Oops

broadinstitute · May 23, 2018 · 3547c12 · 3547c12
1 parent f9a0cc4
commit 3547c12
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
@@ -186,25 +186,25 @@ public void testEntireVariantContext(File input, File expected, List<String> ext
         assertVariantContextsMatch(input, expected, extraArgs, reference);
     }
 
-    @Test
     private void assertVariantContextsMatch(File input, File expected, List<String> extraArgs, String reference) throws IOException {
         try {
-            final VCFHeader header = VCFHeaderReader.readHeaderFrom(new SeekablePathStream( IOUtils.getPath(expected.getAbsolutePath())));
-            runGenotypeGVCFSAndAssertSomething(input, expected, extraArgs, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE ,header), reference);
+            final VCFHeader header = VCFHeaderReader.readHeaderFrom(new SeekablePathStream(IOUtils.getPath(expected.getAbsolutePath())));
+            runGenotypeGVCFSAndAssertSomething(input, expected, extraArgs, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE, header), reference);
         } catch (java.io.IOException e) {
             throw new AssertionError("There was a problem reading your expected input file");
         }
     }
 
+    private void assertGenotypesMatch(File input, File expected, List<String> additionalArguments, String reference) throws IOException {
+        runGenotypeGVCFSAndAssertSomething(input, expected, additionalArguments, VariantContextTestUtils::assertVariantContextsHaveSameGenotypes,
+                                           reference);
+    }
+
     @Test(dataProvider = "gvcfWithPPs")
     public void assertPPsAreStripped(File input, File expected, List<String> extraArgs, String reference) throws IOException {
         runGenotypeGVCFSAndAssertSomething(input, expected, extraArgs, VariantContextTestUtils::assertGenotypeAttributeWasRemoved, reference);
     }
 
-    private void assertGenotypesMatch(File input, File expected, List<String> additionalArguments, String reference) throws IOException {
-        runGenotypeGVCFSAndAssertSomething(input, expected, additionalArguments, VariantContextTestUtils::assertVariantContextsHaveSameGenotypes,
-                                           reference);
-    }
 
     private void runGenotypeGVCFSAndAssertSomething(File input, File expected, List<String> additionalArguments, BiConsumer<VariantContext, VariantContext> assertion, String reference) throws IOException {
         runGenotypeGVCFSAndAssertSomething(input.getAbsolutePath(), expected, additionalArguments, assertion, reference