R/bedEnds.R

In dvera/travis: R Utilities for Bed and BEdgRaphs

bedEnds <- function( bedFiles, end=5, strand=TRUE , threads=getOption("threads",1L) ){

	outnames<-paste0(basename(removeext(bedFiles)),"_",if(end==5){"5p"}else{"3p"},if(strand){"s"},".bed" )

	if(strand){
		if(end==5){awkstring="awk '{if ($6==\"-\"){ $2=$3-1 } else{ $3=$2+1 } ; if($7){$7=$2; $8=$3} ; print $0}'"}
		if(end==3){awkstring="awk '{if ($6==\"-\"){ $3=$2+1 } else{ $2=$3-1 } ; if($7){$7=$2; $8=$3} ; print $0}'"}
	} else{
		if(end==5){awkstring="awk '{ $2=$3-1 ; if($7){$7=$2; $8=$3} ; print $0 }'"}
		if(end==3){awkstring="awk '{ $3=$2+1 ; if($7){$7=$2; $8=$3} ; print $0 }'"}
	}


	cmdString <- paste(
		awkstring, "OFS='\t'", bedFiles,
		"| sort -T . -k1,1 -k2,2n >",
		outnames )

	cmdRun(cmdString,threads)

	return(outnames)

}