From d9270b236334356129a46a03b4d67edecc7163f0 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 4 Jan 2011 19:58:13 +0000
Subject: [PATCH] Fixed recordOriginalLocation option to work properly

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4932 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/liftOverVCF.pl | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index 24d125bb2..a2d7aa91d 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -36,7 +36,10 @@ my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
 
 # lift over the file
 print "Lifting over the vcf...";
-my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict -recordOriginalLocation $recordOriginalLocation";
+my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
+if ($recordOriginalLocation) {
+  $cmd .= " -recordOriginalLocation";
+}
 system($cmd);
 
 # we need to sort the lifted over file now