From f7f67c640bb0c599b89e075d8c85a290a69e4b3d Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Fri, 2 Aug 2019 14:09:58 -0400
Subject: [PATCH] Add a test as supposedly described in #4642

---
 .../tools/walkers/ValidateVariantsIntegrationTest.java | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java
index 99a68ff22cd..4bc7e2e20f5 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java
@@ -37,7 +37,7 @@ public String baseTestStringWithoutReference(boolean sharedFile, String file, bo
     }
 
     private static String excludeValidationTypesButString(ValidateVariants.ValidationType type) {
-        if (type.equals(ALL)) {
+        if (type == null || type.equals(ALL)) {
             return "";
         }
         final StringBuilder sbuilder = new StringBuilder();
@@ -160,6 +160,14 @@ public void testBadChrCount1() throws IOException {
         );
 
         spec.executeTest("test bad chr counts #1", this);
+
+        IntegrationTestSpec spec2 = new IntegrationTestSpec(
+                baseTestStringWithoutReference(false, "validationExampleBad.vcf", false, null),
+                0,
+                UserException.FailsStrictValidation.class
+        );
+
+        spec2.executeTest("test bad chr counts #1", this);
     }
 
     @Test