From ba41f65759724b650d8996185bc4761f50bda466 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 13 Nov 2012 11:53:39 -0500
Subject: [PATCH] Protect against NPEs in SelectVariants by checking for
 missing Genotypes

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

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index d1b7cb96f..d28fe34d6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -659,7 +659,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         return (g !=null && !g.isHomRef() && (g.isCalled() || (g.isFiltered() && !EXCLUDE_FILTERED)));
     }
 
-    private boolean haveSameGenotypes(Genotype g1, Genotype g2) {
+    private boolean haveSameGenotypes(final Genotype g1, final Genotype g2) {
+        if ( g1 == null || g2 == null )
+            return false;
+
         if ((g1.isCalled() && g2.isFiltered()) ||
                 (g2.isCalled() && g1.isFiltered()) ||
                 (g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED))