optimize barcode chunking verbose (e33b97ea) · Commits · github_fork / ZUMIs

zUMIs-dge2.R

+13 −13

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ library(ggplot2)
		myYaml<-commandArgs(trailingOnly = T)
		opt <-read_yaml(myYaml)
		setwd(opt$out_dir)

		#unixtools::set.tempdir(opt$out_dir)
		source(paste0(opt$zUMIs_directory,"/runfeatureCountFUN.R"))
		source(paste0(opt$zUMIs_directory,"/UMIstuffFUN.R"))
		source(paste0(opt$zUMIs_directory,"/barcodeIDFUN.R"))
		@@ -71,8 +71,8 @@ if( opt$counting_opts$introns ){
		########################## assign reads to UB & GENE

		for(i in unique(bccount$chunkID)){
		print(i)
		print( paste( bccount[chunkID==i]$XC ))
		print( paste( "Working on barcode chunk", i, "out of",length(unique(bccount$chunkID)) ))
		print( paste( "Processing",length(bccount[chunkID==i]$XC), "barcodes in this chunk..." ))
		reads<-reads2genes( featfiles = ffiles,
		chunks = bccount[chunkID==i]$XC,
		rgfile = paste0(opt$out_dir,"/zUMIs_output/.currentRGgroup.txt"),