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)
}
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