From c305b41da49eee9c1c5ca9bda1ba545472723775 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 20 Oct 2010 02:39:16 +0000
Subject: [PATCH] Patch for James

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4526 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/createTranscriptToGenomicInfoTables.pl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/perl/createTranscriptToGenomicInfoTables.pl b/perl/createTranscriptToGenomicInfoTables.pl
index 4a7dd7cfb..8787f6ba5 100755
--- a/perl/createTranscriptToGenomicInfoTables.pl
+++ b/perl/createTranscriptToGenomicInfoTables.pl
@@ -42,11 +42,11 @@ open(UNSORTED, "< $unsorted_table") or die "can't open $unsorted_table: $!";
 my $line = <UNSORTED>;
 print SORTED "$line";
 close(UNSORTED);
-
-$cmd = "grep haplotypeReference -v $unsorted_table | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $ref.fai";
-print SORTED `$cmd`;
 close(SORTED);
 
+$cmd = "grep haplotypeReference -v $unsorted_table | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $ref.fai >> $out";
+system($cmd);
+
 # clean up
 unlink $unsorted_table;