#!/software/bin/perl

  
use strict;
use warnings ;
use File::Basename ;
use Getopt::Long;
use File::Basename;
use File::Listing;
use Data::Dumper;
use Algorithm::Permute ;
use Tie::IxHash;
use Array::Each;

GetOptions(
    "if=s" => \my $input_file,
	  "sf=s" => \my $source_file,
		"od=s" => \my $outputdir,
		"d=s"  => \my $date,
		);

if(! $outputdir) {$outputdir = "/nfs/users/nfs_a/aj6/CGP/Sequenom/perl/tests/"};
my $filename  = fileparse($input_file);

#Output locations and names defaults.
my $top_hits = $outputdir . "/$date" ."_seq_comparison_top_hits.csv";
my $out      = $outputdir . "/$date" ."_seq_comparison_summary.csv" ;
my $log      = $outputdir . "/$date" ."_seq_comparison_log.log";

#my ($sample_set,$plex_set) = parseGenotypeFile($input_file) ;
my ($source_set) = ParseSourcefile($source_file);


my @samples = sort keys %{ $source_set };
foreach my $sam(@samples){
	print SUM $sam ,",";
}
#
print SUM "\n";
#
my @redo_samples;
my %rest_samples;
my $samples_report;
for( my $i= 0 ; $i < scalar( @samples ); $i++ ){
	my $s1 = $samples[ $i ];
	#my $rsid1 = $sample_set->{ $s1 };
#get the source genotype results for the sample s1
	my $geno1 = $source_set->{ $s1 };
	my $count = 0;	
	print SUM "$s1,";
#to get the samples with first 20 callrates as NN among the 30 and to get all the samples which has 50 NNs among the 96. 
	my $one_sample1  = Array::Each->new(\@$geno1);
	while(my ($g1, $index) = $one_sample1->each() ) {
		if($g1 =~ /^NN/i) {
			
			$count++;
			if($count >=20 && $index ==30){

				push @redo_samples , $s1;
	#			print "$s1|@$geno1\n";
			}
			if($count >=50 && $index == 96 ) {
				#push @$samples_report, $s1;
				print LOG "$s1|@$geno1\n";
				
			}
		}

	}
}#end of for $i


#get the samples that has first20 pass callrates for samples.
#difference between the @samples and @redo_samples.

%rest_samples = map{$_=>1} @redo_samples;
my @sam2com = grep ( ! defined $rest_samples{$_}, @samples);
#print foreach "@sam2com\n";
my $com_sam = {};
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) ) {

			 
			 	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.













##--------------------------------


sub ParseSourcefile{
 my $file = shift;
 my $source = {};
 open(SFOFN,"$source_file") or usage("FATAL ERROR: could not open file '$input_file' $!\n") ;
					
 while(<SFOFN>){
 	chomp;
	next if /^Sample/;
	my ($sam_name, @genotype ) = split(',', $_);
					
									
	$source->{$sam_name} = \@genotype;
															
 }#end of while <SFOFN> loop
close SFOFN;
return($source);
}#end of sub ParseSourcefile