--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/joinWrapper.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,51 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+use File::Temp "tempfile";
+
+my ($input1, $input2, $field1, $field2, $mode, $OOption, $out_file1) = @ARGV;
+
+die "No arguments\n" unless @ARGV == 7;
+
+my ($fh1, $file1) = tempfile();
+my ($fh2, $file2) = tempfile(); 
+
+`sort -k $field1 $input1 > $file1`;
+`sort -k $field2 $input2 > $file2`;
+
+my $option = "";
+my @fields = ();
+my $line = "";
+
+if ($OOption eq "Y") {
+  if (defined($fh1)) {
+    $line = <$fh1>;
+  } else {
+    die "Failed to create file $file1\n";
+  }
+  @fields = split /\t/, $line;
+  die "The field you selected does not exist in the input file" if (@fields < $field1);
+  my @optionO = ();
+  my $i = 0;
+  foreach (@fields) {
+    ++$i;
+    push(@optionO, "1.$i");
+  }
+  $option = "-o " . join(",", @optionO);
+} else {
+  $option = "";
+}
+
+$ENV{'LC_ALL'} = 'POSIX';
+
+if ($mode eq "V") {
+  `join -v 1 $option -1 $field1 -2 $field2 $file1 $file2 | tr " " "\t" > $out_file1`;
+} else {
+  `join $option -1 $field1 -2 $field2 $file1 $file2 | tr " " "\t" > $out_file1`;
+}
+
+`rm $file1 ; rm $file2`;
+
+
+