use featureCounts threading (21ba6c57) · Commits · github_fork / ZUMIs

runfeatureCountFUN.R

+11 −3

Original line number	Diff line number	Diff line
		@@ -70,20 +70,28 @@ checkRsubreadVersion<- function(){
		rm(se,gr.gene,intron,exon,intron.exon.red,intron.exon.dis,intron.only,ol.ex,ol.in,intron.saf,exon.saf)
		return(saf)
		}
		.runFeatureCount<-function(abamfile,RG,saf,strand,type,primaryOnly){
		.runFeatureCount<-function(abamfile,RG,saf,strand,type,primaryOnly,cpu,mem){
		print(paste0("Assigning reads to features (",type,")"))
		fc.stat<-Rsubread::featureCounts(files=abamfile,
		annot.ext=saf,
		isGTFAnnotationFile=F,
		primaryOnly=primaryOnly,
		nthreads=1,
		nthreads=cpu,
		reportReads="BAM",
		strandSpecific=strand,
		isPairedEnd=T,
		countChimericFragments=F)$stat
		fn<-paste0(abamfile,".featureCounts.bam")
		nfn<-paste0(abamfile,".",type,".featureCounts.bam")
		system(paste("mv",fn,nfn))

		if(is.null(mem)){
		mempercpu <- round(100/cpu,0)
		}else{
		mempercpu <- round(mem/cpu,0)
		}

		system(paste("samtools sort -n -O 'BAM' -@",cpu,paste0("-m ",mempercpu,"G"),"-o",nfn,fn))
		system(paste("rm",fn))
		invisible(suppressWarnings(suppressMessages(gc(verbose=F))))
		return(nfn)
		}

+6 −2

Original line number	Diff line number	Diff line
		@@ -43,7 +43,9 @@ fnex<-.runFeatureCount(abamfile,
		saf=saf$exons,
		strand=opt$counting_opts$strand,
		type="ex",
		primaryOnly = opt$counting_opts$primaryHit)
		primaryOnly = opt$counting_opts$primaryHit,
		cpu = opt$num_threads,
		mem = opt$mem_limit)
		ffiles<-fnex

		if(opt$counting_opts$introns){
		@@ -51,7 +53,9 @@ if(opt$counting_opts$introns){
		saf=saf$introns,
		strand=opt$counting_opts$strand,
		type="in",
		primaryOnly = opt$counting_opts$primaryHit)
		primaryOnly = opt$counting_opts$primaryHit,
		cpu = opt$num_threads,
		mem = opt$mem_limit)
		ffiles<-c(ffiles,fnin)
		}