adapt to read BC from threaded fqfilter (c1a9113d) · Commits · github_fork / ZUMIs

UMIstuffFUN.R

+3 −3

Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@ splitRG<-function(bccount,mem){
		return(bccount)
		}

		.rmRG<-function(b){ gsub("RG:Z:","",b) }
		.rmRG<-function(b){ gsub("BC:Z:","",b) }
		.rmUB<-function(b){ gsub("UB:Z:","",b)}
		.rmXT<-function(b){ gsub("XT:Z:","",b)}

		@@ -53,10 +53,10 @@ reads2genes <- function(featfiles,chunks,rgfile,cores){
		samcommand<-paste("cat freadHeader; samtools view -x NH -x AS -x nM -x HI -x IH -x NM -x uT -x MD -x jM -x jI -x XN -x XS -R",rgfile,"-@",cores)

		if(length(featfiles)==1){
		reads<-data.table::fread(paste(samcommand,featfiles[1],"\| cut -f12,13,14 \| sed 's/RG:Z://' \| sed 's/UB:Z://' \| sed 's/XT:Z://' "), na.strings=c(""),
		reads<-data.table::fread(paste(samcommand,featfiles[1],"\| cut -f12,13,14 \| sed 's/BC:Z://' \| sed 's/UB:Z://' \| sed 's/XT:Z://' "), na.strings=c(""),
		select=c(1,2,3),header=T,fill=T,colClasses = "character" , col.names = c("RG","UB","GE") )
		}else{
		reads<-data.table::fread(paste(samcommand,featfiles[1],"\| cut -f12,13,14 \| sed 's/RG:Z://' \| sed 's/UB:Z://' \| sed 's/XT:Z://' "), na.strings=c(""),
		reads<-data.table::fread(paste(samcommand,featfiles[1],"\| cut -f12,13,14 \| sed 's/BC:Z://' \| sed 's/UB:Z://' \| sed 's/XT:Z://' "), na.strings=c(""),
		select=c(1,2,3),header=T,fill=T,colClasses = "character" , col.names = c("RG","UB","GE") )[
		,"GEin":=fread(paste(samcommand,featfiles[2],"\| cut -f13,14 \| sed 's/XT:Z://'"),select=2,header=T,fill=T,na.strings=c(""),colClasses = "character")
		][ ,"ftype":="NA"

+2 −2

Original line number	Diff line number	Diff line
		.rmRG<-function(b){ gsub("RG:Z:","",b)}
		.rmRG<-function(b){ gsub("BC:Z:","",b)}
		.rmXS<-function(b){ gsub("XS:Z:","",b)}
		.rmXT<-function(b){ gsub("XT:Z:","",b)}
		.rmUnassigned<-function(b){ gsub("Unassigned_","",b)}
		@@ -11,7 +11,7 @@ sumstatBAM <- function(featfiles,cores,outdir,user_seq,bc,outfile){
		write(headerXX,paste(outdir,"freadHeader",sep="/"))
		samcommand<-paste("cat freadHeader; samtools view -x NH -x AS -x nM -x HI -x IH -x NM -x uT -x MD -x jM -x jI -x XN -x UB -@",cores)
		#issue with BC matching
		mapCount<-data.table::fread(paste(samcommand,featfiles[1],"\| cut -f12,13,14 \| sed 's/RG:Z://' \| sed 's/XS:Z://' \| sed 's/XT:Z://' "), na.strings=c(""),
		mapCount<-data.table::fread(paste(samcommand,featfiles[1],"\| cut -f12,13,14 \| sed 's/BC:Z://' \| sed 's/XS:Z://' \| sed 's/XT:Z://' "), na.strings=c(""),
		select=c(1,2,3),header=T,fill=T,colClasses = "character" , col.names = c("RG","XS","GE") )[
		,"GEin":=fread(paste(samcommand,featfiles[2],"\| cut -f13,14 \| sed 's/XT:Z://'"),select=2,header=T,fill=T,na.strings=c(""),colClasses = "character")
		][ ,"ftype":="NA"