my $placeholder = 0;
my $count = 0;

#my $window = "1Mbwindow_overlapping100kb";

my $interval_directory = "/Users/logancurtis-whitchurch/Desktop/IB_Senior_Thesis/galaxy_chrX_data/";

my $input_interval = "$interval_directory"."chrX_"."$window".".txt";

my $cg_input = "/Users/logancurtis-whitchurch/Desktop/IB_Senior_Thesis/CompleteGenomics/All26.females/CGS.All26.txt";

#my $output_directory = "/Users/logancurtis-whitchurch/Desktop/IB_Senior_Thesis/temps/overlapping/1Mb/";

open (INTERVAL, "$input_interval") or die "can't open $input_interval\n"; 
my $interval = <INTERVAL>;

my (@find_interval, $start, $end);

open (CG, "<$cg_input") or die "can't open $cg_input\n";
my @SNPs = <CG>;
close(CG);
			
foreach my $interval (<INTERVAL>){
			
	@find_interval = split(/\t/, $interval);
	$start = $find_interval[1]; 
	$end = $find_interval[2];	
		
	my $tmp = "temp_file_"."$count".".txt";
	my $output_file = "$output_directory" . "$tmp";

	open (OUT, ">>$output_file");	
		
	my $switch = 1; 
	while ($switch == 1) {
		my @get_SNPs = split(/\t/, $SNPs[$placeholder]);
		my $position = $get_SNPs[3];
						
		if (($position < $start) && ($position < $end)) {
			$placeholder++;	
		}
				
		if (($position >= $start) && ($position <= $end)) {
			print OUT "@get_SNPs";
			$placeholder++;
		}
		else {
			$switch =! 1;				
		}
	}
	$count++;
}
close(INTERVAL);