From f4d4969f23ed401cba1093955c2ebfe7b7a4d926 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 30 Mar 2012 00:22:40 -0400
Subject: [PATCH] Don't ever return null for the list of GL models

---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 4a82ed1b7..2675cbb4f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -571,7 +571,7 @@ public class UnifiedGenotyperEngine {
             if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
                 final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
                 if ( vcInput == null )
-                    return null;
+                    return models;
 
                 if ( vcInput.isSNP() )  {
                     // ignore SNPs if the user chose INDEL mode only