--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/script/ReadCluster.pl	Mon Jun 02 07:35:53 2014 -0400
@@ -0,0 +1,191 @@
+#!/usr/bin/perl
+
+=head1 NAME
+   ReadCluster.pl
+
+=head1 SYNOPSIS
+
+    USAGE: ReadCluster.pl --input input_sam_file --output output_prefix [--threshold 10000 --minClusterSize 4]
+
+=head1 OPTIONS
+
+B<--input,-i>
+   Input file
+
+B<--output,-o>
+   output prefix
+
+B<--window, -w>
+    Window size
+
+B<--minClusterSize, -m>
+	Min size of cluster
+
+B<--help,-h>
+   This help message
+
+=head1  DESCRIPTION
+
+
+=head1  INPUT
+
+
+=head1  OUTPUT
+
+
+=head1  CONTACT
+  Jaysheel D. Bhavsar @ bjaysheel[at]gmail[dot]com
+
+
+==head1 EXAMPLE
+   ReadCluster.pl --input=filename.sam --window=10000 --output=PREFIX
+
+=cut
+
+use strict;
+use warnings;
+use Data::Dumper;
+use DBI;
+use Pod::Usage;
+use Scalar::Util qw(looks_like_number);
+use Getopt::Long qw(:config no_ignore_case no_auto_abbrev pass_through);
+
+my %options = ();
+my $results = GetOptions (\%options,
+                          'input|i=s',
+						  'output|o=s',
+                          'window|w=s',
+						  'minClusterSize|m=s',
+						  'help|h') || pod2usage();
+
+## display documentation
+if( $options{'help'} ){
+    pod2usage( {-exitval => 0, -verbose => 2, -output => \*STDERR} );
+}
+#############################################################################
+## make sure everything passed was peachy
+&check_parameters(\%options);
+
+my $r1_start = 0;
+my $r2_start = 0;
+my $r1_end = $r1_start + $options{window};
+my $r2_end = $r2_start + $options{window};
+my $r1_chr = "";
+my $r2_chr = "";
+
+my @cluster = ();
+
+open (FHD, "<", $options{input}) or die "Cound not open file $options{input}\n";
+open (INTRA, ">", $options{output} . ".intra.sam") or die "Cound not open file $options{output}.intra.sam\n";
+open (INTER, ">", $options{output} . ".inter.sam") or die "Cound not open file $options{output}.inter.sam\n";
+
+while (<FHD>){
+	chomp $_;
+
+	#skip processing lines starting with @ just print to output file.
+	if ($_ =~ /^@/){
+		print INTRA $_."\n";
+		print INTER $_."\n";
+		next;
+	}
+#print "$_\n";
+	check_sequence($_);
+}
+
+close(FHD);
+close(INTRA);
+close(INTER);
+
+exit(0);
+
+#############################################################################
+sub check_parameters {
+    my $options = shift;
+
+	my @required = ("input", "output");
+
+	foreach my $key (@required) {
+		unless ($options{$key}) {
+			print STDERR "ARG: $key is required\n";
+			pod2usage({-exitval => 2,  -message => "error message", -verbose => 1, -output => \*STDERR});
+			exit(-1);
+		}
+	}
+
+	unless($options{window}) { $options{window} = 10000; }
+	unless($options{minClusterSize}) { $options{minClusterSize} = 4; }
+}
+
+#############################################################################
+sub check_sequence {
+	my $line = shift;
+
+	my @data = split(/\t/, $line);
+
+	## check if mates are within the window.
+	if ((inWindow($data[3], 1)) && (inWindow($data[7], 2)) &&
+		($r1_chr =~ /$data[2]/) && ($r2_chr =~ /$data[6]/)) {
+
+		## if minClusterSize is reached output
+		if (scalar(@cluster) >= $options{minClusterSize}) {
+
+			## if chr are the same then print intra-chr else inter-chr
+			if ($data[6] =~ /=/) {
+				print INTRA $line."\n";
+			} else {
+				print INTER $line."\n";
+			}
+		} else {
+			push @cluster, $line;
+		}
+	} else {
+
+		if (scalar(@cluster) >= $options{minClusterSize}) {
+			dumpCluster(@cluster);
+		}
+
+		@cluster = ();
+		$r1_start = $data[3];
+		$r2_start = $data[7];
+		$r1_end = $r1_start + $options{window};
+		$r2_end = $r2_start + $options{window};
+		$r1_chr = $data[2];
+		$r2_chr = $data[6];
+	}
+}
+
+#############################################################################
+sub inWindow {
+	my $coord = shift;
+	my $read = shift;
+
+	my $start = 0;
+	my $end = 0;
+
+	if ($read == 1) {
+		$start = $r1_start;
+		$end = $r1_end;
+	} else {
+		$start = $r2_start;
+		$end = $r2_end;
+	}
+
+	if (($coord > $start) && ($coord < $end)){
+		return 1;
+	} else { return 0; }
+}
+
+#############################################################################
+sub dumpCluster {
+	my @cluster = shift;
+
+	foreach (@cluster){
+		my @data = split(/\t/, $_);
+
+		if ($data[6] =~ /=/) {
+			print INTRA $_."\n";
+		} else {
+			print INTER $_."\n";
+		}
+	}
+}