chrM fusions removed by default

Oshlack · Apr 21, 2021 · 3cd61a2 · 3cd61a2
1 parent 2a9ea18
commit 3cd61a2
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/compile_results.R b/compile_results.R
@@ -30,8 +30,6 @@ for(i in 1:length(dir)){
       single_list$sample<-rep(dir[i],length(single_list$transcript))
       #rearrange
       n=dim(single_list)[2]
-      show(n)
-      show(summary_files[i])
       full_list<-rbind(full_list,single_list)
 }
 colnames(full_list)<-gsub("_"," ",colnames(full_list))

diff --git a/make_final_table.R b/make_final_table.R
@@ -39,7 +39,7 @@ REGGAP=200 #fusions with less than this kb gap and no rearanngments will be flag
 TRAN_GAP_MAX=30 #gaps in the blat alignment which are smaller that this will be adjusted for by widening the block size.
 MIN_LOW_SPANNING_READS=2 #LowConfidence calls with less than this many spanning reads will be remove
 REMOVE_ALT=TRUE
-REMOVE_CHRM=FALSE #TRUE
+REMOVE_CHRM=TRUE
 
 #load all the input files to data.frames
 fusion_info<-read.delim(fusion_info_file,stringsAsFactors=F)