INPUT FILE: 

0000000000

-------------

INTERVALS:

chrX	  1	  3
chrX	  5	  6
chrX	  8	  9

------------

DESIRED OUTPUT FILE: 

000N00N00N

-----------------

OUTPUT FILE: 

N00NNNNNNN

----------------

CODE: 

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

my $population = "test";

open( INPUT, "</Users/logancurtis-whitchurch/Desktop/test.mask.txt") or die "can't open masked file\n";

open( OUT, ">/Users/logancurtis-whitchurch/Desktop/filtered.test.mask.txt") or die "can't open output file\n";

my $mask_input = <INPUT>;
close INPUT;

my $filtered_sites = "/Users/logancurtis-whitchurch/Desktop/test.interval";

open (INTERVAL, "<$filtered_sites") or die "can't open $filtered_sites";
my $lastEnd = 1;

while ( <INTERVAL> ) {
    
    my (undef, $start, $end) = split '\s', $_; 

    ## change everything from the end of the last range
    ## to the start of this range to 'N'
    substr( $mask_input, $lastEnd, $start ) =~ tr[\x00-\xff][N];
    $lastEnd = $end;
    
}

close INTERVAL;

## change everything from the end of the last range to the end of string to 'N'
substr( $mask_input, $lastEnd, length( $mask_input ) ) =~ tr[\x00-\xff][N];
	
print OUT "$mask_input";