gffToBedGraph <-
function( gffs, extendbp=NULL, postsort=TRUE, threads=getOption("threads",1L) ){
gffnames<-basename(removeext(gffs))
outnames<-paste0(gffnames,".bg")
cmdString <- paste(
"cut -f 1,4,5,6",
gff,
if(!is.null(extendbp) & is.numeric(extendbp)){paste("| awk '{print $1,$2,$3+",extendbp,",$4}' OFS='\t'")},
"| grep -P -v '^#'",
">",outnames
)
res <- cmdRun(cmdString, threads=threads)
if(postsort){bed.sort(outnames,threads=threads)}
return(outnames)
}
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