#!/usr/bin/perl

use strict;
use Getopt::Long;
use Data::Dumper;

my ($i1, $i2);

GetOptions ('i=s' => \$i1, 't=s' => \$i2);


open (IN, "<", $i1)|| die "$!";
open (IN1, "<", $i2)|| die "$!";


my %hash1;
# set my intervals
while (<IN1>){
	chomp;

	/^([^\t]*)\t([^\t]*)\t([^\t]*)/;
	$hash1{$1}->{$2}->{$3} =0;

}
close IN1;


my %hash2;
my $p =0;
my $id = "";
#count tags per interval
while(<IN>){
	chomp;
	if (/#(.*)/){
		$p=0;
		$id = $1;
		%hash2 = ();
		next;
	}
	$p++; # sometimes the first column is set to 0
	
	/^(\d+)\t(\d+)/;
	if(exists $hash1{$id}->{$p}){
		foreach my $o (keys %{$hash1{$id}->{$p}}){
			$hash2{$p}->{$o}=1;
		}
	}
	foreach my $key1 (keys %hash2){
		foreach my $key2 (keys %{$hash2{$key1}}){
			$hash1{$id}->{$key1}->{$key2}++ if $2 eq '1';
			delete($hash2{$key1}->{$key2}) if $p == $key2;
		}
	}
}
close IN;


print Dumper(\%hash1);