From 4769ef8dad8379744a0b05938c848c2be9328431 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Wed, 2 Sep 2015 09:27:06 -0400
Subject: [PATCH] Fix bug when using --ignoreInputSamples

---
 .../walkers/variantutils/PosteriorLikelihoodsUtils.java      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java
index c96fec979..517ddc3fa 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java
@@ -93,7 +93,10 @@ public class PosteriorLikelihoodsUtils {
             }
 
             //add zero allele counts for any reference alleles not seen in priors (if applicable)
-            totalAlleleCounts.put(vc1.getReference(),totalAlleleCounts.get(vc1.getReference())+numRefSamplesFromMissingResources);
+            int existingRefCounts = 0;
+            if (totalAlleleCounts.containsKey(vc1.getReference()))
+                existingRefCounts += totalAlleleCounts.get(vc1.getReference());
+            totalAlleleCounts.put(vc1.getReference(),existingRefCounts+numRefSamplesFromMissingResources);
         }
 
         // now extract the counts of the alleles present within vc1, and in order