input file looks like this: 0000000NNNN00NNN0NNN0N0N0NN0N

#-------------------------------------------------

my $population = "all28_males";

my $count = 0; 
my $position = 0;
my ($n, $data, @info, $info, $buf);

my $filtered_sites = "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/galaxy_chrX_data/filtered_chrX_rawdata.interval";
open (INTERVAL, "<$filtered_sites") or die "can't open $filtered_sites";

open(MASK, "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/consensus_files/filtered_mask_files/filtered.mask."."$population".".txt") or die "can't open 	masked file\n";

my $mask = <MASK>;
chomp ($mask);

for each (my @interval = <INTERVAL>); { 

	chomp (@interval); 
	my @positions = split(/\t/, $interval[$count]);
	my $start = $positions[1];
	my $end = $positions[2]; 

	while (($n = read MASK, $data, 100000) != 0) {
		
		my @info =  split(//, $data);
		my $length = 1;
									
		foreach $info (@info){
						
			if ( $length < $start]) {
				substr($mask,($info),1,'N');
				$length++;
			}

			if (( $length >= $start) && ($length <= $end)) {
				next; 
				$length++
			}

			if ($length > $end) {
				$count++;
			}
		}
		$buf .= $data;
		print OUT "$mask";
		close OUT; 
		close MASK;
	}
}