lack of Consequence bug

sigven · Nov 15, 2017 · 6975f57 · 6975f57
1 parent 6651f30
commit 6975f57
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/src/R/pcgrr/R/utils.R b/src/R/pcgrr/R/utils.R
@@ -1350,8 +1350,8 @@ get_calls <- function(vcf_gz_file, pcgr_data, sample_id = NULL, tumor_dp_tag = '
     vcf_data_df[!is.na(vcf_data_df$PROTEIN_CHANGE) & stringr::str_detect(vcf_data_df$PROTEIN_CHANGE,"^ENSP"),]$PROTEIN_CHANGE <- NA
   }
   vcf_data_df$CODING_STATUS <- 'noncoding'
-  if(nrow(vcf_data_df[stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]) > 0){
-    vcf_data_df[stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]$CODING_STATUS <- 'coding'
+  if(nrow(vcf_data_df[!is.na(vcf_data_df$CONSEQUENCE) & stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]) > 0){
+    vcf_data_df[!is.na(vcf_data_df$CONSEQUENCE) & stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]$CODING_STATUS <- 'coding'
   }
 
   for(col in c('width','strand','totalDepth','refDepth','altDepth','sampleNames')){

diff --git a/src/pcgr.tgz b/src/pcgr.tgz