#' Convert bed files to bedGraph files
#'
#' \code{bed2bg} converts bed files to bedGraph files by printing bed columns 1,2,3,5.
#'
#' @param bedfiles A character vector of paths to bed files.
#' @param threads A positive integer specifying how many files to process simultaneously.
bedToBedGraph <-
function( bedfiles, sizeScore=FALSE , threads=getOption("threads",1L) ){
outnames<-paste0(basename(removeext(bedfiles)),".bg")
if(any(file.exists(outnames))){stop("files exist already")}
if(sizeScore){
cmdString <- paste( "awk '{print $1,$2,$3,$3-$2}' OFS='\t' ",bedfiles,">",outnames )
} else{
cmdString <- paste( "awk '{print $1,$2,$3,$5}' OFS='\t' ",bedfiles,">",outnames )
}
cmdRun(cmdString,threads)
return(outnames)
}
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