From da641838549f8291e6c449fa8f735e015f602b01 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 25 Oct 2010 15:04:50 +0000
Subject: [PATCH] Fix for the case of the truth VCF file having multiple SNPs
 at the same locus.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4567 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java | 6 ++++--
 .../walkers/variantrecalibration/VariantRecalibrator.java   | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index df737e90f..f12a5e3b8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -186,8 +186,10 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
                     variantDatum.qual = vc.getPhredScaledQual();
 
                     final DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
-                    final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
-                    final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
+                    final Collection<VariantContext> vcsHapMap = tracker.getVariantContexts(ref, "hapmap", null, context.getLocation(), false, true);
+                    final Collection<VariantContext> vcs1KG = tracker.getVariantContexts(ref, "1kg", null, context.getLocation(), false, true);
+                    final VariantContext vcHapMap = ( vcsHapMap.size() != 0 ? vcsHapMap.iterator().next() : null );
+                    final VariantContext vc1KG = ( vcs1KG.size() != 0 ? vcs1KG.iterator().next() : null );
 
                     variantDatum.isKnown = ( dbsnp != null );
                     variantDatum.weight = WEIGHT_NOVELS;                   
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index d9b6d9555..8ffe18c89 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -226,8 +226,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                         variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0;
 
                         final DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
-                        final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
-                        final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
+                        final Collection<VariantContext> vcsHapMap = tracker.getVariantContexts(ref, "hapmap", null, context.getLocation(), false, true);
+                        final Collection<VariantContext> vcs1KG = tracker.getVariantContexts(ref, "1kg", null, context.getLocation(), false, true);
+                        final VariantContext vcHapMap = ( vcsHapMap.size() != 0 ? vcsHapMap.iterator().next() : null );
+                        final VariantContext vc1KG = ( vcs1KG.size() != 0 ? vcs1KG.iterator().next() : null );
 
                         variantDatum.isKnown = ( dbsnp != null );
                         double knownPrior_qScore = PRIOR_NOVELS;