#!/usr/bin/perl

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


my ($optInput1, $optInput2);

GetOptions ('i=s' => \$optInput1, 't=s' => \$optInput2);


open (IN, "<", $optInput1)|| die "$!";
open (IN1, "<", $optInput2)|| die "$!";


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

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

}

close IN1;


my %hash_stop;


my $p =0;
my $id = "";
#count tags per interval
while(my $t = <IN>){
	chomp($t);
	if ($t =~/#(.*)\s/){
		$p=0;
		$id = $1;
		%hash_stop = ();
		next;
	}
	$p++; # sometimes the first column is set to 0
	
	$t =~/^(\d+)\t(\d+)/;
	# set start and stop boundaries for each interval
	# if start position has been reached
	if(exists $hash_pos{$id}->{$p}){
		foreach my $o (keys %{$hash_pos{$id}->{$p}}){
			$hash_stop{$p}->{$o}=1;
		}
	}
    # foreach interval count ++ if tag == 1
	foreach my $keyu (keys %hash_stop){
		foreach my $key (keys %{$hash_stop{$keyu}}){
			$hash_pos{$id}->{$keyu}->{$key}++ if $2 eq '1';
			# if end reached you are don with this 
			# delete it from the hash_stop
			delete($hash_stop{$keyu}->{$key}) if $p == $key;
		}
	}
}
	
	close IN;


print Dumper(\%hash_pos);