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>;

while (($n = read MASK, $data, 100000) != 0) {
	
	my @info =  split(//, $data);
					
	foreach $info (@info){

        if ($#info[$position] < $start) {
		#change the element at that position to an 'N'
		substr($mask,($position),1,'N');
		$position++; 
		}

		if (($#info[$position] >= $start) && ($#info[$position] <= $end) {
			$position++; 
		}

		if ($#info[$position] > $end) {
			$count++;