From f0f4bc336371f905aea7757a29331cb68526c15b Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Mar 2011 21:35:50 +0000
Subject: [PATCH] This was busted because it assumed 1 (and only 1) record at
 each position.  However it's possible to have 0 (which generated a
 NullPointer) or 2+ records (which dropped records).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5361 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/CombineVariants.java       | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 2b91a4b8b..04dc19066 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -131,8 +131,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
 
         if ( ASSUME_IDENTICAL_SAMPLES ) {
-            final VariantContext vc = vcs.iterator().next();
-            if( vc != null ) {
+            for ( final VariantContext vc : vcs ) {
                 vcfWriter.add( vc, ref.getBase() );
             }