From 2fc40a0aedd95086043c69bf1ea7b5eee38b03c4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 7 Nov 2013 09:02:17 -0500
Subject: [PATCH] Fixing the liftover script to not require strict VCF header
 validation.

Apparently no one has used the liftover script for a while (which I guess is a good thing)...
---
 .../sting/gatk/walkers/variantutils/LiftoverVariants.java     | 3 ++-
 public/perl/liftOverVCF.pl                                    | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 379b1c2a3..478a2a351 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.Options;
 import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@@ -118,7 +119,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
 
         final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
-        writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), VariantContextWriterFactory.NO_OPTIONS);
+        writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
         writer.writeHeader(vcfHeader);
     }
 
diff --git a/public/perl/liftOverVCF.pl b/public/perl/liftOverVCF.pl
index ba4198292..a942145d7 100755
--- a/public/perl/liftOverVCF.pl
+++ b/public/perl/liftOverVCF.pl
@@ -36,7 +36,7 @@ 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 -V:variant $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
+my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -V:variant $in -o $unsorted_vcf -chain $chain -dict $newRef.dict -U LENIENT_VCF_PROCESSING";
 if ($recordOriginalLocation) {
   $cmd .= " -recordOriginalLocation";
 }
@@ -66,7 +66,7 @@ system($cmd) == 0 or quit("The sorting step failed.  Please correct the necessar
 
 # Filter the VCF for bad records
 print "\nFixing/removing bad records...\n";
-$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -V:variant $sorted_vcf -o $out";
+$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -V:variant $sorted_vcf -o $out -U LENIENT_VCF_PROCESSING";
 system($cmd) == 0 or quit("The filtering step failed.  Please correct the necessary errors before retrying.");
 
 # clean up