ensure BC correct reading (ddff1a62) · Commits · github_fork / ZUMIs

barcodeIDFUN.R

+2 −4

Original line number	Diff line number	Diff line
		@@ -178,9 +178,7 @@ setDownSamplingOption<-function( down ,bccount, filename=NULL){

		#bccount needs to be read
		cellBC<-function(bcfile, bcnum, bcauto, bccount_file, outfilename=NULL){
		bccount<-data.table::fread( bccount_file )
		names(bccount)<-c("XC","n")
		bccount <- bccount[,list(n=sum(n)),by=XC]
		bccount<-data.table::fread( bccount_file, header = FALSE, col.names = c("XC","n") )[, .(n = sum(n)), by = XC]
		bccount<-bccount[n>=opt$barcodes$nReadsperCell][order(-n)][,cellindex:=1:(.N)][,keep:=FALSE]

		if(is.null(bcfile)==FALSE & bcauto){
		@@ -232,7 +230,7 @@ plotReadCountSelection<-function(bccount , mads, filename){

		BCbin <- function(bccount_file, bc_detected) {
		true_BCs <- bc_detected[,XC]
		nocell_bccount<-data.table::fread( bccount_file, col.names = c("XC","n"))[
		nocell_bccount<-data.table::fread( bccount_file, header = FALSE, col.names = c("XC","n"))[
		,list(n=sum(n)),by=XC][
		n>=opt$barcodes$nReadsperCell][
		order(-n)][