From 9ffdfeccd53e37428d5cbc711f53f561ed59cc95 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Tue, 15 Mar 2016 11:06:48 -0400
Subject: [PATCH] Add test case for fix

---
 .../gatk/tools/walkers/genotyper/GenotypingEngine.java   | 2 +-
 .../variantutils/GenotypeGVCFsIntegrationTest.java       | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
index 0a0debff9..6c1b28cb2 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
@@ -210,7 +210,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
      * @param vc                                 Input VC
      * @param model                              GL calculation model
      * @param inheritAttributesFromInputVC       Output VC will contain attributes inherited from input vc
-     * @return                                   VC with assigned genotypes
+     * @return                                   VC with assigned genotypes (may be null if QUAL<emit threshold or MLEAF==0)
      */
     protected VariantCallContext calculateGenotypes(final RefMetaDataTracker tracker, final ReferenceContext refContext,
                                                  final AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts,
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 049da9bba..2de0af25b 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -612,6 +612,15 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         executeTest("testAlleleSpecificAnnotations_elevenSamples", spec);
     }
 
+    @Test
+    public void testMonomorphicVCwithAlt() {
+        final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V "
+                + privateTestDir + "monomorphicGVCwithAlt.vcf";
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("080951cdb5d4903dd58b1e753b9378d5"));
+        spec.disableShadowBCF();
+        executeTest("testAlleleSpecificAnnotations", spec);
+    }
+
     @Test
     public void testFractionInformativeReads() {
         final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V "