- oops fixed failing tests

broadinstitute · Oct 17, 2018 · 3eeec7d · 3eeec7d
1 parent 232addf
commit 3eeec7d
Showing 1 changed file with 12 additions and 12 deletions.
diff --git a/src/test/java/picard/fingerprint/CheckFingerprintTest.java b/src/test/java/picard/fingerprint/CheckFingerprintTest.java
@@ -198,36 +198,36 @@ public void setup() throws IOException {
     @DataProvider(name = "samsToFingerprint")
     Object[][] samsToFingerprint() {
         return new Object[][]{
-                {NA12891_r1_sam, na12891_fp},
-                {NA12892_r1_sam, na12891_fp},
+                {NA12891_r1_sam, na12891_fp, 0},
+                {NA12892_r1_sam, na12891_fp, 1},
         };
     }
 
     @DataProvider(name = "vcfsToFingerprint")
     Object[][] vcfsToFingerprint() {
         return new Object[][]{
-                {NA12891_named_NA12892_vcf, na12892_fp},
-                {NA12892_1_vcf, na12892_fp},
+                {NA12891_named_NA12892_vcf, na12892_fp, 0},
+                {NA12892_1_vcf, na12892_fp, 0},
         };
     }
 
     @Test(dataProvider = "samsToFingerprint")
-    void testCheckFingerprintSam(File file, File genotypes) throws IOException {
-        tester(false, file, genotypes);
+    void testCheckFingerprintSam(final File file, final File genotypes, final int expectedRetVal) throws IOException {
+        tester(false, file, genotypes, expectedRetVal);
 
     }
 
     @Test(dataProvider = "vcfsToFingerprint")
-    void testCheckFingerprintVcf(File file, File genotypes) throws IOException {
-        tester(false, file, genotypes);
+    void testCheckFingerprintVcf(final File file, final File genotypes, final int expectedRetVal) throws IOException {
+        tester(false, file, genotypes, expectedRetVal);
     }
 
     @Test(dataProvider = "samsToFingerprint")
-    void testCheckFingerprintNoRg(File file, File genotypes) throws IOException {
-        tester(true, file, genotypes);
+    void testCheckFingerprintNoRg(final File file, final File genotypes, final int expectedRetVal) throws IOException {
+        tester(true, file, genotypes, expectedRetVal);
     }
 
-    private File tester(boolean ignoreRG, File file, File genotypes) throws IOException {
+    private File tester(boolean ignoreRG, final File file, final File genotypes, final int expectedRetVal) throws IOException {
         final List<String> args = new ArrayList<>();
         final File outputSummary = File.createTempFile("fingerprint", "summary_metrics");
         outputSummary.deleteOnExit();
@@ -241,7 +241,7 @@ private File tester(boolean ignoreRG, File file, File genotypes) throws IOExcept
         args.add("SUMMARY_OUTPUT=" + outputSummary.getAbsolutePath());
         args.add("DETAIL_OUTPUT=" + outputDetail.getAbsolutePath());
 
-        Assert.assertEquals(runPicardCommandLine(args), 0);
+        Assert.assertEquals(runPicardCommandLine(args), expectedRetVal);
 
         Assert.assertTrue(outputSummary.exists(), "Expected output file " + outputSummary.getAbsolutePath() + " to exist.");
         Assert.assertTrue(outputDetail.exists(), "Expected output file " + outputDetail.getAbsolutePath() + " to exist.");