#!/usr/bin/env perl -l

use strict;
use warnings;
use autodie;

use Text::CSV;

my $ref_file = 'pm_1079751_reference.csv';
my @gen_files = qw{pm_1079751_source1.gen pm_1079751_source2.gen};
my $allele_sep = '-';

my %ref_data;

my $ref_csv = Text::CSV::->new;
open my $ref_fh, '<', $ref_file;
while (my $row = $ref_csv->getline($ref_fh)) {
    $ref_data{$row->[0]} = join $allele_sep, @$row[1,2];
} 
close $ref_fh;

for my $gen_file (@gen_files) {
    my $gen_csv = Text::CSV::->new({allow_whitespace => 1});
    open my $gen_fh, '<', $gen_file;
    while (my $row = $gen_csv->getline($gen_fh)) {
        next unless exists $ref_data{$row->[2]};
        if ($ref_data{$row->[2]} eq join $allele_sep, @$row[3,4]) {
            print join(',' => @$row[2,3,4]),
                    "\n\tfound in '$gen_file':\n\t\t", join ', ' => @$row;
        }
    }
    close $gen_fh;
}