From 762f184262347262cdea1e494a2bc2a5e177c92d Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 17 Dec 2012 10:32:41 -0500
Subject: [PATCH] Bug fix for strict validation: rsID checking wasn't working
 if there were multiple IDs

---
 .../sting/gatk/walkers/variantutils/ValidateVariants.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 3e6ab050a..189772f01 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -34,12 +34,14 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.Set;
@@ -149,7 +151,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
         if ( tracker.hasValues(dbsnp.dbsnp) ) {
             rsIDs = new HashSet<String>();
             for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) )
-                rsIDs.add(rsID.getID());
+                rsIDs.addAll(Arrays.asList(rsID.getID().split(VCFConstants.ID_FIELD_SEPARATOR)));
         }
 
         try {