Add some statusCallback to VcfTabixAdapter

plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -1,7 +1,7 @@
 import { TabixIndexedFile } from '@gmod/tabix'
 import VcfParser from '@gmod/vcf'
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { fetchAndMaybeUnzipText } from '@jbrowse/core/util'
+import { fetchAndMaybeUnzipText, updateStatus } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 
@@ -17,22 +17,28 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     parser: VcfParser
   }>
 
-  private async configurePre() {
-    const pm = this.pluginManager
+  private async configurePre(opts?: BaseOptions) {
+    const { statusCallback = () => {} } = opts || {}
     const vcfGzLocation = this.getConf('vcfGzLocation')
     const location = this.getConf(['index', 'location'])
     const indexType = this.getConf(['index', 'indexType'])
 
-    const filehandle = openLocation(vcfGzLocation, pm)
+    const filehandle = openLocation(vcfGzLocation, this.pluginManager)
     const isCSI = indexType === 'CSI'
     const vcf = new TabixIndexedFile({
       filehandle,
-      csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
-      tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
+      csiFilehandle: isCSI
+        ? openLocation(location, this.pluginManager)
+        : undefined,
+      tbiFilehandle: !isCSI
+        ? openLocation(location, this.pluginManager)
+        : undefined,
       chunkCacheSize: 50 * 2 ** 20,
     })
 
-    const header = await vcf.getHeader()
+    const header = await updateStatus('Downloading index', statusCallback, () =>
+      vcf.getHeader(),
+    )
     return {
       vcf,
       parser: new VcfParser({ header }),
@@ -67,19 +73,23 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
   public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
       const { refName, start, end } = query
+      const { statusCallback = () => {} } = opts || {}
       const { vcf, parser } = await this.configure()
-      await vcf.getLines(refName, start, end, {
-        lineCallback: (line, fileOffset) => {
-          observer.next(
-            new VcfFeature({
-              variant: parser.parseLine(line),
-              parser,
-              id: `${this.id}-vcf-${fileOffset}`,
-            }),
-          )
-        },
-        ...opts,
-      })
+
+      await updateStatus('Downloading variants', statusCallback, () =>
+        vcf.getLines(refName, start, end, {
+          lineCallback: (line, fileOffset) => {
+            observer.next(
+              new VcfFeature({
+                variant: parser.parseLine(line),
+                parser,
+                id: `${this.id}-vcf-${fileOffset}`,
+              }),
+            )
+          },
+          ...opts,
+        }),
+      )
       observer.complete()
     }, opts.stopToken)
   }