#!/usr/bin/env perl

use strict;
use warnings;


die "usage:perl $0 vcf1r vcf2r outvcf" unless @ARGV == 3;
my ($vcf1r, $vcf2r, $outvcf) = @ARGV;

# open R1, "${outputdir}/mutation/${tumor}.1r.snp.indel.vcf";
# open R2, "${outputdir}/mutation/${tumor}.2r.snp.indel.vcf";
# open OUT, ">${outputdir}/mutation/${tumor}.snp.indel.vcf";

open R1, "$vcf1r";
open R2, "$vcf2r";
open OUT, ">$outvcf";

my (%r1, %r2);
while (<R2>) {
    next if /^#/;
    chomp;
    my @line = split;
    my $key = join("_", @line[0, 1, 3, 4]);
    $r2{$key} = $_;
}

while (<R1>) {
    if (/^#/) {
        print OUT;
        next;
    }
    chomp;
    my @line = split;
    my $freq = (split(":", $line[-1]))[4];
    my $dp = (split(":", $line[-1]))[1];
    next if $dp < 50;

    if ($freq < 0.01) {
        my $key = join("_", @line[0, 1, 3, 4]);
        if (exists $r2{$key}) {
            print OUT "$_\n";
        }
    }
    else {
        print OUT "$_\n";
    }
}