chrM fusions removed by default

Nadia Davidson · Nadia Davidson · commit 3cd61a2f2a6c · 2021-04-22T09:32:22.000+10:00
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)

Original file line number	Diff line number	Diff line change
`@@ -30,8 +30,6 @@ for(i in 1:length(dir)){`
`30`	`30`	`single_list$sample<-rep(dir[i],length(single_list$transcript))`
`31`	`31`	`#rearrange`
`32`	`32`	`n=dim(single_list)[2]`
`33`		`- show(n)`
`34`		`- show(summary_files[i])`
`35`	`33`	`full_list<-rbind(full_list,single_list)`
`36`	`34`	`}`
`37`	`35`	`colnames(full_list)<-gsub("_"," ",colnames(full_list))`