From 1d6756fbd09f14d31e0bd9bec4e22eb357211aad Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Fri, 12 May 2017 17:07:05 -0400
Subject: [PATCH] Add assert to testMissingAlleleSpecificAnnotationGroup
 (#1587)

---
 .../tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java | 1 +
 1 file changed, 1 insertion(+)

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 3639f236f..0a7eb5d0f 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 +612,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList(""));
         spec.disableShadowBCF();
         executeTest("testMissingAlleleSpecificAnnotationGroup", spec);
+        Assert.assertTrue(FileUtils.readFileToString(logFile).contains(ReferenceConfidenceVariantContextMerger.ADD_AS_STANDARD_MSG));
     }
 
     @Test