File 1: 

ID  start  stop

a    12    15
a    12    17
a    13    14
a    14    19
b    10    15
b    12    15
...

##</code><code>##

file 2:

Position  Tag

#a
1          0
2          1
3          0
4          0
...
10         0
11         1
12         1
13         0
14         0
...
#b
1          0
2          1
3          0
4          0
...
10         0
11         0
12         1
13         1
14         1
...

##</code><code>##

#!/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);
	

##</code><code>##

a	12	15
a 	12	17
a	13	14
a	14	19
b	10	15
b	12	15

##</code><code>##

#a
1	0
2	1
3	0
4	0
5	0
6	1
7	0
8	1
9	1
10	1
11	0
12	0
13	0
14	1
15	1
16	1
17	1
18	1
19	0
20	0
21	0
#b
1	0
2	1
3	0
4	0
5	0
6	1
7	0
8	1
9	1
10	1
11	0
12	1
13	1
14	1
15	1
16	1
17	1
18	1
19	0
20	0
21	0


##</code><code>##

./test.pl -i file.2 -t file.1

##</code><code>##

$VAR1 = {
          'a ' => {
                    '12' => {
                              '17' => 0
                            }
                  },
          'a' => {
                   '13' => {
                             '14' => 1
                           },
                   '12' => {
                             '15' => 2
                           },
                   '14' => {
                             '19' => 5
                           }
                 },
          'b' => {
                   '10' => {
                             '15' => 5
                           },
                   '12' => {
                             '15' => 4
                           }
                 }
        };


##</code><code>##

without the mistake in my input file 1

$VAR1 = {
          'a' => {
                   '13' => {
                             '14' => 1
                           },
                   '12' => {
                             '17' => 4,
                             '15' => 2
                           },
                   '14' => {
                             '19' => 5
                           }
                 },
          'b' => {
                   '10' => {
                             '15' => 5
                           },
                   '12' => {
                             '15' => 4
                           }
                 }
        };


##</code><code>##

#!/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);