my $total_coverage = 0; #looping variable

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 );  
	
	my $coverage = $included_length =~ tr[0][];
	$total_coverage = $total_coverage + $coverage;
}

print "$total_coverage\n";