writeBed.bsh

#!/usr/bin/bash
TH=$1

## Create bed files larger than the specified threshold.
for i in `ls $2`
do
  j=$i #`echo $i | cut -d \. -f 1,2`
  echo $j

  ## Merge into peaks.
  zcat $i | awk 'BEGIN{OFS="\t"} ($4 > '"$TH"') {print $1,$2-50,$3+51}' | sort-bed - | bedops --merge - | bed_merge.pl 500 > $j.no_score.bed

  ## Get max score in each peak. 
  zcat $i | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,"n",$4}' | sort-bed - | bedmap --echo --max $j.no_score.bed - | sed "s/|/\t/g" | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,"n",$4}' | gzip > $j.bed.gz

  ## Clean temporary files.  
  rm $j.no_score.bed
done