my $input_dir = "/Users/logancurtis-whitchurch/Desktop/IB_Senior_Thesis/consensus_files/mask_files/"; #directory with mask files
my $input_file = "$input_dir"."mask."."$population".".txt";	
open(CGS, "<$input_file") or die "can't open input_file\n";
my $cgs = <CGS>;

my $interval = "/Users/logancurtis-whitchurch/Desktop/chrX_divisions/"."$region"."_$filter".".txt"; #specifiecs intervals by region and filter version
open (INTERVAL, "<$interval") or die "can't open interval file\n";
foreach ( <INTERVAL> ) {
	
	my (undef, $start, $end) = split '\s+', $_;
	my $subs_length = $end-$start;
	my $included_length = substr( $cgs, $start, $subs_length );  
		
	print length $included_length;

	printf "found %d zeros\n", $included_length =~ tr[0][];
}