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chrX    1    1000000
...
chrX    2000001    3000001

...etc.

open (INTERVAL, "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/g
+alaxy_chrX_data/chrX_1Mbwindow_nonoverlapping.interval") or die "can'
+t open file\n";

while (my $interval = <INTERVAL>){ 
...
        my @find_interval = split(/\t/, $interval);
        my $start = $find_interval[1];
        my $end = $find_interval[2];

    
        my $switch = 1; 
        
...
        
        my $output_file = "/Users/logancurtis-whitchurch/Desktop/temp_
+$count.txt";
            open(OUT, ">$output_file");

   my @SNPs = <CG>; 
        my @get_SNP = split(/\t/, $SNPs[$placeholder]); 
        my $position = $get_SNP[3];

 my $switch = 1; 
        
        while ($switch == 1) {
...

        }
        }