From 80a70ccf0336b89074769bd5815a297ed8b6e31a Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 Aug 2010 17:07:18 +0000
Subject: [PATCH] Repopulating rodsToSamples.  Code reviewed by Eric.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4027 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/BatchedCallsMerger.java    | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
index 12b93b019..17676a166 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
@@ -83,8 +83,12 @@ public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> imp
         // get all of the sample names and meta data
         Map<String, VCFHeader> headers = VCFUtils.getVCFHeadersFromRods(getToolkit(), targetRods);
         Set<String> samples = SampleUtils.getSampleList(headers);
-        for ( VCFHeader header : headers.values() )
+        for ( String rodName : headers.keySet() ) {
+            VCFHeader header = headers.get(rodName);
             headerLines.addAll(header.getMetaData());
+            HashSet<String> mySamples = new HashSet<String>(header.getGenotypeSamples());
+            rodsToSamples.put(rodName, mySamples);
+        }
 
         // update the engine
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, null, null);