Examples with IntegrationTestSpec org.broadinstitute.hellbender.utils.test.IntegrationTestSpec used on opensource projects

Example 96 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk-protected by broadinstitute.

the class CalculateGenotypePosteriorsIntegrationTest method testSingleParentFamily.

@Test
public void testSingleParentFamily() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(" -O %s" + " -ped " + threeMemberNonTrioFamilyFile + " -V " + getThreeMemberNonTrioTest + " -skipPop" + " -addOutputVCFCommandLine false", Collections.singletonList(dir + "expectedCGP_testSingleParentFamily_chr1.vcf"));
    spec.executeTest("testFamilyPriors", this);
}

Example 97 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class VariantWalkerGCSSupportIntegrationTest method testReadVCFOnGCS.

@Test(dataProvider = "GCSTestCases", groups = { "bucket" })
public void testReadVCFOnGCS(final String vcf, final List<SimpleInterval> intervals, final String expectedOutput) throws IOException {
    String intervalArg = "";
    if (intervals != null) {
        final StringBuilder intervalArgBuilder = new StringBuilder();
        for (final SimpleInterval interval : intervals) {
            intervalArgBuilder.append(" -L ");
            intervalArgBuilder.append(interval.toString());
        }
        intervalArg = intervalArgBuilder.toString();
    }
    final IntegrationTestSpec testSpec = new IntegrationTestSpec(" -V " + getGCPTestInputPath() + vcf + intervalArg + " -O %s " + " --addOutputVCFCommandLine false ", Collections.singletonList(expectedOutput));
    testSpec.executeTest("testReadVCFOnGCS", this);
}

Example 98 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ValidateVariantsIntegrationTest method testGoodFile.

@Test
public void testGoodFile() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationExampleGood.vcf", false, ALL), Collections.emptyList());
    spec.executeTest("test good file", this);
}

Example 99 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ExampleVariantWalkerIntegrationTest method testExampleVariantWalker.

@Test
public void testExampleVariantWalker() throws IOException {
    final IntegrationTestSpec testSpec = new IntegrationTestSpec(" -L 1:100-200" + " -R " + hg19MiniReference + " -I " + TEST_DATA_DIRECTORY + "reads_data_source_test1.bam" + " -V " + TEST_DATA_DIRECTORY + "example_variants_withSequenceDict.vcf" + " -auxiliaryVariants " + TEST_DATA_DIRECTORY + "feature_data_source_test.vcf" + " -O %s", Arrays.asList(TEST_OUTPUT_DIRECTORY + "expected_ExampleVariantWalkerIntegrationTest_output.txt"));
    testSpec.executeTest("testExampleVariantWalker", this);
}

Example 100 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ValidateVariantsIntegrationTest method testBadRefBase2.

@Test
public void testBadRefBase2() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationExampleBad2.vcf", false, REF), 0, UserException.FailsStrictValidation.class);
    spec.executeTest("test bad ref base #2", this);
}