From 0a37e199987dcb2d89b9f548f7165022e3602568 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 8 Jun 2012 11:51:28 -0400
Subject: [PATCH] Bug fix in VQSR so that the VCF index will be created for the
 recalFile.

---
 .../walkers/variantrecalibration/VariantRecalibrator.java    | 5 +----
 .../VariantRecalibrationWalkersIntegrationTest.java          | 2 ++
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 813f20e57..3666cfd12 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -139,7 +139,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     // Outputs
     /////////////////////////////
     @Output(fullName="recal_file", shortName="recalFile", doc="The output recal file used by ApplyRecalibration", required=true)
-    protected File recalFile = null;
     protected VariantContextWriter recalWriter = null;
 
     @Output(fullName="tranches_file", shortName="tranchesFile", doc="The output tranches file used by ApplyRecalibration", required=true)
@@ -230,9 +229,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }
 
-        final VCFHeader vcfHeader = new VCFHeader();
-        recalWriter = VariantContextWriterFactory.create(recalFile, getMasterSequenceDictionary());
-        recalWriter.writeHeader(vcfHeader);
+        recalWriter.writeHeader( new VCFHeader() );
     }
 
     //---------------------------------------------------------------------------------------------------------------
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 82751d9e3..47baeefb7 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -47,6 +47,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -T VariantRecalibrator" +
                         " -input " + params.inVCF +
                         " -L 20:1,000,000-40,000,000" +
+                        " --no_cmdline_in_header" +
                         " -an QD -an HaplotypeScore -an HRun" +
                         " -percentBad 0.07" +
                         " --minNumBadVariants 0" +
@@ -92,6 +93,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -T VariantRecalibrator" +
                         " -input " + params.inVCF +
                         " -L 20:1,000,000-40,000,000" +
+                        " --no_cmdline_in_header" +
                         " -an QD -an ReadPosRankSum -an HaplotypeScore" +
                         " -percentBad 0.08" +
                         " -mode INDEL -mG 3" +