#!/usr/bin/perl

open(IN, "NISC_SNVs.mm9_canonAuto.txt.pre");
open(OUT, ">NISC_SNVs.mm9_canonAuto.bed");
while (<IN>) {
  next if ($_ =~ /^\#/);
  ($chr, $pos, $mm9, $bl6, $c3h, $type) = split/\t/, $_;
  $p0 = $pos-1;
  print OUT "$chr\t$p0\t$pos\tmm9:$mm9\_B6:$bl6\_C3:$c3h\t999\t.\t$p0\t$pos\t";
  if ($bl6 =~ /\,/ || $c3h =~ /\,/) { print OUT "0,0,0\n"; }
  elsif ($bl6 eq $c3h) { print OUT "0,0,255\n"; }
  else { print OUT "255,0,0\n"; }
}
close(IN); close(OUT);
system "/ddn/gs1/home/grimmsa/tools/ucsc/bedToBigBed NISC_SNVs.mm9_canonAuto.bed /ddn/gs1/project/mousemeth/reference/mm9/mm9assembly.chromSizes NISC_SNVs.mm9_canonAuto.bigBed";