Add a test as supposedly described in #4642

broadinstitute · Aug 5, 2019 · db893e5 · db893e5
1 parent 1a290ae
commit db893e5
Showing 1 changed file with 9 additions and 1 deletion.
diff --git a/...est/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java b/...est/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