From d7928ad669b0a6877923eeb3f4a724fae464eca5 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 27 Feb 2012 21:31:54 -0500
Subject: [PATCH] Drat, missed one: handle null alleles being passed in.

---
 .../broadinstitute/sting/utils/variantcontext/Genotype.java  | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
index 13c4ff3d8..8712788bf 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -29,8 +29,9 @@ public class Genotype implements Comparable<Genotype> {
     }
 
     public Genotype(String sampleName, List<Allele> alleles, double log10PError, Set<String> filters, Map<String, Object> attributes, boolean isPhased, double[] log10Likelihoods) {
-        if ( alleles != null )
-            this.alleles = Collections.unmodifiableList(alleles);
+        if ( alleles == null )
+            alleles = new ArrayList<Allele>(0);
+        this.alleles = Collections.unmodifiableList(alleles);
         commonInfo = new CommonInfo(sampleName, log10PError, filters, attributes);
         if ( log10Likelihoods != null )
             commonInfo.putAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));