#!/usr/bin/perl
#use strict;
#use warnings;

die "usage:perl $0 outputDir tumor" if @ARGV!=2; 
my (${outputDir},${tumor})=@ARGV;
open L,"${outputDir}/mutation/hotspot/${tumor}.hotspot.L.snp.indel.vcf";
open H,"${outputDir}/mutation/hotspot/${tumor}.hotspot.H.snp.indel.vcf";

my %high;
my %low;
my @head;
while(<L>){
	if(/^#/){
		push @head,$_;
	}else{
		my @line=split;
		$low{"$line[0]_$line[1]"}=$_;	
	}
}

while(<H>){
        unless(/^#/){
                my @line=split;
                $high{"$line[0]_$line[1]"}=$_;
        }
}

my @content;
foreach my $key(keys %low){
	if(not exists $high{$key}){
		push @content,$low{$key};	
	}
}

if (@content){
	open OUT,">${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.vcf";
	print OUT @head;
	print OUT @content;
}