created an interface for the haploytpe caller integraiton tests betwe…

…en spark and non-spark versions
broadinstitute · Nov 27, 2018 · 6fbdbbe · 6fbdbbe
1 parent e4bd5da
commit 6fbdbbe
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Showing 3 changed files with 675 additions and 631 deletions.
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java
@@ -12,6 +12,7 @@
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection;
+import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AbstractHaplotypeCallerIntegrationTest;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.GATKBaseTest;
@@ -23,12 +24,13 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.Collections;
+import java.util.List;
 
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest;
 
 @Test(groups = {"variantcalling"})
 // Selected tests copied from HaplotypeCallerIntegrationTest
-public class HaplotypeCallerSparkIntegrationTest extends CommandLineProgramTest {
+public class HaplotypeCallerSparkIntegrationTest extends AbstractHaplotypeCallerIntegrationTest {
 
     // If true, update the expected outputs in tests that assert an exact match vs. prior output,
     // instead of actually running the tests. Can be used with "./gradlew test -Dtest.single=HaplotypeCallerIntegrationTest"
@@ -46,6 +48,11 @@ public void assertThatExpectedOutputUpdateToggleIsDisabled() {
         Assert.assertFalse(UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS, "The toggle to update expected outputs should not be left enabled");
     }
 
+    @Override
+    public List<String> getToolSpecificArguments() {
+        return Collections.singletonList("--strict");
+    }
+
     @DataProvider(name = "HaplotypeCallerTestInputs")
     public Object[][] getHaplotypCallerTestInputs() {
         return new Object[][]{