for (my $j = 0; $j<=scalar(@sam2com);$j++){

	my $s1 = $sam2com[ $j ] ;
	my $geno1 = $source_set->{$s1};
	
	my $top_percent = 0;
	my $top = '';
	for (my $k = 0;$k<=scalar(@sam2com);$k++){
		
		my $match = 0;
		my $s2 = $sam2com[ $k ];
		my $geno2 = $source_set->{$s2};

		my $set = Array::Each->new(\@$geno1, \@$geno2);

		while (my($g1, $g2, $index2) = $set->each() ){

			#print "$s1|$s2|$g1|$g2|$index2\n";
			next if $g1 eq "" || $g2 eq "";
			next if $g1 =~ /^NN/i || $g2 =~ /^NN/i;
			if($g1 eq $g2){

				$match++;
				#print "$s1|$s2|$g1|$g2|$match|$index2\n";
			}#end of if $g1 eq $g2
		}#end of while loop $set->each
		
		my $percentage = sprintf "%.2f", ($match * 100)/( scalar @$geno1 ) ; 
		
		print SUM $percentage, ",";
		next if ($percentage < 75);
		#print "$s1|$s2|$percentage\n";
		if( ( $percentage >=$top_percent) and ($top ne $s1 ) ){
		
			$top_percent= $percentage;
			$top = $s2;

		} #end of if $percentage >=$top_percent) and $top ne $s1
		
		push @{ $com_sam->{ $s1 }->{ $percentage } }, {
			sample  =>$s2,
			percent =>$percentage,
			match   =>$match


		};


		my $ge1 = join "", @$geno1;
		my $ge2 = join "", @$geno2;

		if( ( $ge1 eq $ge2 ) and ( $s1 ne $s2 ) ) {

			print LOG "$s1|$s2|$ge1  |  $ge2\n";
			
		}

	}#end of for $k sam2com
	
print SUM "\n";

#sort by percentage in desending order. Get the samples match to other sample percentage of match and top hit .
	foreach my $percent ( sort { $b <=> $a } keys %{ $com_sam->{ $s1 } } ){
	
		my $match_samples = $com_sam->{ $s1 }->{ $percent };
		
		foreach my $matSam( @ { $match_samples } ){
			
			if( ( $s1 ne $matSam->{ sample } ) and ($matSam->{ percent } >= $top_percent) ) {#check the sample1 matches with a different sample with a higher percntage.

			 
			 	print LOG  "Sample $s1 matches with $matSam->{ sample } with $matSam->{ percent }\n";
				
				
				
				
			}	#else{

				
				my $l = sprintf "%s, %s, %0.2f, %s, %0.2f ", $s1, $matSam->{ sample }, $matSam->{ percent }, $top, $top_percent;
				print OUT $l,"\n";

			#}
		}#end of forach $match->sample

	}#end of percentage foreach loop

}#end of for $j @sam2com.