From 48772a9d012b6ae1a44c39dba9428b3910117a71 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 5 Jan 2011 23:12:14 +0000
Subject: [PATCH] Fixed bug that required users to use the
 recordOriginalLocation option

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4944 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/liftOverVCF.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index a2d7aa91d..a03a4fe16 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -12,7 +12,7 @@ my $newRef = undef;
 my $oldRef = undef;
 my $out = undef;
 my $tmp = "/tmp";
-my $recordOriginalLocation = undef;
+my $recordOriginalLocation = 0;
 GetOptions( "vcf=s" => \$in,
 	    "gatk=s" => \$gatk,
 	    "chain=s" => \$chain,
@@ -22,7 +22,7 @@ GetOptions( "vcf=s" => \$in,
 	    "tmp=s" => \$tmp,
 	    "recordOriginalLocation" => \$recordOriginalLocation);
 
-if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out || !defined($recordOriginalLocation)) {
+if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
     print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-tmp \t\t<temp file location; defaults to /tmp>\n\t-recordOriginalLocation \t\t<Should we record what the original location was in the INFO field?; defaults to false>\n";
     print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /humgen/1kg/reference/human_b36_both\n";
     exit(1);