#!perl
use strict;
use warnings;

my $extension = '.txt';
my @files = glob("*.tmp");

for my $file (@files) { 
  open IN, '<', $file or die "$!";
  $file =~ s/\..*//;
  my $outfile = $file.$extension;
  open OUT, '>', $outfile or die "$!";
  
  <IN> for (1..45); # skip 45 lines
  while (<IN>) {
    next unless /\S/; # skip blanks
    chomp $_;
    my @F = split ' ', $_;
    my @array = split m[[:,/]+], $F[9];
    my $check = index $F[4],',';
    if ($check == -1) {
      my $ratio = $array[3] / $array[4]; 
      print OUT join "\t",@F[0,1,3,4],$ratio,$array[4];
      print OUT "\n";
    } elsif ($check > 0) {
      my @allele = split ',', $F[4];
      my $ratio1 = $array[3] / $array[5]; 
      my $ratio2 = $array[4] / $array[5]; 
      print OUT join "\t",@F[0,1,3],$allele[0],$ratio1,$array[5];
      print OUT "\n";
      print OUT join "\t",@F[0,1,3],$allele[1],$ratio2,$array[5];
      print OUT "\n";
    }
    print $_;
  }
}
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