#!/usr/local/perl
#we modified the main program by removing processing the likelihoods so we get faster program to count dif in two individuals from same population
#$chunk =$ARGV[3]*100000 +1;
$chunk = $ARGV[2]*1000000 +1;
$dir = 'InterpopulationDifferences';
#print "$chunk \n";
mkdir "./$dir", 0750 unless -d "./$dir";

open(OUT1, ">./$dir/$ARGV[0]_$ARGV[1]_$ARGV[2]_A")|| die "Can't open 1_1 output : $!\n";
#	open(OUT2, ">./$dir/$ARGV[0]_$ARGV[2]_$ARGV[3]_B")|| die "Can't open 2_2 output : $!\n";

#$str = localtime();
#print OUT1 "$str\n";
#@pair_id = ();
#new addition to make arrays of teh IDS for each population 10_15_2013, $ARGV[1] for example will be LWK_IDs.txt
open (POP1, "$ARGV[0]") || die "Can't open POP1 : $!\n";
	while (<POP1>){
		chomp $_;
		@e=split(/\t/, $_); push (@pop1, $e[0]);
	}
for $n(0..$#pop1){
	print "$pop1[$n]";
}
open (POP2, "$ARGV[1]") || die "Can't open POP2 : $!\n";
        while (<POP2>){
                chomp $_;
                @e2=split(/\t/, $_); push (@pop2, $e2[0]);
        }
#here we open the main file that has the heterozygous differences only for the two populations combined.
open (FILE1, "JPT_CHB_Genome_HET.txt") || die "Can't open File1 : $!\n";
$line_N = 0;
while (<FILE1>){
	$line_N++;
	if ($line_N == 1){
		chop $_;	
		@ID = split(/\t/, $_);
	#	$n = 1;
		foreach (@ID) {
 			print "$n\t$_\n";$n++;
 		} 
		last;
	}
}
#for $n(0..$#pop1){
#print " $pop1[$n]\n"
#}
#new edit to test for two individuals.
#@pair_id = ('NA19328', 'NA19312');#TWo GBR individual to test
for $x (0..$#pop1) {
        for $y (0..$#ID) {
                        if ($pop1[$x] eq $ID[$y]) {   
	#			print "$pop1[$x]$ID[$y]MYMYMY\n";
				 push(@columns1, $y);
#                        #end of the edit.
                        }
         }   
}

#for $n(0..$#columns1){
#	print "$columns1[$n]\n";
#}
for $x (0..$#pop2) {
        for $y (0..$#ID) {
                        if ($pop2[$x] eq $ID[$y]) {    push(@columns2, $y);
#                        #end of the edit.
                         }
         }
}

for $n(0..$#columns2){
print "$columns2[$n]\n";
}

open (FILE, "JPT_CHB_Genome_HET.txt") || die "Can't open zipped file chr21 : $!\n";
$line_N = 0;
#$w, $z two individuals from the analyzed population(e.g. GBR)
@diff = ();
while (<FILE>){

	$line_N++;print "$line_N\n";
	if ($line_N >= $chunk + 1000000) {last;}
 	       if ($line_N > 1 && $line_N >= $chunk) {
#                 print $line_N "\n";
#	print $line_N."\n";_
#	if ($line_N > 1){
#		print "my god\n";
		@e = split(/\t/, $_);
#		print $e[1]."\n";
			for $w (0..$#columns1){
				for $z (0..$#columns2){
				#	if ($w < $z){
				#	@e = split(/\t/, $_);
						if ($e[$columns1[$w]] =~/^(\d)\|(\d)\:(.+)\:(.+)\,(.+)\,(.+)/){
						$p1 = $1 + $2;
		#			print $p1."\n";	
						}
						if ($e[$columns2[$z]] =~/^(\d)\|(\d)\:(.+)\:(.+)\,(.+)\,(.+)/){
                                       		$p2 = $1 + $2;
	#				print $p2."\n";
                                       		}
						$diff[$w][$z] += abs ($p1 - $p2);
				#	$my = abs ($p1 - $p2);
#					}
#print   "$columns1[$w]\t$ID[$columns1[$w]]\t$columns2[$z]\t$ID[$columns2[$z]]\t$diff[$w][$z]\n";
#				print $my."\n";
		#		}
			}
		}
	
	}
}
for $w (0..$#columns1) {
         for $z (0..$#columns2) {
             #   if ($w < $z) {
  			print  OUT1 "$columns1[$w]\t$ID[$columns1[$w]]\t$columns2[$z]\t$ID[$columns2[$z]]\t$diff[$w][$z]\n";
         #	}
         } 
}
#$str2 = localtime();
#print OUT1 "$str2\n";