From f532f1f843ed3e79cf063b5f91018f4a2b741982 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Thu, 7 Aug 2014 10:00:14 -0400
Subject: [PATCH] Fix nullPointerException

---
 .../gatk/tools/walkers/annotator/InbreedingCoeff.java           | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java
index 4dd6448c5..813945e50 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java
@@ -108,6 +108,8 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
         for ( final Genotype g : genotypes ) {
             if ( g.isCalled() && g.hasLikelihoods() && g.getPloidy() == 2)  // only work for diploid samples
                 sampleCount++;
+            else
+                continue;
             final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10( g.getLikelihoods().getAsVector() );
             if (doMultiallelicMapping)
             {