0 26 2 2699645 1 3 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

0 21 7 2699676 3 1 1 1 3 1 3 1 1 3 1 1 1 1 3 1 1 3 1 1 3 1 1 1 1 1 1 1

0 14 14 2699968 1 1 3 3 1 1 1 3 3 1 3 1 1 3 1 3 3 1 1 3 1 3 3 3 1 1 3 3

0 13 15 2700027 1 1 3 3 1 1 1 3 3 1 3 1 1 3 1 3 3 1 1 3 1 3 3 3 3 1 3 3

0 26 2 2700157 1 3 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

0 17 11 2700202 3 3 1 1 3 3 3 1 1 3 3 1 1 1 3 1 3 3 1 1 3 1 1 1 1 1 1 1

0 18 10 2700302 3 1 1 1 3 1 3 3 1 3 3 1 1 1 3 1 3 3 1 1 3 1 1 1 1 1 1 1

0 15 13 2700608 1 3 3 3 1 3 1 1 3 1 1 3 1 3 1 3 1 1 1 3 1 1 1 3 1 3 3 3

0 15 13 2700613 1 1 3 3 1 3 1 1 3 1 1 3 1 3 3 3 1 1 1 3 1 1 1 3 1 3 3 3



##</code><code>##

2699645	2
	0
2699676	7
	0
2699968	14

##</code><code>##

while($count < 155){

	my $output_file = "$output_dir"."compute_minor_alleles_28_males."."$count".".txt";
	open(OUT, ">$output_file");
	print OUT "position\tminor allele frequency\n";

	my $input_file = "$input_dir"."temp_file_". "$count."."txt";
	
	open (CG, "<$input_file") or die "Cannot open $input_file:$!\n";
	while (my $cg = <CG>){
		
		if ($cg =~ /NA/){
			next;
		}
		
		chomp($cg);	#get rid of newline character
		@info =  split(" ", $cg);