0.2" - es-abstract "^1.20.0" for-each "^0.3.3" + gopd "^1.0.1" has-tostringtag "^1.0.0" is-typedarray@^1.0.0: @@ -12681,6 +12658,11 @@ is-utf8@^0.2.0: resolved "https://registry.yarnpkg.com/is-utf8/-/is-utf8-0.2.1.tgz#4b0da1442104d1b336340e80797e865cf39f7d72" integrity sha512-rMYPYvCzsXywIsldgLaSoPlw5PfoB/ssr7hY4pLfcodrA5M/eArza1a9VmTiNIBNMjOGr1Ow9mTyU2o69U6U9Q== +is-weakmap@^2.0.1: + version "2.0.1" + resolved "https://registry.yarnpkg.com/is-weakmap/-/is-weakmap-2.0.1.tgz#5008b59bdc43b698201d18f62b37b2ca243e8cf2" + integrity sha512-NSBR4kH5oVj1Uwvv970ruUkCV7O1mzgVFO4/rev2cLRda9Tm9HrL70ZPut4rOHgY0FNrUu9BCbXA2sdQ+x0chA== + is-weakref@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/is-weakref/-/is-weakref-1.0.2.tgz#9529f383a9338205e89765e0392efc2f100f06f2" @@ -12688,6 +12670,14 @@ is-weakref@^1.0.2: dependencies: call-bind "^1.0.2" +is-weakset@^2.0.1: + version "2.0.2" + resolved "https://registry.yarnpkg.com/is-weakset/-/is-weakset-2.0.2.tgz#4569d67a747a1ce5a994dfd4ef6dcea76e7c0a1d" + integrity sha512-t2yVvttHkQktwnNNmBQ98AhENLdPUTDTE21uPqAQ0ARwQfGeQKRVS0NNurH7bTf7RrvcVn1OOge45CnBeHCSmg== + dependencies: + call-bind "^1.0.2" + get-intrinsic "^1.1.1" + is-whitespace-character@^1.0.0: version "1.0.4" resolved "https://registry.yarnpkg.com/is-whitespace-character/-/is-whitespace-character-1.0.4.tgz#0858edd94a95594c7c9dd0b5c174ec6e45ee4aa7" @@ -12720,11 +12710,6 @@ is-wsl@^2.1.1, is-wsl@^2.2.0: dependencies: is-docker "^2.0.0" -is-yarn-global@^0.3.0: - version "0.3.0" - resolved "https://registry.yarnpkg.com/is-yarn-global/-/is-yarn-global-0.3.0.tgz#d502d3382590ea3004893746754c89139973e232" - integrity sha512-VjSeb/lHmkoyd8ryPVIKvOCn4D1koMqY+vqyjjUfc3xyKtP4dYOxM44sZrnqQSzSds3xyOrUTLTC9LVCVgLngw== - isarray@0.0.1: version "0.0.1" resolved "https://registry.yarnpkg.com/isarray/-/isarray-0.0.1.tgz#8a18acfca9a8f4177e09abfc6038939b05d1eedf" @@ -12788,9 +12773,9 @@ istanbul-lib-coverage@^3.0.0, istanbul-lib-coverage@^3.2.0: integrity sha512-eOeJ5BHCmHYvQK7xt9GkdHuzuCGS1Y6g9Gvnx3Ym33fz/HpLRYxiS0wHNr+m/MBC8B647Xt608vCDEvhl9c6Mw== istanbul-lib-instrument@^5.0.4, istanbul-lib-instrument@^5.1.0: - version "5.2.0" - resolved "https://registry.yarnpkg.com/istanbul-lib-instrument/-/istanbul-lib-instrument-5.2.0.tgz#31d18bdd127f825dd02ea7bfdfd906f8ab840e9f" - integrity sha512-6Lthe1hqXHBNsqvgDzGO6l03XNeu3CrG4RqQ1KM9+l5+jNGpEJfIELx1NS3SEHmJQA8np/u+E4EPRKRiu6m19A== + version "5.2.1" + resolved "https://registry.yarnpkg.com/istanbul-lib-instrument/-/istanbul-lib-instrument-5.2.1.tgz#d10c8885c2125574e1c231cacadf955675e1ce3d" + integrity sha512-pzqtp31nLv/XFOzXGuvhCb8qhjmTVo5vjVk19XE4CRlSWz0KoeJ3bw9XsA7nOp9YBf4qHjwBxkDzKcME/J29Yg== dependencies: "@babel/core" "^7.12.3" "@babel/parser" "^7.14.7" @@ -12837,12 +12822,12 @@ iterate-value@^1.0.2: es-get-iterator "^1.0.2" iterate-iterator "^1.0.1" -ixixx@^1.0.19, ixixx@^1.0.20: - version "1.0.21" - resolved "https://registry.yarnpkg.com/ixixx/-/ixixx-1.0.21.tgz#907b3f416ff63f75f0d3aeefe02d2330bba52fb5" - integrity sha512-OW7tLHM8EQKC/rlkMk4LOoy8JGwnyYSmUsPP7DoRL7lxKwSyym7Z4lGLvo0qPGUHob03ieCPUCUUXTs4c+ymmA== +ixixx@^2.0.1: + version "2.0.1" + resolved "https://registry.yarnpkg.com/ixixx/-/ixixx-2.0.1.tgz#8ed4388fc46a155f5bd6692f0b55b028310bee46" + integrity sha512-I1SvJVVAzjM0OhdnJMW67zv2Du/8+diIIYVl07muN1U/ZGulaviDynY4E27YYSpzXEohnxkI2v/7lZJ/tTU4gg== dependencies: - external-sorting "^1.2.1" + external-sorting "^1.3.1" split2 "^4.1.0" tmp "^0.2.1" @@ -12865,10 +12850,10 @@ jest-changed-files@^27.5.1: execa "^5.0.0" throat "^6.0.1" -jest-changed-files@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-changed-files/-/jest-changed-files-28.1.3.tgz#d9aeee6792be3686c47cb988a8eaf82ff4238831" - integrity sha512-esaOfUWJXk2nfZt9SPyC8gA1kNfdKLkQWyzsMlqq8msYSlNKfmZxfRgZn4Cd4MGVUF+7v6dBs0d5TOAKa7iIiA== +jest-changed-files@^29.2.0: + version "29.2.0" + resolved "https://registry.yarnpkg.com/jest-changed-files/-/jest-changed-files-29.2.0.tgz#b6598daa9803ea6a4dce7968e20ab380ddbee289" + integrity sha512-qPVmLLyBmvF5HJrY7krDisx6Voi8DmlV3GZYX0aFNbaQsZeoz1hfxcCMbqDGuQCxU1dJy9eYc2xscE8QrCCYaA== dependencies: execa "^5.0.0" p-limit "^3.1.0" @@ -12898,28 +12883,28 @@ jest-circus@^27.5.1: stack-utils "^2.0.3" throat "^6.0.1" -jest-circus@^28.1.3: - 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pretty-format "^28.1.3" + pretty-format "^29.3.1" slash "^3.0.0" stack-utils "^2.0.3" @@ -12941,21 +12926,21 @@ jest-cli@^27.5.1: prompts "^2.0.1" yargs "^16.2.0" -jest-cli@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-cli/-/jest-cli-28.1.3.tgz#558b33c577d06de55087b8448d373b9f654e46b2" - integrity sha512-roY3kvrv57Azn1yPgdTebPAXvdR2xfezaKKYzVxZ6It/5NCxzJym6tUI5P1zkdWhfUYkxEI9uZWcQdaFLo8mJQ== +jest-cli@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-cli/-/jest-cli-29.3.1.tgz#e89dff427db3b1df50cea9a393ebd8640790416d" + integrity sha512-TO/ewvwyvPOiBBuWZ0gm04z3WWP8TIK8acgPzE4IxgsLKQgb377NYGrQLc3Wl/7ndWzIH2CDNNsUjGxwLL43VQ== dependencies: - "@jest/core" "^28.1.3" - "@jest/test-result" "^28.1.3" - "@jest/types" "^28.1.3" + "@jest/core" "^29.3.1" + "@jest/test-result" "^29.3.1" + "@jest/types" "^29.3.1" chalk "^4.0.0" exit "^0.1.2" graceful-fs "^4.2.9" import-local "^3.0.2" - jest-config "^28.1.3" - jest-util "^28.1.3" - jest-validate "^28.1.3" + jest-config "^29.3.1" + jest-util "^29.3.1" + jest-validate "^29.3.1" prompts "^2.0.1" yargs "^17.3.1" @@ -12989,44 +12974,34 @@ jest-config@^27.5.1: slash "^3.0.0" strip-json-comments "^3.1.1" -jest-config@^28.1.3: - 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pretty-format "^28.1.3" + pretty-format "^29.3.1" slash "^3.0.0" strip-json-comments "^3.1.1" -jest-diff@^25.2.1: - version "25.5.0" - resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-25.5.0.tgz#1dd26ed64f96667c068cef026b677dfa01afcfa9" - integrity sha512-z1kygetuPiREYdNIumRpAHY6RXiGmp70YHptjdaxTWGmA085W3iCnXNx0DhflK3vwrKmrRWyY1wUpkPMVxMK7A== - dependencies: - chalk "^3.0.0" - diff-sequences "^25.2.6" - jest-get-type "^25.2.6" - pretty-format "^25.5.0" - jest-diff@^27.5.1: version "27.5.1" resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-27.5.1.tgz#a07f5011ac9e6643cf8a95a462b7b1ecf6680def" @@ -13037,25 +13012,15 @@ jest-diff@^27.5.1: jest-get-type "^27.5.1" pretty-format "^27.5.1" -jest-diff@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-28.1.3.tgz#948a192d86f4e7a64c5264ad4da4877133d8792f" - integrity sha512-8RqP1B/OXzjjTWkqMX67iqgwBVJRgCyKD3L9nq+6ZqJMdvjE8RgHktqZ6jNrkdMT+dJuYNI3rhQpxaz7drJHfw== - dependencies: - chalk "^4.0.0" - 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integrity sha512-3wayBVNiOYx0cwAbl9rwm5kKFP8yHH3d/fkEaL02NPTkDojPtheGB7HZSFY4wzX+DxyrvhXz0KSCVksmCknCuA== +jest-docblock@^29.2.0: + version "29.2.0" + resolved "https://registry.yarnpkg.com/jest-docblock/-/jest-docblock-29.2.0.tgz#307203e20b637d97cee04809efc1d43afc641e82" + integrity sha512-bkxUsxTgWQGbXV5IENmfiIuqZhJcyvF7tU4zJ/7ioTutdz4ToB5Yx6JOFBpgI+TphRY4lhOyCWGNH/QFQh5T6A== dependencies: detect-newline "^3.0.0" @@ -13082,16 +13047,16 @@ jest-each@^27.5.1: jest-util "^27.5.1" pretty-format "^27.5.1" -jest-each@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-each/-/jest-each-28.1.3.tgz#bdd1516edbe2b1f3569cfdad9acd543040028f81" - integrity sha512-arT1z4sg2yABU5uogObVPvSlSMQlDA48owx07BDPAiasW0yYpYHYOo4HHLz9q0BVzDVU4hILFjzJw0So9aCL/g== +jest-each@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-each/-/jest-each-29.3.1.tgz#bc375c8734f1bb96625d83d1ca03ef508379e132" + integrity sha512-qrZH7PmFB9rEzCSl00BWjZYuS1BSOH8lLuC0azQE9lQrAx3PWGKHTDudQiOSwIy5dGAJh7KA0ScYlCP7JxvFYA== dependencies: - 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chalk "^1.1.3" + chalk "^4.0.0" get-stdin "^5.0.1" glur "^1.1.2" lodash "^4.17.4" @@ -13278,18 +13233,18 @@ jest-leak-detector@^27.5.1: jest-get-type "^27.5.1" pretty-format "^27.5.1" -jest-leak-detector@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-leak-detector/-/jest-leak-detector-28.1.3.tgz#a6685d9b074be99e3adee816ce84fd30795e654d" - integrity sha512-WFVJhnQsiKtDEo5lG2mM0v40QWnBM+zMdHHyJs8AWZ7J0QZJS59MsyKeJHWhpBZBH32S48FOVvGyOFT1h0DlqA== +jest-leak-detector@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-leak-detector/-/jest-leak-detector-29.3.1.tgz#95336d020170671db0ee166b75cd8ef647265518" + integrity sha512-3DA/VVXj4zFOPagGkuqHnSQf1GZBmmlagpguxEERO6Pla2g84Q1MaVIB3YMxgUaFIaYag8ZnTyQgiZ35YEqAQA== dependencies: - jest-get-type "^28.0.2" - pretty-format "^28.1.3" + jest-get-type "^29.2.0" + pretty-format "^29.3.1" jest-localstorage-mock@^2.4.3: - version "2.4.22" - resolved "https://registry.yarnpkg.com/jest-localstorage-mock/-/jest-localstorage-mock-2.4.22.tgz#9d70be92bfc591c0be289ee2f71de1b4b2a5ca9b" - 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version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-resolve-dependencies/-/jest-resolve-dependencies-28.1.3.tgz#8c65d7583460df7275c6ea2791901fa975c1fe66" - integrity sha512-qa0QO2Q0XzQoNPouMbCc7Bvtsem8eQgVPNkwn9LnS+R2n8DaVDPL/U1gngC0LTl1RYXJU0uJa2BMC2DbTfFrHA== +jest-resolve-dependencies@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-resolve-dependencies/-/jest-resolve-dependencies-29.3.1.tgz#a6a329708a128e68d67c49f38678a4a4a914c3bf" + integrity sha512-Vk0cYq0byRw2WluNmNWGqPeRnZ3p3hHmjJMp2dyyZeYIfiBskwq4rpiuGFR6QGAdbj58WC7HN4hQHjf2mpvrLA== dependencies: - jest-regex-util "^28.0.2" - jest-snapshot "^28.1.3" + jest-regex-util "^29.2.0" + jest-snapshot "^29.3.1" jest-resolve@^27.4.2, jest-resolve@^27.5.1: version "27.5.1" @@ -13435,17 +13386,17 @@ jest-resolve@^27.4.2, jest-resolve@^27.5.1: resolve.exports "^1.1.0" slash "^3.0.0" -jest-resolve@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-resolve/-/jest-resolve-28.1.3.tgz#cfb36100341ddbb061ec781426b3c31eb51aa0a8" - 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integrity sha512-vPCk9F353i0Ymx3WQq3+a4lZ07NXu9Ca8wya6o4Fe4/aO1e1awMMprZ3woPFpKwghEOW+UXgd15vVotuNN9ONQ== +jest-util@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-util/-/jest-util-29.3.1.tgz#1dda51e378bbcb7e3bc9d8ab651445591ed373e1" + integrity sha512-7YOVZaiX7RJLv76ZfHt4nbNEzzTRiMW/IiOG7ZOKmTXmoGBxUDefgMAxQubu6WPVqP5zSzAdZG0FfLcC7HOIFQ== dependencies: - "@jest/types" "^29.1.2" + "@jest/types" "^29.3.1" "@types/node" "*" chalk "^4.0.0" ci-info "^3.2.0" @@ -13693,17 +13645,17 @@ jest-validate@^27.5.1: leven "^3.1.0" pretty-format "^27.5.1" -jest-validate@^28.1.3: - version "28.1.3" - resolved "https://registry.yarnpkg.com/jest-validate/-/jest-validate-28.1.3.tgz#e322267fd5e7c64cea4629612c357bbda96229df" - integrity sha512-SZbOGBWEsaTxBGCOpsRWlXlvNkvTkY0XxRfh7zYmvd8uL5Qzyg0CHAXiXKROflh801quA6+/DsT4ODDthOC/OA== +jest-validate@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-validate/-/jest-validate-29.3.1.tgz#d56fefaa2e7d1fde3ecdc973c7f7f8f25eea704a" + integrity sha512-N9Lr3oYR2Mpzuelp1F8negJR3YE+L1ebk1rYA5qYo9TTY3f9OWdptLoNSPP9itOCBIRBqjt/S5XHlzYglLN67g== dependencies: - "@jest/types" "^28.1.3" + "@jest/types" "^29.3.1" camelcase "^6.2.0" chalk "^4.0.0" - jest-get-type "^28.0.2" + jest-get-type "^29.2.0" leven "^3.1.0" - pretty-format "^28.1.3" + pretty-format "^29.3.1" jest-watch-typeahead@^1.0.0: version "1.1.0" @@ -13731,7 +13683,7 @@ jest-watcher@^27.5.1: jest-util "^27.5.1" string-length "^4.0.1" -jest-watcher@^28.0.0, jest-watcher@^28.1.3: +jest-watcher@^28.0.0: version "28.1.3" resolved "https://registry.yarnpkg.com/jest-watcher/-/jest-watcher-28.1.3.tgz#c6023a59ba2255e3b4c57179fc94164b3e73abd4" integrity sha512-t4qcqj9hze+jviFPUN3YAtAEeFnr/azITXQEMARf5cMwKY2SMBRnCQTXLixTl20OR6mLh9KLMrgVJgJISym+1g== @@ -13745,6 +13697,20 @@ jest-watcher@^28.0.0, jest-watcher@^28.1.3: jest-util "^28.1.3" string-length "^4.0.1" +jest-watcher@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-watcher/-/jest-watcher-29.3.1.tgz#3341547e14fe3c0f79f9c3a4c62dbc3fc977fd4a" + integrity sha512-RspXG2BQFDsZSRKGCT/NiNa8RkQ1iKAjrO0//soTMWx/QUt+OcxMqMSBxz23PYGqUuWm2+m2mNNsmj0eIoOaFg== + dependencies: + "@jest/test-result" "^29.3.1" + "@jest/types" "^29.3.1" + "@types/node" "*" + ansi-escapes "^4.2.1" + chalk "^4.0.0" + emittery "^0.13.1" + jest-util "^29.3.1" + string-length "^4.0.1" + jest-worker@^26.2.1, jest-worker@^26.5.0, jest-worker@^26.6.2: version "26.6.2" resolved "https://registry.yarnpkg.com/jest-worker/-/jest-worker-26.6.2.tgz#7f72cbc4d643c365e27b9fd775f9d0eaa9c7a8ed" @@ -13763,7 +13729,7 @@ jest-worker@^27.0.2, jest-worker@^27.4.5, jest-worker@^27.5.1: merge-stream "^2.0.0" supports-color "^8.0.0" -jest-worker@^28.0.2, jest-worker@^28.1.3: +jest-worker@^28.0.2: version "28.1.3" resolved "https://registry.yarnpkg.com/jest-worker/-/jest-worker-28.1.3.tgz#7e3c4ce3fa23d1bb6accb169e7f396f98ed4bb98" integrity sha512-CqRA220YV/6jCo8VWvAt1KKx6eek1VIHMPeLEbpcfSfkEeWyBNppynM/o6q+Wmw+sOhos2ml34wZbSX3G13//g== @@ -13772,6 +13738,16 @@ jest-worker@^28.0.2, jest-worker@^28.1.3: merge-stream "^2.0.0" supports-color "^8.0.0" +jest-worker@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/jest-worker/-/jest-worker-29.3.1.tgz#e9462161017a9bb176380d721cab022661da3d6b" + integrity sha512-lY4AnnmsEWeiXirAIA0c9SDPbuCBq8IYuDVL8PMm0MZ2PEs2yPvRA/J64QBXuZp7CYKrDM/rmNrc9/i3KJQncw== + dependencies: + "@types/node" "*" + jest-util "^29.3.1" + merge-stream "^2.0.0" + supports-color "^8.0.0" + jest@^27.4.3: version "27.5.1" resolved "https://registry.yarnpkg.com/jest/-/jest-27.5.1.tgz#dadf33ba70a779be7a6fc33015843b51494f63fc" @@ -13781,15 +13757,15 @@ jest@^27.4.3: import-local "^3.0.2" jest-cli "^27.5.1" -jest@^28.1.1: - 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version "4.1.5" - resolved "https://registry.yarnpkg.com/js-sdsl/-/js-sdsl-4.1.5.tgz#1ff1645e6b4d1b028cd3f862db88c9d887f26e2a" - integrity sha512-08bOAKweV2NUC1wqTtf3qZlnpOX/R2DU9ikpjOHs0H+ibQv3zpncVQg6um4uYtRtrwIX8M4Nh3ytK4HGlYAq7Q== + version "4.2.0" + resolved "https://registry.yarnpkg.com/js-sdsl/-/js-sdsl-4.2.0.tgz#278e98b7bea589b8baaf048c20aeb19eb7ad09d0" + integrity sha512-dyBIzQBDkCqCu+0upx25Y2jGdbTGxE9fshMsCdK0ViOongpV+n5tXRcZY9v7CaVQ79AGS9KA1KHtojxiM7aXSQ== js-string-escape@^1.0.1: version "1.0.1" @@ -13877,37 +13853,36 @@ jsdom@^16.6.0: ws "^7.4.6" xml-name-validator "^3.0.0" -jsdom@^19.0.0: - version "19.0.0" - resolved "https://registry.yarnpkg.com/jsdom/-/jsdom-19.0.0.tgz#93e67c149fe26816d38a849ea30ac93677e16b6a" - integrity sha512-RYAyjCbxy/vri/CfnjUWJQQtZ3LKlLnDqj+9XLNnJPgEGeirZs3hllKR20re8LUZ6o1b1X4Jat+Qd26zmP41+A== +jsdom@^20.0.0, jsdom@^20.0.3: + version "20.0.3" + resolved "https://registry.yarnpkg.com/jsdom/-/jsdom-20.0.3.tgz#886a41ba1d4726f67a8858028c99489fed6ad4db" + integrity sha512-SYhBvTh89tTfCD/CRdSOm13mOBa42iTaTyfyEWBdKcGdPxPtLFBXuHR8XHb33YNYaP+lLbmSvBTsnoesCNJEsQ== dependencies: - 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jsonify "~0.0.0" + jsonify "^0.0.1" json-stringify-nice@^1.1.4: version "1.1.4" @@ -13980,9 +13955,9 @@ json5@^1.0.1: minimist "^1.2.0" json5@^2.1.2, json5@^2.1.3, json5@^2.2.0, json5@^2.2.1: - version "2.2.1" - resolved "https://registry.yarnpkg.com/json5/-/json5-2.2.1.tgz#655d50ed1e6f95ad1a3caababd2b0efda10b395c" - integrity sha512-1hqLFMSrGHRHxav9q9gNjJ5EXznIxGVO09xQRrwplcS8qs28pZ8s8hupZAmqDwZUmVZ2Qb2jnyPOWcDH8m8dlA== + version "2.2.2" + resolved "https://registry.yarnpkg.com/json5/-/json5-2.2.2.tgz#64471c5bdcc564c18f7c1d4df2e2297f2457c5ab" + integrity sha512-46Tk9JiOL2z7ytNQWFLpj99RZkVgeHf87yGQKsIkaPz1qSH9UczKH1rO7K3wgRselo0tYMUNfecYpm/p1vC7tQ== jsonc-parser@3.2.0: version "3.2.0" @@ -14005,10 +13980,10 @@ jsonfile@^6.0.1: optionalDependencies: graceful-fs "^4.1.6" -jsonify@~0.0.0: - version "0.0.0" - resolved "https://registry.yarnpkg.com/jsonify/-/jsonify-0.0.0.tgz#2c74b6ee41d93ca51b7b5aaee8f503631d252a73" - integrity sha512-trvBk1ki43VZptdBI5rIlG4YOzyeH/WefQt5rj1grasPn4iiZWKet8nkgc4GlsAylaztn0qZfUYOiTsASJFdNA== +jsonify@^0.0.1: + version "0.0.1" + resolved "https://registry.yarnpkg.com/jsonify/-/jsonify-0.0.1.tgz#2aa3111dae3d34a0f151c63f3a45d995d9420978" + integrity sha512-2/Ki0GcmuqSrgFyelQq9M05y7PS0mEwuIzrf3f1fPqkVDVRvZrPZtVSMHxdgo8Aq0sxAOb/cr2aqqA3LeWHVPg== jsonparse@^1.2.0, jsonparse@^1.3.1: version "1.3.1" @@ -14034,14 +14009,14 @@ junk@^3.1.0: integrity sha512-pBxcB3LFc8QVgdggvZWyeys+hnrNWg4OcZIU/1X59k5jQdLBlCsYGRQaz234SqoRLTCgMH00fY0xRJH+F9METQ== just-diff-apply@^5.2.0: - 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version "1.0.1" - resolved "https://registry.yarnpkg.com/lowercase-keys/-/lowercase-keys-1.0.1.tgz#6f9e30b47084d971a7c820ff15a6c5167b74c26f" - integrity sha512-G2Lj61tXDnVFFOi8VZds+SoQjtQC3dgokKdDG2mTm1tx4m50NUHBOZSBwQQHyy0V12A0JTG4icfZQH+xPyh8VA== - lowercase-keys@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/lowercase-keys/-/lowercase-keys-2.0.0.tgz#2603e78b7b4b0006cbca2fbcc8a3202558ac9479" @@ -14455,9 +14421,9 @@ lru-cache@^6.0.0: yallist "^4.0.0" lru-cache@^7.4.4, lru-cache@^7.5.1, lru-cache@^7.7.1: - version "7.14.0" - resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-7.14.0.tgz#21be64954a4680e303a09e9468f880b98a0b3c7f" - integrity sha512-EIRtP1GrSJny0dqb50QXRUNBxHJhcpxHC++M5tD7RYbvLLn5KVWKsbyswSSqDuU15UFi3bgTQIY8nhDMeF6aDQ== + version "7.14.1" + resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-7.14.1.tgz#8da8d2f5f59827edb388e63e459ac23d6d408fea" + integrity sha512-ysxwsnTKdAx96aTRdhDOCQfDgbHnt8SK0KY8SEjO0wHinhWOFTESbjVCMPbU1uGXg/ch4lifqx0wfjOawU2+WA== lz-string@^1.4.4: version "1.4.4" @@ -14678,9 +14644,9 @@ mem@^8.1.1: mimic-fn "^3.1.0" memfs@^3.1.2, memfs@^3.2.2, memfs@^3.4.3: - version "3.4.7" - resolved "https://registry.yarnpkg.com/memfs/-/memfs-3.4.7.tgz#e5252ad2242a724f938cb937e3c4f7ceb1f70e5a" - integrity sha512-ygaiUSNalBX85388uskeCyhSAoOSgzBbtVCr9jA2RROssFL9Q19/ZXFqS+2Th2sr1ewNIWgFdLzLC3Yl1Zv+lw== + version "3.4.12" + resolved "https://registry.yarnpkg.com/memfs/-/memfs-3.4.12.tgz#d00f8ad8dab132dc277c659dc85bfd14b07d03bd" + integrity sha512-BcjuQn6vfqP+k100e0E9m61Hyqa//Brp+I3f0OBmN0ATHlFA8vx3Lt8z57R3u2bPqe3WGDBC+nF72fTH7isyEw== dependencies: fs-monkey "^1.0.3" @@ -14842,7 +14808,7 @@ mimic-fn@^3.1.0: resolved "https://registry.yarnpkg.com/mimic-fn/-/mimic-fn-3.1.0.tgz#65755145bbf3e36954b949c16450427451d5ca74" integrity sha512-Ysbi9uYW9hFyfrThdDEQuykN4Ey6BuwPD2kpI5ES/nFTDn/98yxYNLZJcgUAKPT/mcrLLKaGzJR9YVxJrIdASQ== -mimic-response@^1.0.0, mimic-response@^1.0.1: +mimic-response@^1.0.0: version "1.0.1" resolved "https://registry.yarnpkg.com/mimic-response/-/mimic-response-1.0.1.tgz#4923538878eef42063cb8a3e3b0798781487ab1b" integrity sha512-j5EctnkH7amfV/q5Hgmoal1g2QHFJRraOtmx0JpIqkxhBhI/lJSl1nMpQ45hVarwNETOoWEimndZ4QK0RHxuxQ== @@ -14852,6 +14818,11 @@ mimic-response@^2.0.0: resolved "https://registry.yarnpkg.com/mimic-response/-/mimic-response-2.1.0.tgz#d13763d35f613d09ec37ebb30bac0469c0ee8f43" integrity sha512-wXqjST+SLt7R009ySCglWBCFpjUygmCIfD790/kVbiGmUgfYGuB14PiTd5DwVxSV4NcYHjzMkoj5LjQZwTQLEA== +mimic-response@^3.1.0: + version "3.1.0" + resolved "https://registry.yarnpkg.com/mimic-response/-/mimic-response-3.1.0.tgz#2d1d59af9c1b129815accc2c46a022a5ce1fa3c9" + integrity sha512-z0yWI+4FDrrweS8Zmt4Ej5HdJmky15+L2e6Wgn3+iK5fWzb6T3fhNFq2+MeTRb064c6Wr4N/wv0DzQTjNzHNGQ== + min-document@^2.19.0: version "2.19.0" resolved "https://registry.yarnpkg.com/min-document/-/min-document-2.19.0.tgz#7bd282e3f5842ed295bb748cdd9f1ffa2c824685" @@ -14865,9 +14836,9 @@ min-indent@^1.0.0: integrity sha512-I9jwMn07Sy/IwOj3zVkVik2JTvgpaykDZEigL6Rx6N9LbMywwUSMtxET+7lVoDLLd3O3IXwJwvuuns8UB/HeAg== mini-css-extract-plugin@^2.4.5: - 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version "5.1.0" - resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-5.1.0.tgz#1717b464f4971b144f6aabe8f2d0b8e4511e09c7" - integrity sha512-9TPBGGak4nHfGZsPBohm9AWg6NoT7QTCehS3BIJABslyZbzxfV78QM2Y6+i741OPZIafFAaiiEMh5OyIrJPgtg== + version "5.1.1" + resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-5.1.1.tgz#6c9dffcf9927ff2a31e74b5af11adf8b9604b022" + integrity sha512-362NP+zlprccbEt/SkxKfRMHnNY85V74mVnpUpNyr3F35covl09Kec7/sEFLt3RA4oXmewtoaanoIf67SE5Y5g== dependencies: brace-expansion "^2.0.1" @@ -14919,9 +14890,9 @@ minimist-options@4.1.0: kind-of "^6.0.3" minimist@^1.1.1, minimist@^1.1.3, minimist@^1.2.0, minimist@^1.2.5, minimist@^1.2.6: - version "1.2.6" - resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.6.tgz#8637a5b759ea0d6e98702cfb3a9283323c93af44" - integrity sha512-Jsjnk4bw3YJqYzbdyBiNsPWHPfO++UGG749Cxs6peCu5Xg4nrena6OVxOYxrQTqww0Jmwt+Ref8rggumkTLz9Q== + version "1.2.7" + resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.7.tgz#daa1c4d91f507390437c6a8bc01078e7000c4d18" + integrity sha512-bzfL1YUZsP41gmu/qjrEk0Q6i2ix/cVeAhbCbqH9u3zYutS1cLg00qhrD0M2MVdCcx4Sc0UpP2eBWo9rotpq6g== minipass-collect@^1.0.2: version "1.0.2" @@ -14982,9 +14953,16 @@ minipass-sized@^1.0.3: minipass "^3.0.0" minipass@^3.0.0, minipass@^3.1.0, minipass@^3.1.1, minipass@^3.1.3, minipass@^3.1.6: - 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domain-browser "^4.19.0" + domain-browser "^4.22.0" events "^3.3.0" filter-obj "^2.0.2" https-browserify "^1.0.0" @@ -15332,20 +15315,21 @@ node-polyfill-webpack-plugin@^1.1.4: process "^0.11.10" punycode "^2.1.1" querystring-es3 "^0.2.1" - readable-stream "^3.6.0" + readable-stream "^4.0.0" stream-browserify "^3.0.0" stream-http "^3.2.0" string_decoder "^1.3.0" timers-browserify "^2.0.12" tty-browserify "^0.0.1" + type-fest "^2.14.0" url "^0.11.0" util "^0.12.4" vm-browserify "^1.1.2" node-releases@^2.0.6: - version "2.0.6" - resolved "https://registry.yarnpkg.com/node-releases/-/node-releases-2.0.6.tgz#8a7088c63a55e493845683ebf3c828d8c51c5503" - integrity sha512-PiVXnNuFm5+iYkLBNeq5211hvO38y63T0i2KKh2KnUs3RpzJ+JtODFjkD8yjLwnDkTYF1eKXheUwdssR+NRZdg== + version "2.0.8" + resolved "https://registry.yarnpkg.com/node-releases/-/node-releases-2.0.8.tgz#0f349cdc8fcfa39a92ac0be9bc48b7706292b9ae" + integrity sha512-dFSmB8fFHEH/s81Xi+Y/15DQY6VHW81nXRj86EMSL3lmuTmK1e+aT4wrFCkTbm+gSwkw4KpX+rT/pMM2c1mF+A== nopt@^5.0.0: version "5.0.0" @@ -15354,6 +15338,13 @@ nopt@^5.0.0: dependencies: abbrev "1" +nopt@^6.0.0: + version "6.0.0" + resolved "https://registry.yarnpkg.com/nopt/-/nopt-6.0.0.tgz#245801d8ebf409c6df22ab9d95b65e1309cdb16d" + integrity sha512-ZwLpbTgdhuZUnZzjd7nb1ZV+4DoiC6/sfiVKok72ym/4Tlf+DFdlHYmT2JPmcNNWV6Pi3SDf1kT+A4r9RTuT9g== + dependencies: + abbrev "^1.0.0" + normalize-package-data@^2.3.2, normalize-package-data@^2.3.4, normalize-package-data@^2.5.0: version "2.5.0" resolved "https://registry.yarnpkg.com/normalize-package-data/-/normalize-package-data-2.5.0.tgz#e66db1838b200c1dfc233225d12cb36520e234a8" @@ -15401,11 +15392,6 @@ normalize-range@^0.1.2: resolved "https://registry.yarnpkg.com/normalize-range/-/normalize-range-0.1.2.tgz#2d10c06bdfd312ea9777695a4d28439456b75942" integrity sha512-bdok/XvKII3nUpklnV6P2hxtMNrCboOjAcyBuQnWEhO665FwrSNRxU+AqpsyvO6LgGYPspN+lu5CLtw4jPRKNA== -normalize-url@^4.1.0: - version "4.5.1" - resolved "https://registry.yarnpkg.com/normalize-url/-/normalize-url-4.5.1.tgz#0dd90cf1288ee1d1313b87081c9a5932ee48518a" - integrity sha512-9UZCFRHQdNrfTpGg8+1INIg93B6zE0aXMVFkw1WFwvO4SlZywU6aLg5Of0Ap/PgcbSw4LNxvMWXMeugwMCX0AA== - normalize-url@^6.0.1: version "6.1.0" resolved "https://registry.yarnpkg.com/normalize-url/-/normalize-url-6.1.0.tgz#40d0885b535deffe3f3147bec877d05fe4c5668a" @@ -15430,14 +15416,6 @@ npm-bundled@^2.0.0: dependencies: npm-normalize-package-bin "^2.0.0" -npm-conf@^1.1.3: - version "1.1.3" - resolved "https://registry.yarnpkg.com/npm-conf/-/npm-conf-1.1.3.tgz#256cc47bd0e218c259c4e9550bf413bc2192aff9" - integrity sha512-Yic4bZHJOt9RCFbRP3GgpqhScOY4HH3V2P8yBj6CeYq118Qr+BLXqT2JvpJ00mryLESpgOxf5XlFv4ZjXxLScw== - dependencies: - config-chain "^1.1.11" - pify "^3.0.0" - npm-install-checks@^5.0.0: version "5.0.0" resolved "https://registry.yarnpkg.com/npm-install-checks/-/npm-install-checks-5.0.0.tgz#5ff27d209a4e3542b8ac6b0c1db6063506248234" @@ -15575,22 +15553,23 @@ num2fraction@^1.2.2: resolved "https://registry.yarnpkg.com/num2fraction/-/num2fraction-1.2.2.tgz#6f682b6a027a4e9ddfa4564cd2589d1d4e669ede" integrity sha512-Y1wZESM7VUThYY+4W+X4ySH2maqcA+p7UR+w8VWNWVAd6lwuXXWz/w/Cz43J/dI2I+PS6wD5N+bJUF+gjWvIqg== -nwsapi@^2.2.0: +nwsapi@^2.2.0, nwsapi@^2.2.2: version "2.2.2" resolved "https://registry.yarnpkg.com/nwsapi/-/nwsapi-2.2.2.tgz#e5418863e7905df67d51ec95938d67bf801f0bb0" integrity sha512-90yv+6538zuvUMnN+zCr8LuV6bPFdq50304114vJYJ8RDyK8D5O9Phpbd6SZWgI7PwzmmfN1upeOJlvybDSgCw== -nx@14.8.2, "nx@>=14.6.1 < 16": - 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define-properties "^1.1.3" - es-abstract "^1.19.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" object.getownpropertydescriptors@^2.0.3, object.getownpropertydescriptors@^2.1.0, object.getownpropertydescriptors@^2.1.2: - version "2.1.4" - resolved "https://registry.yarnpkg.com/object.getownpropertydescriptors/-/object.getownpropertydescriptors-2.1.4.tgz#7965e6437a57278b587383831a9b829455a4bc37" - integrity sha512-sccv3L/pMModT6dJAYF3fzGMVcb38ysQ0tEE6ixv2yXJDtEIPph268OlAdJj5/qZMZDq2g/jqvwppt36uS/uQQ== + version "2.1.5" + resolved "https://registry.yarnpkg.com/object.getownpropertydescriptors/-/object.getownpropertydescriptors-2.1.5.tgz#db5a9002489b64eef903df81d6623c07e5b4b4d3" + integrity sha512-yDNzckpM6ntyQiGTik1fKV1DcVDRS+w8bvpWNCBanvH5LfRX9O8WTHqQzG4RZwRAM4I0oU7TV11Lj5v0g20ibw== dependencies: - array.prototype.reduce "^1.0.4" + array.prototype.reduce "^1.0.5" call-bind "^1.0.2" define-properties "^1.1.4" - es-abstract "^1.20.1" + es-abstract "^1.20.4" -object.hasown@^1.1.1: - 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define-properties "^1.1.3" - es-abstract "^1.19.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" objectorarray@^1.0.5: version "1.0.5" @@ -15850,10 +15829,10 @@ p-all@^2.1.0: dependencies: p-map "^2.0.0" -p-cancelable@^1.0.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/p-cancelable/-/p-cancelable-1.1.0.tgz#d078d15a3af409220c886f1d9a0ca2e441ab26cc" - integrity sha512-s73XxOZ4zpt1edZYZzvhqFa6uvQc1vwUa0K0BdtIZgQMAJj9IbebH+JkgKZc9h+B05PKHLOTl4ajG1BmNrVZlw== +p-cancelable@^2.0.0: + version "2.1.1" + resolved "https://registry.yarnpkg.com/p-cancelable/-/p-cancelable-2.1.1.tgz#aab7fbd416582fa32a3db49859c122487c5ed2cf" + integrity sha512-BZOr3nRQHOntUjTrH8+Lh54smKHoHyur8We1V8DSMVrl5A2malOOwuJRnKRDjSnkoeBh4at6BwEnb5I7Jl31wg== p-defer@^1.0.0: version "1.0.0" @@ -16026,16 +16005,6 @@ pac-resolver@^5.0.0: ip "^1.1.5" netmask "^2.0.2" -package-json@^6.3.0: - version "6.5.0" - resolved "https://registry.yarnpkg.com/package-json/-/package-json-6.5.0.tgz#6feedaca35e75725876d0b0e64974697fed145b0" - integrity sha512-k3bdm2n25tkyxcjSKzB5x8kfVxlMdgsbPr0GkZcwHsLpba6cBjqCt1KlcChKEvxHIcTB1FVMuwoijZ26xex5MQ== - dependencies: - got "^9.6.0" - registry-auth-token "^4.0.0" - registry-url "^5.0.0" - semver "^6.2.0" - pacote@^13.0.3, pacote@^13.6.1: version "13.6.2" resolved "https://registry.yarnpkg.com/pacote/-/pacote-13.6.2.tgz#0d444ba3618ab3e5cd330b451c22967bbd0ca48a" @@ -16069,9 +16038,9 @@ pako@^1.0.10, pako@^1.0.11, pako@^1.0.4, pako@~1.0.5: integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw== pako@^2.0.0: - version "2.0.4" - resolved "https://registry.yarnpkg.com/pako/-/pako-2.0.4.tgz#6cebc4bbb0b6c73b0d5b8d7e8476e2b2fbea576d" - integrity sha512-v8tweI900AUkZN6heMU/4Uy4cXRc2AYNRggVmTR+dEncawDJgCdLMximOVA2p4qO57WMynangsfGRb5WD6L1Bg== + version "2.1.0" + resolved "https://registry.yarnpkg.com/pako/-/pako-2.1.0.tgz#266cc37f98c7d883545d11335c00fbd4062c9a86" + integrity sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug== parallel-transform@^1.1.0: version "1.2.0" @@ -16190,6 +16159,13 @@ parse5@^5.1.1: resolved "https://registry.yarnpkg.com/parse5/-/parse5-5.1.1.tgz#f68e4e5ba1852ac2cadc00f4555fff6c2abb6178" integrity sha512-ugq4DFI0Ptb+WWjAdOK16+u/nHfiIrcE+sh8kZMaM0WllQKLI9rOUq6c2b7cwPkXdzfQESqvoqK6ug7U/Yyzug== +parse5@^7.0.0, parse5@^7.1.1: + version "7.1.2" + resolved "https://registry.yarnpkg.com/parse5/-/parse5-7.1.2.tgz#0736bebbfd77793823240a23b7fc5e010b7f8e32" + integrity sha512-Czj1WaSVpaoj0wbhMzLmWD69anp2WH7FXMB9n1Sy8/ZFF9jolSQVMu1Ij5WIyGmcBmhk7EOndpO4mIpihVqAXw== + dependencies: + entities "^4.4.0" + parseurl@~1.3.2, parseurl@~1.3.3: version "1.3.3" resolved "https://registry.yarnpkg.com/parseurl/-/parseurl-1.3.3.tgz#9da19e7bee8d12dff0513ed5b76957793bc2e8d4" @@ -16517,12 +16493,12 @@ postcss-colormin@^5.3.0: colord "^2.9.1" postcss-value-parser "^4.2.0" -postcss-convert-values@^5.1.2: - version "5.1.2" - resolved "https://registry.yarnpkg.com/postcss-convert-values/-/postcss-convert-values-5.1.2.tgz#31586df4e184c2e8890e8b34a0b9355313f503ab" - integrity sha512-c6Hzc4GAv95B7suy4udszX9Zy4ETyMCgFPUDtWjdFTKH1SE9eFY/jEpHSwTH1QPuwxHpWslhckUQWbNRM4ho5g== +postcss-convert-values@^5.1.3: + version "5.1.3" + resolved "https://registry.yarnpkg.com/postcss-convert-values/-/postcss-convert-values-5.1.3.tgz#04998bb9ba6b65aa31035d669a6af342c5f9d393" + integrity sha512-82pC1xkJZtcJEfiLw6UXnXVXScgtBrjlO5CBmuDQc+dlb88ZYheFsjTn40+zBVi3DkfF7iezO0nJUPLcJK3pvA== dependencies: - browserslist "^4.20.3" + browserslist "^4.21.4" postcss-value-parser "^4.2.0" postcss-custom-media@^8.0.2: @@ -16532,10 +16508,10 @@ postcss-custom-media@^8.0.2: dependencies: postcss-value-parser "^4.2.0" -postcss-custom-properties@^12.1.9: - version "12.1.9" - resolved "https://registry.yarnpkg.com/postcss-custom-properties/-/postcss-custom-properties-12.1.9.tgz#0883429a7ef99f1ba239d1fea29ce84906daa8bd" - integrity sha512-/E7PRvK8DAVljBbeWrcEQJPG72jaImxF3vvCNFwv9cC8CzigVoNIpeyfnJzphnN3Fd8/auBf5wvkw6W9MfmTyg== +postcss-custom-properties@^12.1.10: + version "12.1.11" + resolved "https://registry.yarnpkg.com/postcss-custom-properties/-/postcss-custom-properties-12.1.11.tgz#d14bb9b3989ac4d40aaa0e110b43be67ac7845cf" + integrity sha512-0IDJYhgU8xDv1KY6+VgUwuQkVtmYzRwu+dMjnmdMafXYv86SWqfxkc7qdDvWS38vsjaEtv8e0vGOUQrAiMBLpQ== dependencies: postcss-value-parser "^4.2.0" @@ -16698,20 +16674,20 @@ postcss-media-minmax@^5.0.0: resolved "https://registry.yarnpkg.com/postcss-media-minmax/-/postcss-media-minmax-5.0.0.tgz#7140bddec173e2d6d657edbd8554a55794e2a5b5" integrity sha512-yDUvFf9QdFZTuCUg0g0uNSHVlJ5X1lSzDZjPSFaiCWvjgsvu8vEVxtahPrLMinIDEEGnx6cBe6iqdx5YWz08wQ== -postcss-merge-longhand@^5.1.6: - version "5.1.6" - resolved "https://registry.yarnpkg.com/postcss-merge-longhand/-/postcss-merge-longhand-5.1.6.tgz#f378a8a7e55766b7b644f48e5d8c789ed7ed51ce" - integrity sha512-6C/UGF/3T5OE2CEbOuX7iNO63dnvqhGZeUnKkDeifebY0XqkkvrctYSZurpNE902LDf2yKwwPFgotnfSoPhQiw== +postcss-merge-longhand@^5.1.7: + version "5.1.7" + resolved "https://registry.yarnpkg.com/postcss-merge-longhand/-/postcss-merge-longhand-5.1.7.tgz#24a1bdf402d9ef0e70f568f39bdc0344d568fb16" + integrity sha512-YCI9gZB+PLNskrK0BB3/2OzPnGhPkBEwmwhfYk1ilBHYVAZB7/tkTHFBAnCrvBBOmeYyMYw3DMjT55SyxMBzjQ== dependencies: postcss-value-parser "^4.2.0" - stylehacks "^5.1.0" + stylehacks "^5.1.1" -postcss-merge-rules@^5.1.2: - version "5.1.2" - resolved "https://registry.yarnpkg.com/postcss-merge-rules/-/postcss-merge-rules-5.1.2.tgz#7049a14d4211045412116d79b751def4484473a5" - integrity sha512-zKMUlnw+zYCWoPN6yhPjtcEdlJaMUZ0WyVcxTAmw3lkkN/NDMRkOkiuctQEoWAOvH7twaxUUdvBWl0d4+hifRQ== +postcss-merge-rules@^5.1.3: + version "5.1.3" + resolved "https://registry.yarnpkg.com/postcss-merge-rules/-/postcss-merge-rules-5.1.3.tgz#8f97679e67cc8d08677a6519afca41edf2220894" + integrity sha512-LbLd7uFC00vpOuMvyZop8+vvhnfRGpp2S+IMQKeuOZZapPRY4SMq5ErjQeHbHsjCUgJkRNrlU+LmxsKIqPKQlA== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" caniuse-api "^3.0.0" cssnano-utils "^3.1.0" postcss-selector-parser "^6.0.5" @@ -16732,12 +16708,12 @@ postcss-minify-gradients@^5.1.1: cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" -postcss-minify-params@^5.1.3: - version "5.1.3" - resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.3.tgz#ac41a6465be2db735099bbd1798d85079a6dc1f9" - integrity sha512-bkzpWcjykkqIujNL+EVEPOlLYi/eZ050oImVtHU7b4lFS82jPnsCb44gvC6pxaNt38Els3jWYDHTjHKf0koTgg== +postcss-minify-params@^5.1.4: + version "5.1.4" + resolved "https://registry.yarnpkg.com/postcss-minify-params/-/postcss-minify-params-5.1.4.tgz#c06a6c787128b3208b38c9364cfc40c8aa5d7352" + integrity sha512-+mePA3MgdmVmv6g+30rn57USjOGSAyuxUmkfiWpzalZ8aiBkdPYjXWtHuwJGm1v5Ojy0Z0LaSYhHaLJQB0P8Jw== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" cssnano-utils "^3.1.0" postcss-value-parser "^4.2.0" @@ -16809,12 +16785,12 @@ postcss-modules-values@^4.0.0: dependencies: icss-utils "^5.0.0" -postcss-nested@5.0.6: - version "5.0.6" - resolved "https://registry.yarnpkg.com/postcss-nested/-/postcss-nested-5.0.6.tgz#466343f7fc8d3d46af3e7dba3fcd47d052a945bc" - integrity sha512-rKqm2Fk0KbA8Vt3AdGN0FB9OBOMDVajMG6ZCf/GoHgdxUJ4sBFp0A/uMIRm+MJUdo33YXEtjqIz8u7DAp8B7DA== +postcss-nested@6.0.0: + version "6.0.0" + resolved "https://registry.yarnpkg.com/postcss-nested/-/postcss-nested-6.0.0.tgz#1572f1984736578f360cffc7eb7dca69e30d1735" + integrity sha512-0DkamqrPcmkBDsLn+vQDIrtkSbNkv5AD/M322ySo9kqFkCIYklym2xEmWkwo+Y3/qZo34tzEPNUw4y7yMCdv5w== dependencies: - postcss-selector-parser "^6.0.6" + postcss-selector-parser "^6.0.10" postcss-nesting@^10.2.0: version "10.2.0" @@ -16864,12 +16840,12 @@ postcss-normalize-timing-functions@^5.1.0: dependencies: postcss-value-parser "^4.2.0" -postcss-normalize-unicode@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/postcss-normalize-unicode/-/postcss-normalize-unicode-5.1.0.tgz#3d23aede35e160089a285e27bf715de11dc9db75" - integrity sha512-J6M3MizAAZ2dOdSjy2caayJLQT8E8K9XjLce8AUQMwOrCvjCHv24aLC/Lps1R1ylOfol5VIDMaM/Lo9NGlk1SQ== +postcss-normalize-unicode@^5.1.1: + version "5.1.1" + resolved "https://registry.yarnpkg.com/postcss-normalize-unicode/-/postcss-normalize-unicode-5.1.1.tgz#f67297fca3fea7f17e0d2caa40769afc487aa030" + integrity sha512-qnCL5jzkNUmKVhZoENp1mJiGNPcsJCs1aaRmURmeJGES23Z/ajaln+EPTD+rBeNkSryI+2WTdW+lwcVdOikrpA== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" postcss-value-parser "^4.2.0" postcss-normalize-url@^5.1.0: @@ -16897,9 +16873,9 @@ postcss-normalize@^10.0.1: sanitize.css "*" postcss-opacity-percentage@^1.1.2: - version "1.1.2" - resolved "https://registry.yarnpkg.com/postcss-opacity-percentage/-/postcss-opacity-percentage-1.1.2.tgz#bd698bb3670a0a27f6d657cc16744b3ebf3b1145" - integrity sha512-lyUfF7miG+yewZ8EAk9XUBIlrHyUE6fijnesuz+Mj5zrIHIEw6KcIZSOk/elVMqzLvREmXB83Zi/5QpNRYd47w== + version "1.1.3" + resolved "https://registry.yarnpkg.com/postcss-opacity-percentage/-/postcss-opacity-percentage-1.1.3.tgz#5b89b35551a556e20c5d23eb5260fbfcf5245da6" + integrity sha512-An6Ba4pHBiDtyVpSLymUUERMo2cU7s+Obz6BTrS+gxkbnSBNKSuD0AVUc+CpBMrpVPKKfoVz0WQCX+Tnst0i4A== postcss-ordered-values@^5.1.3: version "5.1.3" @@ -16929,11 +16905,11 @@ postcss-place@^7.0.5: postcss-value-parser "^4.2.0" postcss-preset-env@^7.0.1: - version "7.8.2" - resolved "https://registry.yarnpkg.com/postcss-preset-env/-/postcss-preset-env-7.8.2.tgz#4c834d5cbd2e29df2abf59118947c456922b79ba" - integrity sha512-rSMUEaOCnovKnwc5LvBDHUDzpGP+nrUeWZGWt9M72fBvckCi45JmnJigUr4QG4zZeOHmOCNCZnd2LKDvP++ZuQ== + version "7.8.3" + resolved "https://registry.yarnpkg.com/postcss-preset-env/-/postcss-preset-env-7.8.3.tgz#2a50f5e612c3149cc7af75634e202a5b2ad4f1e2" + integrity sha512-T1LgRm5uEVFSEF83vHZJV2z19lHg4yJuZ6gXZZkqVsqv63nlr6zabMH3l4Pc01FQCyfWVrh2GaUeCVy9Po+Aag== dependencies: - "@csstools/postcss-cascade-layers" "^1.1.0" + "@csstools/postcss-cascade-layers" "^1.1.1" "@csstools/postcss-color-function" "^1.1.1" "@csstools/postcss-font-format-keywords" "^1.0.1" "@csstools/postcss-hwb-function" "^1.0.2" @@ -16947,19 +16923,19 @@ postcss-preset-env@^7.0.1: "@csstools/postcss-text-decoration-shorthand" "^1.0.0" "@csstools/postcss-trigonometric-functions" "^1.0.2" "@csstools/postcss-unset-value" "^1.0.2" - autoprefixer "^10.4.11" - browserslist "^4.21.3" + autoprefixer "^10.4.13" + browserslist "^4.21.4" css-blank-pseudo "^3.0.3" css-has-pseudo "^3.0.4" css-prefers-color-scheme "^6.0.3" - cssdb "^7.0.1" + cssdb "^7.1.0" postcss-attribute-case-insensitive "^5.0.2" postcss-clamp "^4.1.0" postcss-color-functional-notation "^4.2.4" postcss-color-hex-alpha "^8.0.4" postcss-color-rebeccapurple "^7.1.1" postcss-custom-media "^8.0.2" - postcss-custom-properties "^12.1.9" + postcss-custom-properties "^12.1.10" postcss-custom-selectors "^6.0.3" postcss-dir-pseudo-class "^6.0.5" postcss-double-position-gradients "^3.1.2" @@ -16990,12 +16966,12 @@ postcss-pseudo-class-any-link@^7.1.6: dependencies: postcss-selector-parser "^6.0.10" -postcss-reduce-initial@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/postcss-reduce-initial/-/postcss-reduce-initial-5.1.0.tgz#fc31659ea6e85c492fb2a7b545370c215822c5d6" - integrity sha512-5OgTUviz0aeH6MtBjHfbr57tml13PuedK/Ecg8szzd4XRMbYxH4572JFG067z+FqBIf6Zp/d+0581glkvvWMFw== +postcss-reduce-initial@^5.1.1: + version "5.1.1" + resolved "https://registry.yarnpkg.com/postcss-reduce-initial/-/postcss-reduce-initial-5.1.1.tgz#c18b7dfb88aee24b1f8e4936541c29adbd35224e" + integrity sha512-//jeDqWcHPuXGZLoolFrUXBDyuEGbr9S2rMo19bkTIjBQ4PqkaO+oI8wua5BOUxpfi97i3PCoInsiFIEBfkm9w== dependencies: - browserslist "^4.16.6" + browserslist "^4.21.4" caniuse-api "^3.0.0" postcss-reduce-transforms@^5.1.0: @@ -17017,10 +16993,10 @@ postcss-selector-not@^6.0.1: dependencies: postcss-selector-parser "^6.0.10" -postcss-selector-parser@^6.0.0, postcss-selector-parser@^6.0.10, postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4, postcss-selector-parser@^6.0.5, postcss-selector-parser@^6.0.6, postcss-selector-parser@^6.0.9: - version "6.0.10" - resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-6.0.10.tgz#79b61e2c0d1bfc2602d549e11d0876256f8df88d" - integrity sha512-IQ7TZdoaqbT+LCpShg46jnZVlhWD2w6iQYAcYXfHARZ7X1t/UGhhceQDs5X0cGqKvYlHNOuv7Oa1xmb0oQuA3w== +postcss-selector-parser@^6.0.0, postcss-selector-parser@^6.0.10, postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4, postcss-selector-parser@^6.0.5, postcss-selector-parser@^6.0.9: + version "6.0.11" + resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-6.0.11.tgz#2e41dc39b7ad74046e1615185185cd0b17d0c8dc" + integrity sha512-zbARubNdogI9j7WY4nQJBiNqQf3sLS3wCP4WfOidu+p28LofJqDH1tcXypGrcmMHhDk2t9wGhCsYe/+szLTy1g== dependencies: cssesc "^3.0.0" util-deprecate "^1.0.2" @@ -17053,10 +17029,10 @@ postcss@^7.0.14, postcss@^7.0.26, postcss@^7.0.32, postcss@^7.0.35, postcss@^7.0 picocolors "^0.2.1" source-map "^0.6.1" -postcss@^8.2.15, postcss@^8.3.5, postcss@^8.4.14, postcss@^8.4.4, postcss@^8.4.7: - version "8.4.17" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.17.tgz#f87863ec7cd353f81f7ab2dec5d67d861bbb1be5" - integrity sha512-UNxNOLQydcOFi41yHNMcKRZ39NeXlr8AxGuZJsdub8vIb12fHzcq37DTU/QtbI6WLxNg2gF9Z+8qtRwTj1UI1Q== +postcss@^8.2.15, postcss@^8.3.5, postcss@^8.4.18, postcss@^8.4.19, postcss@^8.4.4: + version "8.4.20" + resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.20.tgz#64c52f509644cecad8567e949f4081d98349dc56" + integrity sha512-6Q04AXR1212bXr5fh03u8aAwbLxAQNGQ/Q1LNa0VfOI06ZAlhPHtQvE4OIdpj4kLThXilalPnmDSOD65DcHt+g== dependencies: nanoid "^3.3.4" picocolors "^1.0.0" @@ -17072,11 +17048,6 @@ prelude-ls@~1.1.2: resolved "https://registry.yarnpkg.com/prelude-ls/-/prelude-ls-1.1.2.tgz#21932a549f5e52ffd9a827f570e04be62a97da54" integrity sha512-ESF23V4SKG6lVSGZgYNpbsiaAkdab6ZgOxe52p7+Kid3W3u3bxR4Vfd/o21dmN7jSt0IwgZ4v5MUd26FEtXE9w== -prepend-http@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/prepend-http/-/prepend-http-2.0.0.tgz#e92434bfa5ea8c19f41cdfd401d741a3c819d897" - integrity sha512-ravE6m9Atw9Z/jjttRUZ+clIXogdghyZAuWJ3qEzjT+jI/dL1ifAqhZeC5VHzQp1MSt1+jxKkFNemj/iO7tVUA== - prettier-linter-helpers@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/prettier-linter-helpers/-/prettier-linter-helpers-1.0.0.tgz#d23d41fe1375646de2d0104d3454a3008802cf7b" @@ -17090,9 +17061,9 @@ prettier-linter-helpers@^1.0.0: integrity sha512-kXtO4s0Lz/DW/IJ9QdWhAf7/NmPWQXkFr/r/WkR3vyI+0v8amTDxiaQSLzs8NBlytfLWX/7uQUMIW677yLKl4w== prettier@^2.5.1: - version "2.7.1" - resolved "https://registry.yarnpkg.com/prettier/-/prettier-2.7.1.tgz#e235806850d057f97bb08368a4f7d899f7760c64" - integrity sha512-ujppO+MkdPqoVINuDFDRLClm7D78qbDt0/NR+wp5FqEZOoTNAjPHWj17QRhu7geIHJfcNhRk1XVQmF8Bp3ye+g== + version "2.8.1" + resolved "https://registry.yarnpkg.com/prettier/-/prettier-2.8.1.tgz#4e1fd11c34e2421bc1da9aea9bd8127cd0a35efc" + integrity sha512-lqGoSJBQNJidqCHE80vqZJHWHRFoNYsSpP9AjFhlhi9ODCJA541svILes/+/1GM3VaL/abZi7cpFzOpdR9UPKg== pretty-bytes@^5.3.0, pretty-bytes@^5.4.1: version "5.6.0" @@ -17115,16 +17086,6 @@ pretty-error@^4.0.0: lodash "^4.17.20" renderkid "^3.0.0" -pretty-format@^25.2.1, pretty-format@^25.5.0: - version "25.5.0" - resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-25.5.0.tgz#7873c1d774f682c34b8d48b6743a2bf2ac55791a" - integrity sha512-kbo/kq2LQ/A/is0PQwsEHM7Ca6//bGPPvU6UnsdDRSKTWxT/ru/xb88v4BJf6a69H+uTytOEsTusT9ksd/1iWQ== - dependencies: - "@jest/types" "^25.5.0" - ansi-regex "^5.0.0" - ansi-styles "^4.0.0" - react-is "^16.12.0" - pretty-format@^27.0.2, pretty-format@^27.5.1: version "27.5.1" resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-27.5.1.tgz#2181879fdea51a7a5851fb39d920faa63f01d88e" @@ -17144,10 +17105,10 @@ pretty-format@^28.1.3: ansi-styles "^5.0.0" react-is "^18.0.0" -pretty-format@^29.0.0, pretty-format@^29.1.2: - version "29.1.2" - resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-29.1.2.tgz#b1f6b75be7d699be1a051f5da36e8ae9e76a8e6a" - integrity sha512-CGJ6VVGXVRP2o2Dorl4mAwwvDWT25luIsYhkyVQW32E4nL+TgW939J7LlKT/npq5Cpq6j3s+sy+13yk7xYpBmg== +pretty-format@^29.0.0, pretty-format@^29.3.1: + version "29.3.1" + resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-29.3.1.tgz#1841cac822b02b4da8971dacb03e8a871b4722da" + integrity sha512-FyLnmb1cYJV8biEIiRyzRFvs2lry7PPIvOqKVe1GCUEYg4YGmlx1qG9EJNMxArYm7piII4qb8UV1Pncq5dxmcg== dependencies: "@jest/schemas" "^29.0.0" ansi-styles "^5.0.0" @@ -17207,30 +17168,30 @@ promise-retry@^2.0.1: retry "^0.12.0" promise.allsettled@^1.0.0: - version "1.0.5" - resolved "https://registry.yarnpkg.com/promise.allsettled/-/promise.allsettled-1.0.5.tgz#2443f3d4b2aa8dfa560f6ac2aa6c4ea999d75f53" - integrity sha512-tVDqeZPoBC0SlzJHzWGZ2NKAguVq2oiYj7gbggbiTvH2itHohijTp7njOUA0aQ/nl+0lr/r6egmhoYu63UZ/pQ== + version "1.0.6" + resolved "https://registry.yarnpkg.com/promise.allsettled/-/promise.allsettled-1.0.6.tgz#8dc8ba8edf429feb60f8e81335b920e109c94b6e" + integrity sha512-22wJUOD3zswWFqgwjNHa1965LvqTX87WPu/lreY2KSd7SVcERfuZ4GfUaOnJNnvtoIv2yXT/W00YIGMetXtFXg== dependencies: - array.prototype.map "^1.0.4" + array.prototype.map "^1.0.5" call-bind "^1.0.2" - define-properties "^1.1.3" - es-abstract "^1.19.1" - get-intrinsic "^1.1.