#!/usr/bin/perl

for ($i=1; $i<5; $i++) {
  if ($i == 1) { $infile = "male1"; $outfile = "AM.male-1.bed"; }
  if ($i == 2) { $infile = "male2"; $outfile = "AM.male-2.bed"; }
  if ($i == 3) { $infile = "female1"; $outfile = "AM.female-1.bed"; }
  if ($i == 4) { $infile = "female2"; $outfile = "AM.female-2.bed"; }
  $bbfile = $outfile; $bbfile =~ s/\.bed/\.bigBed/;
  open(IN, "$infile");
  open(OUT, ">$outfile");
  while (<IN>) {
    chomp $_; @ar = split/\t/, $_;
    print OUT "chr$ar[2]\t$ar[3]\t$ar[4]\n";
  }
  close(IN); close(OUT);
  system "/ddn/gs1/home/grimmsa/tools/ucsc/bedToBigBed $outfile /ddn/gs1/shared/dirib/reference_genomes/mm10/mm10ordered.chromSizes $bbfile";
}