From bf17f92b64a549a8109e0870fd12674ac739361e Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Oct 2010 17:36:38 +0000
Subject: [PATCH] Do not look for samples in dbsnp binding

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4543 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/varianteval/VariantEvalWalker.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 6b6f956dd..ff1fbde4e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -672,7 +672,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
 
             VariantContext vc = contexts.size() == 1 ? contexts.iterator().next() : null;
 
-            if ( vc != null && vc.hasGenotypes(SAMPLES_LIST) && SAMPLES_LIST.size() > 0 ) {
+            if ( vc != null && vc.hasGenotypes(SAMPLES_LIST) && SAMPLES_LIST.size() > 0 && !name.equals("dbsnp") ) {
                 //if ( ! name.equals("eval") ) logger.info(String.format("subsetting VC %s", vc));
                 vc = vc.subContextFromGenotypes(vc.getGenotypes(SAMPLES_LIST).values());
                 HashMap<String,Object> newAts = new HashMap<String,Object>(vc.getAttributes());