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HaplotypeCallerIntegrationTest: add a boolean toggle to update the expected outputs for all exact-match-based tests #5324

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Oct 19, 2018
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HaplotypeCallerIntegrationTest: add a boolean toggle to update the expected outputs for all exact-match-based tests #5324

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62 changes: 50 additions & 12 deletions ...oadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,22 @@
@Test(groups = {"variantcalling"})
public class HaplotypeCallerIntegrationTest extends CommandLineProgramTest {

// 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"
// to update all of the exact-match tests at once. After you do this, you should look at the
// diffs in the new expected outputs in git to confirm that they are consistent with expectations.
public static final boolean UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS = false;

public static final String TEST_FILES_DIR = toolsTestDir + "haplotypecaller/";

/*
* Make sure that someone didn't leave the UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS toggle turned on
*/
@Test
public void assertThatExpectedOutputUpdateToggleIsDisabled() {
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So elegantly simple.

Assert.assertFalse(UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS, "The toggle to update expected outputs should not be left enabled");
}

@DataProvider(name="HaplotypeCallerTestInputs")
public Object[][] getHaplotypCallerTestInputs() {
return new Object[][] {
Expand All @@ -61,19 +75,23 @@ public void testVCFModeIsConsistentWithPastResults(final String inputFileName, f
final File output = createTempFile("testVCFModeIsConsistentWithPastResults", ".vcf");
final File expected = new File(TEST_FILES_DIR, "expected.testVCFMode.gatk4.vcf");

final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

final String[] args = {
"-I", inputFileName,
"-R", referenceFileName,
"-L", "20:10000000-10100000",
"-O", output.getAbsolutePath(),
"-O", outputPath,
"-pairHMM", "AVX_LOGLESS_CACHING",
"--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
};

runCommandLine(args);

// Test for an exact match against past results
IntegrationTestSpec.assertEqualTextFiles(output, expected);
if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
IntegrationTestSpec.assertEqualTextFiles(output, expected);
}
}

/*
Expand All @@ -90,11 +108,13 @@ public void testVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations(fin
final File output = createTempFile("testVCFModeIsConsistentWithPastResults", ".vcf");
final File expected = new File(TEST_FILES_DIR + "expected.testVCFMode.gatk4.alleleSpecific.vcf");

final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

final String[] args = {
"-I", inputFileName,
"-R", referenceFileName,
"-L", "20:10000000-10100000",
"-O", output.getAbsolutePath(),
"-O", outputPath,
"-G", "StandardAnnotation",
"-G", "StandardHCAnnotation",
"-G", "AS_StandardAnnotation",
Expand All @@ -105,7 +125,9 @@ public void testVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations(fin
runCommandLine(args);

// Test for an exact match against past results
IntegrationTestSpec.assertEqualTextFiles(output, expected);
if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
IntegrationTestSpec.assertEqualTextFiles(output, expected);
}
}

/*
Expand Down Expand Up @@ -186,11 +208,13 @@ public void testGVCFModeIsConsistentWithPastResults(final String inputFileName,
final File output = createTempFile("testGVCFModeIsConsistentWithPastResults", ".g.vcf");
final File expected = new File(TEST_FILES_DIR, "expected.testGVCFMode.gatk4.g.vcf");

final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

final String[] args = {
"-I", inputFileName,
"-R", referenceFileName,
"-L", "20:10000000-10100000",
"-O", output.getAbsolutePath(),
"-O", outputPath,
"-ERC", "GVCF",
"-pairHMM", "AVX_LOGLESS_CACHING",
"--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
Expand All @@ -199,7 +223,9 @@ public void testGVCFModeIsConsistentWithPastResults(final String inputFileName,
runCommandLine(args);

// Test for an exact match against past results
IntegrationTestSpec.assertEqualTextFiles(output, expected);
if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
IntegrationTestSpec.assertEqualTextFiles(output, expected);
}
}

/*
Expand All @@ -214,11 +240,13 @@ public void testGVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations(fi
final File output = createTempFile("testGVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations", ".g.vcf");
final File expected = new File(TEST_FILES_DIR + "expected.testGVCFMode.gatk4.alleleSpecific.g.vcf");

final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

final String[] args = {
"-I", inputFileName,
"-R", referenceFileName,
"-L", "20:10000000-10100000",
"-O", output.getAbsolutePath(),
"-O", outputPath,
"-G", "StandardAnnotation",
"-G", "StandardHCAnnotation",
"-G", "AS_StandardAnnotation",
Expand All @@ -230,7 +258,9 @@ public void testGVCFModeIsConsistentWithPastResults_AlleleSpecificAnnotations(fi
runCommandLine(args);

// Test for an exact match against past results
IntegrationTestSpec.assertEqualTextFiles(output, expected);
if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
IntegrationTestSpec.assertEqualTextFiles(output, expected);
}
}

/*
Expand Down Expand Up @@ -342,11 +372,13 @@ public void testGenotypeGivenAllelesMode() throws IOException {
final File output = createTempFile("testGenotypeGivenAllelesMode", ".vcf");
final File expected = new File(TEST_FILES_DIR, "expected.testGenotypeGivenAllelesMode.gatk4.vcf");

final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

final String[] args = {
"-I", NA12878_20_21_WGS_bam,
"-R", b37_reference_20_21,
"-L", "20:10000000-10010000",
"-O", output.getAbsolutePath(),
"-O", outputPath,
"-pairHMM", "AVX_LOGLESS_CACHING",
"--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false",
"--genotyping-mode", "GENOTYPE_GIVEN_ALLELES",
Expand All @@ -356,7 +388,9 @@ public void testGenotypeGivenAllelesMode() throws IOException {
runCommandLine(args);

// Test for an exact match against past results
IntegrationTestSpec.assertEqualTextFiles(output, expected);
if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
IntegrationTestSpec.assertEqualTextFiles(output, expected);
}
}

@Test(expectedExceptions = CommandLineException.BadArgumentValue.class)
Expand Down Expand Up @@ -522,18 +556,22 @@ public void testHaplotypeCallerRemoveAltAlleleBasedOnHaptypeScores() throws IOEx
final File output = createTempFile("testHaplotypeCallerRemoveAltAlleleBasedOnHaptypeScoresResults", ".vcf");
final File expected = new File(TEST_FILES_DIR, "expected.testHaplotypeCallerRemoveAltAlleleBasedOnHaptypeScores.gatk4.vcf");

final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

final String[] args = {
"-I", testBAM.getAbsolutePath(),
"-R", b37_reference_20_21,
"-L", "20:11363580-11363600",
"-O", output.getAbsolutePath(),
"-O", outputPath,
"-ploidy", "4",
"--max-genotype-count", "15",
"--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false"
};
runCommandLine(args);

IntegrationTestSpec.assertEqualTextFiles(output, expected);
if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
IntegrationTestSpec.assertEqualTextFiles(output, expected);
}
}

// test that ReadFilterLibrary.NON_ZERO_REFERENCE_LENGTH_ALIGNMENT removes reads that consume zero reference bases
Expand Down