input format for intervals: 

chrX    1    6000
chrX    6045    6302
chrX    7204    8239

...etc until all 155e6 positions have been covered. 


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";
;;
my @interval = <INTERVAL>; 
;;
close (INTERVAL);
;;
chomp (@interval); 
;;
my @site_info= split(/\t/, $interval[$count]);
;;
my $start = $site_info[1];
;;
my $end = $site_info[2];
;;