open (CG, "<$cg_input") or die "can't open $cg_input\n";
my @SNPs = <CG>;
close(CG); 

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 $switch = 1; 
	while ($switch == 1) {		 
	
		my @get_SNPs = split('\s+', $SNPs[$placeholder]);
		my $position = $get_SNPs[3];
				
		if (($position < $start) && ($position < $end)) {
			$placeholder++;
		}
		
		if (($position >= $start) && ($position <= $end)) {
			print OUT "@get_SNPs\n";
			$placeholder++;
		}
		if (($position > $start) && ($position > $end)) {
			$switch =! 1;	
		}
	}
}
close(INTERVAL);



##</code><code>##

 Use of uninitialized value in split at filter.CGS.pl line 43, <INTERVAL> line 264.
Use of uninitialized value $position in numeric lt (<) at filter.CGS.pl line 46, <INTERVAL> line 264.
Use of uninitialized value $position in numeric lt (<) at filter.CGS.pl line 46, <INTERVAL> line 264.
Use of uninitialized value $position in numeric ge (>=) at filter.CGS.pl line 50, <INTERVAL> line 264.
Use of uninitialized value $position in numeric gt (>) at filter.CGS.pl line 54, <INTERVAL> line 264.
Use of uninitialized value in split at filter.CGS.pl line 43, <INTERVAL> line 264.