--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyFastqDuplicateRemover.pl	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,34 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+
+my %opt;
+
+
+GetOptions(\%opt, "f=s", "r=s", "o=s", "out2=s", "version","id=s");
+
+my $cmnd;
+
+if (exists $opt{version}){
+	$cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py --version";
+}
+else{
+	$cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py -f $opt{f} -o $opt{id}";
+
+	if(defined $opt{r}){
+		$cmnd.= " -r $opt{r}";
+	}
+}
+
+system $cmnd;
+
+
+
+if(defined $opt{r}){
+	system "mv $opt{id}"."_1.fasta $opt{o}";
+	system "mv $opt{id}"."_2.fasta $opt{out2}";
+}
+else{
+	system "mv $opt{id} $opt{o}";
+}
+