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" + get-intrinsic "^1.1.3" iterate-value "^1.0.2" promise.prototype.finally@^3.1.0: - version "3.1.3" - resolved "https://registry.yarnpkg.com/promise.prototype.finally/-/promise.prototype.finally-3.1.3.tgz#d3186e58fcf4df1682a150f934ccc27b7893389c" - integrity sha512-EXRF3fC9/0gz4qkt/f5EP5iW4kj9oFpBICNpCNOb/52+8nlHIX07FPLbi/q4qYBQ1xZqivMzTpNQSnArVASolQ== + version "3.1.4" + resolved "https://registry.yarnpkg.com/promise.prototype.finally/-/promise.prototype.finally-3.1.4.tgz#4e756a154e4db27fae24c6b18703495c31da3927" + integrity sha512-nNc3YbgMfLzqtqvO/q5DP6RR0SiHI9pUPGzyDf1q+usTwCN2kjvAnJkBb7bHe3o+fFSBPpsGMoYtaSi+LTNqng== dependencies: call-bind "^1.0.2" - define-properties "^1.1.3" - es-abstract "^1.19.1" + define-properties "^1.1.4" + es-abstract "^1.20.4" promise@^8.1.0: - version "8.2.0" - resolved "https://registry.yarnpkg.com/promise/-/promise-8.2.0.tgz#a1f6280ab67457fbfc8aad2b198c9497e9e5c806" - integrity sha512-+CMAlLHqwRYwBMXKCP+o8ns7DN+xHDUiI+0nArsiJ9y+kJVPLFxEaSw6Ha9s9H0tftxg2Yzl25wqj9G7m5wLZg== + version "8.3.0" + resolved "https://registry.yarnpkg.com/promise/-/promise-8.3.0.tgz#8cb333d1edeb61ef23869fbb8a4ea0279ab60e0a" + integrity sha512-rZPNPKTOYVNEEKFaq1HqTgOwZD+4/YHS5ukLzQCypkj+OkYx7iv0mA91lJlpPPZ8vMau3IIGj5Qlwrx+8iiSmg== dependencies: asap "~2.0.6" @@ -17302,7 +17263,7 @@ proxy-agent@^5.0.0: proxy-from-env "^1.0.0" socks-proxy-agent "^5.0.0" -proxy-from-env@^1.0.0: +proxy-from-env@^1.0.0, proxy-from-env@^1.1.0: version "1.1.0" resolved "https://registry.yarnpkg.com/proxy-from-env/-/proxy-from-env-1.1.0.tgz#e102f16ca355424865755d2c9e8ea4f24d58c3e2" integrity sha512-D+zkORCbA9f1tdWRK0RaCR3GPv50cMxcrz4X8k5LTSUD1Dkw47mKJEZQNunItRTkWwgtaUSo1RVFRIG9ZXiFYg== @@ -17369,13 +17330,6 @@ punycode@^2.1.0, punycode@^2.1.1: resolved "https://registry.yarnpkg.com/punycode/-/punycode-2.1.1.tgz#b58b010ac40c22c5657616c8d2c2c02c7bf479ec" integrity sha512-XRsRjdf+j5ml+y/6GKHPZbrF/8p2Yga0JPtdqTIY2Xe5ohJPD9saDJJLPvp9+NSBprVvevdXZybnj2cv8OEd0A== -pupa@^2.1.1: - version "2.1.1" - resolved "https://registry.yarnpkg.com/pupa/-/pupa-2.1.1.tgz#f5e8fd4afc2c5d97828faa523549ed8744a20d62" - integrity sha512-l1jNAspIBSFqbT+y+5FosojNpVpF94nlI+wDUpqP9enwOTfHx9f0gh5nB96vl+6yTpsJsypeNrwfzPrKuHB41A== - dependencies: - escape-goat "^2.0.0" - q@^1.1.2, q@^1.5.1: version "1.5.1" resolved "https://registry.yarnpkg.com/q/-/q-1.5.1.tgz#7e32f75b41381291d04611f1bf14109ac00651d7" @@ -17400,14 +17354,7 @@ qqjs@^0.3.10: tmp "^0.1.0" write-json-file "^4.1.1" -qs@6.10.3: - version "6.10.3" - resolved "https://registry.yarnpkg.com/qs/-/qs-6.10.3.tgz#d6cde1b2ffca87b5aa57889816c5f81535e22e8e" - integrity sha512-wr7M2E0OFRfIfJZjKGieI8lBKb7fRCH4Fv5KNPEs7gJ8jadvotdsS08PzOKR7opXhZ/Xkjtt3WF9g38drmyRqQ== - dependencies: - side-channel "^1.0.4" - -qs@^6.10.0: +qs@6.11.0, qs@^6.10.0: version "6.11.0" resolved "https://registry.yarnpkg.com/qs/-/qs-6.11.0.tgz#fd0d963446f7a65e1367e01abd85429453f0c37a" integrity sha512-MvjoMCJwEarSbUYk5O+nmoSzSutSsTwF85zcHPQ9OrlFoZOYIjaqBAJIqIXjptyD5vThxGq52Xu/MaJzRkIk4Q== @@ -17511,16 +17458,6 @@ rbush@^3.0.1: dependencies: quickselect "^2.0.0" -rc@1.2.8, rc@^1.2.8: - version "1.2.8" - resolved "https://registry.yarnpkg.com/rc/-/rc-1.2.8.tgz#cd924bf5200a075b83c188cd6b9e211b7fc0d3ed" - integrity sha512-y3bGgqKj3QBdxLbLkomlohkvsA8gdAiUQlSBJnBhfn+BPxg4bc62d8TcBW15wavDfgexCgccckhcZvywyQYPOw== - dependencies: - deep-extend "^0.6.0" - ini "~1.3.0" - minimist "^1.2.0" - strip-json-comments "~2.0.1" - react-app-polyfill@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/react-app-polyfill/-/react-app-polyfill-3.0.0.tgz#95221e0a9bd259e5ca6b177c7bb1cb6768f68fd7" @@ -17607,9 +17544,9 @@ react-draggable@^4.4.5: prop-types "^15.8.1" react-dropzone@^14.2.1: - version "14.2.2" - resolved "https://registry.yarnpkg.com/react-dropzone/-/react-dropzone-14.2.2.tgz#a75a0676055fe9e2cb78578df4dedb4c42b54f98" - integrity sha512-5oyGN/B5rNhop2ggUnxztXBQ6q6zii+OMEftPzsxAR2hhpVWz0nAV+3Ktxo2h5bZzdcCKrpd8bfWAVsveIBM+w== + version "14.2.3" + resolved "https://registry.yarnpkg.com/react-dropzone/-/react-dropzone-14.2.3.tgz#0acab68308fda2d54d1273a1e626264e13d4e84b" + integrity sha512-O3om8I+PkFKbxCukfIR3QAGftYXDZfOE2N1mr/7qebQJHs7U+/RSL/9xomJNpRg9kM5h9soQSdf0Gc7OHF5Fug== dependencies: attr-accept "^2.2.2" file-selector "^0.6.0" @@ -17655,7 +17592,7 @@ react-is@17.0.2, react-is@^17.0.1: resolved "https://registry.yarnpkg.com/react-is/-/react-is-17.0.2.tgz#e691d4a8e9c789365655539ab372762b0efb54f0" integrity sha512-w2GsyukL62IJnlaff/nRegPQR94C/XXamvMWmSHRJ4y7Ts/4ocGRmTHvOs8PSE6pB3dWOrD/nueuU5sduBsQ4w== -react-is@^16.12.0, react-is@^16.13.1, react-is@^16.7.0: +react-is@^16.13.1, react-is@^16.7.0: version "16.13.1" resolved "https://registry.yarnpkg.com/react-is/-/react-is-16.13.1.tgz#789729a4dc36de2999dc156dd6c1d9c18cea56a4" integrity sha512-24e6ynE2H+OKt4kqsOvNd8kBpV65zoxbA4BVsEOB3ARVWQki/DHzaUoC5KuON/BiccDaCCTZBuOcfZs70kR8bQ== @@ -17774,9 +17711,9 @@ react-vtree@^3.0.0-beta.1: react-merge-refs "^1.1.0" react-window@^1.8.6: - version "1.8.7" - resolved "https://registry.yarnpkg.com/react-window/-/react-window-1.8.7.tgz#5e9fd0d23f48f432d7022cdb327219353a15f0d4" - integrity sha512-JHEZbPXBpKMmoNO1bNhoXOOLg/ujhL/BU4IqVU9r8eQPcy5KQnGHIHDRkJ0ns9IM5+Aq5LNwt3j8t3tIrePQzA== + version "1.8.8" + resolved "https://registry.yarnpkg.com/react-window/-/react-window-1.8.8.tgz#1b52919f009ddf91970cbdb2050a6c7be44df243" + integrity sha512-D4IiBeRtGXziZ1n0XklnFGu7h9gU684zepqyKzgPNzrsrk7xOCxni+TCckjg2Nr/DiaEEGVVmnhYSlT2rB47dQ== dependencies: "@babel/runtime" "^7.0.0" memoize-one ">=3.1.1 <6" @@ -17922,6 +17859,16 @@ readable-stream@3, readable-stream@^3.0.0, readable-stream@^3.0.2, readable-stre string_decoder "^1.1.1" util-deprecate "^1.0.1" +readable-stream@^4.0.0: + version "4.2.0" + resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-4.2.0.tgz#a7ef523d3b39e4962b0db1a1af22777b10eeca46" + integrity sha512-gJrBHsaI3lgBoGMW/jHZsQ/o/TIWiu5ENCJG1BB7fuCKzpFM8GaS2UoBVt9NO+oI+3FcrBNbUkl3ilDe09aY4A== + dependencies: + abort-controller "^3.0.0" + buffer "^6.0.3" + events "^3.3.0" + process "^0.11.10" + readdir-scoped-modules@^1.1.0: version "1.1.0" resolved "https://registry.yarnpkg.com/readdir-scoped-modules/-/readdir-scoped-modules-1.1.0.tgz#8d45407b4f870a0dcaebc0e28670d18e74514309" @@ -17948,19 +17895,19 @@ readdirp@~3.6.0: dependencies: picomatch "^2.2.1" -rechoir@^0.7.0: - 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-webpack-merge@^5.7.3: +webpack-merge@^5.7.3, webpack-merge@^5.8.0: version "5.8.0" resolved "https://registry.yarnpkg.com/webpack-merge/-/webpack-merge-5.8.0.tgz#2b39dbf22af87776ad744c390223731d30a68f61" integrity sha512-/SaI7xY0831XwP6kzuwhKWVKDP9t1QY1h65lAFLbZqMPIuYcD9QAW4u9STIbU9kaJbPBB/geU/gLr1wDjOhQ+Q== @@ -21011,9 +20903,9 @@ webpack-virtual-modules@^0.2.2: debug "^3.0.0" webpack-virtual-modules@^0.4.1: - version "0.4.5" - resolved "https://registry.yarnpkg.com/webpack-virtual-modules/-/webpack-virtual-modules-0.4.5.tgz#e476842dab5eafb7beb844aa2f747fc12ebbf6ec" - integrity sha512-8bWq0Iluiv9lVf9YaqWQ9+liNgXSHICm+rg544yRgGYaR8yXZTVBaHZkINZSB2yZSWo4b0F6MIxqJezVfOEAlg== + version "0.4.6" + resolved "https://registry.yarnpkg.com/webpack-virtual-modules/-/webpack-virtual-modules-0.4.6.tgz#3e4008230731f1db078d9cb6f68baf8571182b45" + integrity sha512-5tyDlKLqPfMqjT3Q9TAqf2YqjwmnUleZwzJi1A5qXnlBCdj2AtOJ6wAWdglTIDOPgOiOrXeBeFcsQ8+aGQ6QbA== webpack@4: version "4.46.0" @@ -21044,10 +20936,10 @@ webpack@4: watchpack "^1.7.4" webpack-sources "^1.4.1" -"webpack@>=4.43.0 <6.0.0", webpack@^5.64.4, webpack@^5.72.0, webpack@^5.9.0: - version "5.74.0" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.74.0.tgz#02a5dac19a17e0bb47093f2be67c695102a55980" - integrity sha512-A2InDwnhhGN4LYctJj6M1JEaGL7Luj6LOmyBHjcI8529cm5p6VXiTIW2sn6ffvEAKmveLzvu4jrihwXtPojlAA== +"webpack@>=4.43.0 <6.0.0", webpack@^5.0.0, webpack@^5.64.4, webpack@^5.72.0, webpack@^5.9.0: + version "5.75.0" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.75.0.tgz#1e440468647b2505860e94c9ff3e44d5b582c152" + integrity sha512-piaIaoVJlqMsPtX/+3KTTO6jfvrSYgauFVdt8cr9LTHKmcq/AMd4mhzsiP7ZF/PGRNPGA8336jldh9l2Kt2ogQ== dependencies: "@types/eslint-scope" "^3.7.3" "@types/estree" "^0.0.51" @@ -21117,14 +21009,6 @@ whatwg-mimetype@^3.0.0: resolved "https://registry.yarnpkg.com/whatwg-mimetype/-/whatwg-mimetype-3.0.0.tgz#5fa1a7623867ff1af6ca3dc72ad6b8a4208beba7" integrity sha512-nt+N2dzIutVRxARx1nghPKGv1xHikU7HKdfafKkLNLindmPU/ch3U31NOCGGA/dmPcmb1VlofO0vnKAcsm0o/Q== -whatwg-url@^10.0.0: - version "10.0.0" - resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-10.0.0.tgz#37264f720b575b4a311bd4094ed8c760caaa05da" - integrity sha512-CLxxCmdUby142H5FZzn4D8ikO1cmypvXVQktsgosNy4a4BHrDHeciBBGZhb0bNoR5/MltoCatso+vFjjGx8t0w== - dependencies: - tr46 "^3.0.0" - webidl-conversions "^7.0.0" - whatwg-url@^11.0.0: version "11.0.0" resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-11.0.0.tgz#0a849eebb5faf2119b901bb76fd795c2848d4018" @@ -21170,17 +21054,27 @@ which-boxed-primitive@^1.0.2: is-string "^1.0.5" is-symbol "^1.0.3" -which-typed-array@^1.1.2: - version "1.1.8" - resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.8.tgz#0cfd53401a6f334d90ed1125754a42ed663eb01f" - integrity sha512-Jn4e5PItbcAHyLoRDwvPj1ypu27DJbtdYXUa5zsinrUx77Uvfb0cXwwnGMTn7cjUfhhqgVQnVJCwF+7cgU7tpw== +which-collection@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/which-collection/-/which-collection-1.0.1.tgz#70eab71ebbbd2aefaf32f917082fc62cdcb70906" + integrity sha512-W8xeTUwaln8i3K/cY1nGXzdnVZlidBcagyNFtBdD5kxnb4TvGKR7FfSIS3mYpwWS1QUCutfKz8IY8RjftB0+1A== + dependencies: + is-map "^2.0.1" + is-set "^2.0.1" + is-weakmap "^2.0.1" + is-weakset "^2.0.1" + +which-typed-array@^1.1.2, which-typed-array@^1.1.8: + version "1.1.9" + resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.9.tgz#307cf898025848cf995e795e8423c7f337efbde6" + integrity sha512-w9c4xkx6mPidwp7180ckYWfMmvxpjlZuIudNtDf4N/tTAUB8VJbX25qZoAsrtGuYNnGw3pa0AXgbGKRB8/EceA== dependencies: available-typed-arrays "^1.0.5" call-bind "^1.0.2" - es-abstract "^1.20.0" for-each "^0.3.3" + gopd "^1.0.1" has-tostringtag "^1.0.0" - is-typed-array "^1.1.9" + is-typed-array "^1.1.10" which@^1.2.9, which@^1.3.1: version "1.3.1" @@ -21501,10 +21395,10 @@ ws@^7.4.6: resolved "https://registry.yarnpkg.com/ws/-/ws-7.5.9.tgz#54fa7db29f4c7cec68b1ddd3a89de099942bb591" integrity sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q== -ws@^8.2.3, ws@^8.4.2: - version "8.9.0" - resolved "https://registry.yarnpkg.com/ws/-/ws-8.9.0.tgz#2a994bb67144be1b53fe2d23c53c028adeb7f45e" - integrity sha512-Ja7nszREasGaYUYCI2k4lCKIRTt+y7XuqVoHR44YpI49TtryyqbqvDMn5eqfW7e6HzTukDRIsXqzVHScqRcafg== +ws@^8.11.0, ws@^8.2.3, ws@^8.4.2: + version "8.11.0" + resolved "https://registry.yarnpkg.com/ws/-/ws-8.11.0.tgz#6a0d36b8edfd9f96d8b25683db2f8d7de6e8e143" + integrity sha512-HPG3wQd9sNQoT9xHyNCXoDUa+Xw/VevmY9FoHyQ+g+rrMn4j6FB4np7Z0OhdTgjx6MgQLK7jwSy1YecU1+4Asg== x-default-browser@^0.4.0: version "0.4.0" @@ -21513,11 +21407,6 @@ x-default-browser@^0.4.0: optionalDependencies: default-browser-id "^1.0.4" -xdg-basedir@^4.0.0: - version "4.0.0" - resolved "https://registry.yarnpkg.com/xdg-basedir/-/xdg-basedir-4.0.0.tgz#4bc8d9984403696225ef83a1573cbbcb4e79db13" - integrity sha512-PSNhEJDejZYV7h50BohL09Er9VaIefr2LMAf3OEmpCkjOi34eYyQYAXUTjEQtZJTKcF0E2UKTh+osDLsgNim9Q== - xml-name-validator@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/xml-name-validator/-/xml-name-validator-3.0.0.tgz#6ae73e06de4d8c6e47f9fb181f78d648ad457c6a" @@ -21578,21 +21467,16 @@ yargs-parser@20.2.4: resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-20.2.4.tgz#b42890f14566796f85ae8e3a25290d205f154a54" integrity sha512-WOkpgNhPTlE73h4VFAFsOnomJVaovO8VqLDzy5saChRBFQFBoMYirowyW+Q9HB4HFF4Z7VZTiG3iSzJJA29yRA== -yargs-parser@21.0.1: - version "21.0.1" - resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.0.1.tgz#0267f286c877a4f0f728fceb6f8a3e4cb95c6e35" - integrity sha512-9BK1jFpLzJROCI5TzwZL/TU4gqjK5xiHV/RfWLOahrjAko/e4DJkRDZQXfvqAsiZzzYhgAzbgz6lg48jcm4GLg== +yargs-parser@21.1.1, yargs-parser@^21.1.1: + version "21.1.1" + resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" + integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== yargs-parser@^20.2.2, yargs-parser@^20.2.3, yargs-parser@^20.2.9: version "20.2.9" resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-20.2.9.tgz#2eb7dc3b0289718fc295f362753845c41a0c94ee" integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w== -yargs-parser@^21.0.0: - version "21.1.1" - resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" - integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== - yargs@^16.0.0, yargs@^16.2.0: version "16.2.0" resolved "https://registry.yarnpkg.com/yargs/-/yargs-16.2.0.tgz#1c82bf0f6b6a66eafce7ef30e376f49a12477f66" @@ -21606,10 +21490,10 @@ yargs@^16.0.0, yargs@^16.2.0: y18n "^5.0.5" yargs-parser "^20.2.2" -yargs@^17.0.1, yargs@^17.1.0, yargs@^17.3.0, yargs@^17.3.1, yargs@^17.4.0: - version "17.6.0" - resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.6.0.tgz#e134900fc1f218bc230192bdec06a0a5f973e46c" - integrity sha512-8H/wTDqlSwoSnScvV2N/JHfLWOKuh5MVla9hqLjK3nsfyy6Y4kDSYSvkU5YCUEPOSnRXfIyx3Sq+B/IWudTo4g== +yargs@^17.1.0, yargs@^17.3.0, yargs@^17.3.1, yargs@^17.5.1, yargs@^17.6.2: + version "17.6.2" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.6.2.tgz#2e23f2944e976339a1ee00f18c77fedee8332541" + integrity sha512-1/9UrdHjDZc0eOU0HxOHoS78C69UD3JRMvzlJ7S79S2nTaWRA/whGCTV8o9e/N/1Va9YIV7Q4sOxD8VV4pCWOw== dependencies: cliui "^8.0.1" escalade "^3.1.1" @@ -21617,7 +21501,7 @@ yargs@^17.0.1, yargs@^17.1.0, yargs@^17.3.0, yargs@^17.3.1, yargs@^17.4.0: require-directory "^2.1.1" string-width "^4.2.3" y18n "^5.0.5" - yargs-parser "^21.0.0" + yargs-parser "^21.1.1" yauzl@^2.10.0: version "2.10.0"