#!/usr/bin/env/perl

#use strict;
#use warnings;

my $InSam = $ARGV[0];
my $SampleID = $ARGV[1];
chomp $InSam;
chomp $SampleID;


open(DATA, "$InSam") || die "Can't open $InSam: $!\n";
open my $OFILE, '>', $SampleID.'.cluster_ChrPos.txt' or die "Cannot create file for output: $!";

use strict;
my %seen=();
my @flds;
my $UMI;

my @cluster_ChrPos;
while (<DATA>)
{
chomp;
@flds=split /\t/;

my $POS;




	if ($seen{$flds[0]}++)
		{
				$UMI=$flds[2];
				my @subpats;
				for my $i (0..length($UMI)-1) {
				for my $j ($i+1..length($UMI)-1) {
				my $subpat = join('',
				substr($UMI, 0, $i),
				'.',  # or '\\w'
				substr($UMI, $i+1, $j-$i-1),
				'.',  # or '\\w'
				substr($UMI, $j+1),
				);
				push @subpats, $subpat;
				}
				}

				my $pat = join('|', @subpats);
						
		if($flds[0] =~ m/"$pat"/)
			{
			#print "$pat\t$flds[0]";
			push (@cluster_ChrPos, "$_");
			push (@cluster_ChrPos, "\n");
			}
		else
			{
			#push (@cluster_ChrPos, "DELIMIT\n");
			push (@cluster_ChrPos, "$_");
			push (@cluster_ChrPos, "\n");	
			}
		}	
		else
			{
			push (@cluster_ChrPos, "DELIMIT\n");
			push (@cluster_ChrPos, "$_");
			push (@cluster_ChrPos, "\n");
			}
}
push (@cluster_ChrPos, "DELIMIT");

print  $OFILE  "@cluster_ChrPos\n";
print  "@cluster_ChrPos\n";
close $OFILE;
close DATA;