From da6a07ad3b29574ea4eb7890066e251a384f0c76 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Dec 2010 02:48:09 +0000
Subject: [PATCH] First round of critical fixes to indel genotyper (more to
 come tomorrow): a) Avoid complete crash of caller that broke due to a recent
 refactoring by someone who must not be named <cough>EB<cough>... an
 integration test to avoid this in the future coming soon. b) Fixed up strand
 bias computation for indels

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4779 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/DindelGenotypeLikelihoodsCalculationModel.java | 3 ++-
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 5 ++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
index 2e9da3595..3690ae8dc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
@@ -88,7 +88,8 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
         if (!vc.isIndel())
             return null;
 
-        if (sitesVisited.contains(new Integer(vc.getStart())))
+        if (sitesVisited.contains(new Integer(vc.getStart())) &&
+                contextType.equals(StratifiedAlignmentContext.StratifiedContextType.COMPLETE))
              return null;
 
         sitesVisited.add(new Integer(vc.getStart()));
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 84a4ffed7..c0d0c061c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -177,7 +177,10 @@ public class UnifiedGenotyperEngine {
         Map<String, BiallelicGenotypeLikelihoods> GLs = new HashMap<String, BiallelicGenotypeLikelihoods>();
         Allele refAllele = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, type, genotypePriors, GLs);
 
-        return createVariantContextFromLikelihoods(refContext, refAllele, GLs);
+        if (refAllele != null)
+            return createVariantContextFromLikelihoods(refContext, refAllele, GLs);
+        else
+            return null;
     }
 
     private VariantContext createVariantContextFromLikelihoods(ReferenceContext refContext, Allele refAllele, Map<String, BiallelicGenotypeLikelihoods> GLs) {