pairsamtoolsSplit <- function( pairsamFiles , outputSam=FALSE , outputBam=FALSE , compressOut=TRUE, inThreads=1, outThreads=1, pipe=FALSE, threads=getOption("threads",1L) ){
numfiles <- length(pairsamFiles)
outnames <- paste0(basename(removeext(gsub(".gz$","",pairsamFiles))),".pairs")
outsams <- paste0(basename(removeext(gsub(".gz$","",pairsamFiles))),".sam")
outbams <- paste0(basename(removeext(gsub(".gz$","",pairsamFiles))),".bam")
if(compressOut){outnames=paste0(outnames,".gz")}
if(outputSam & outputBam){stop("can only output sams or bams, not both")}
cmdString <- paste(
"pairsamtools", "split",
"--nproc-out",inThreads,
"--nproc-in",outThreads,
if(outputSam){paste("--output-sam",outsams)},
if(outputBam){paste("--output-sam",outbams)},
if(!pipe){paste("--output-pairs",outnames)},
if(!pipe){pairsamFiles}
)
res <- cmdRun(cmdString,threads=threads)
return(outnames)
}
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