#!/usr/bin/perl
open I, "$ARGV[0]";
while (<I>){
  @F=split;
  $start=$F[1] if $F[1]-1!=$prev;                      # extract range starting number by comparing value of second column with it's value from previous line
  $r{$F[0]}{$start}{$F[1]}=($F[4]=="-1")?$F[2]:$F[4];  # if 5th column is equal "-1" then Ref value is taken from 3rd field, otherwise take it from 5th column
  $g{$F[0]}{$start}{$F[1]}=($F[4]=="-1")?$F[3]:$F[5];  # the same for Gen, just other columns
  $prev=$F[1];                                         # save 1st column value for comparison with next line
}
END{                                                   # this part is in the essence the same as the old code, it just contains another "for" loop(red), that goes through the starting numbers for the ranges.
  for $i (keys %r){
    for $j (keys %{$r{$i}}){
      @x=sort{$a <=> $b} keys %{$r{$i}{$j}};
      print "$i\n";
      print "$x[0]-$x[$#x]\n";
      print "Ref:\n";
      for $k (@x){
        print "$r{$i}{$j}{$k}";
      }
      print "\n\n";
      print "Gen:\n";
      for $k (@x){
        print "$g{$i}{$j}{$k}";
      }
      print "\n\n";
    }
  }
}

%r = {
          'SK1.chr10' => {
                           '3181' => {
                                       '3181' => 'C',
                                       '3193' => 'G',
                                       '3182' => 'C',
                                       '3189' => 'T',
                                       '3188' => 'T',
                                       '3194' => 'C',
                                       '3185' => 'A',
                                       '3183' => 'T',
                                       '3190' => 'G',
                                       '3184' => 'G',
                                       '3191' => 'A',
                                       '3187' => 'G',
                                       '3192' => 'T',
                                       '3186' => 'C'
                                     },
                           '5503' => {
                                       '5503' => 'C',
                                       '5504' => 'A',
                                       '5506' => 'A',
                                       '5505' => 'A'
                                     }
                         }
        };