From 5889138f4a93796ae42ac2c326f5be45a1bb44ef Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 17 Oct 2010 05:36:29 +0000
Subject: [PATCH] *facepalm*

forgot to add the samples to the header. How could the VCFWriter let me get away with something so boneheaded?!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4513 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/oneoffprojects/walkers/vcftools/FixRefBases.java    | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java
index 2bb238c4d..605d0b223 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java
@@ -17,6 +17,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.SampleUtils;
 
 import java.util.*;
 
@@ -34,9 +35,10 @@ public class FixRefBases extends RodWalker<Integer,Integer> {
 
     public void initialize() {
         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
+	Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
         Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
         headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
-        out.writeHeader(new VCFHeader(headerLines));
+        out.writeHeader(new VCFHeader(headerLines,vcfSamples));
     }
 
     public Integer reduceInit() {