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

Example 1 with IntegrationTestSpec

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

the class BQSRPipelineSparkIntegrationTest method testBlowUpOnBroadcastIncompatibleReference.

@Test(groups = "spark")
public void testBlowUpOnBroadcastIncompatibleReference() throws IOException {
    //this should blow up because broadcast requires a 2bit reference
    final String hiSeqBam_chr20 = getResourceDir() + WGS_B37_CH20_1M_1M1K_BAM;
    final String dbSNPb37_chr20 = getResourceDir() + DBSNP_138_B37_CH20_1M_1M1K_VCF;
    BQSRTest params = new BQSRTest(b37_reference_20_21, hiSeqBam_chr20, dbSNPb37_chr20, ".bam", "-indelBQSR -enableBAQ " + "--joinStrategy BROADCAST", getResourceDir() + BQSRTestData.EXPECTED_WGS_B37_CH20_1M_1M1K_RECAL);
    ArgumentsBuilder ab = new ArgumentsBuilder().add(params.getCommandLineNoApiKey());
    IntegrationTestSpec spec = new IntegrationTestSpec(ab.getString(), 1, UserException.Require2BitReferenceForBroadcast.class);
    spec.executeTest("testBQSR-" + params.args, this);
}

Example 2 with IntegrationTestSpec

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

the class BaseRecalibratorSparkIntegrationTest method testBQSRSpark.

@Test(dataProvider = "BQSRTest", groups = "spark")
public void testBQSRSpark(BQSRTest params) throws IOException {
    ArgumentsBuilder ab = new ArgumentsBuilder().add(params.getCommandLineNoApiKey());
    IntegrationTestSpec spec = new IntegrationTestSpec(ab.getString(), Arrays.asList(params.expectedFileName));
    spec.executeTest("testBQSRSpark-" + params.args, this);
}

Example 3 with IntegrationTestSpec

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

the class BaseRecalibratorSparkShardedIntegrationTest method testBQSRFailWithIncompatibleReference.

@Test(groups = { "spark", "cloud" })
public void testBQSRFailWithIncompatibleReference() throws IOException {
    final String resourceDir = getTestDataDir() + "/" + "BQSR" + "/";
    final String localResources = getResourceDir();
    final String hg19Ref = ReferenceAPISource.URL_PREFIX + ReferenceAPISource.HG19_REF_ID;
    final String HiSeqBam = resourceDir + "NA12878.chr17_69k_70k.dictFix.bam";
    final String dbSNPb37 = getResourceDir() + "dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf";
    final BQSRTest params = new BQSRTest(hg19Ref, HiSeqBam, dbSNPb37, "-indelBQSR -enableBAQ ", localResources + BQSRTestData.EXPECTED_WGS_B37_CH20_1M_1M1K_RECAL);
    IntegrationTestSpec spec = new IntegrationTestSpec(params.getCommandLine(), 1, UserException.IncompatibleSequenceDictionaries.class);
    spec.executeTest("testBQSRFailWithIncompatibleReference", this);
}

Example 4 with IntegrationTestSpec

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

the class BaseRecalibratorSparkShardedIntegrationTest method testBQSRLocal.

// "local", but we're still getting the reference from the cloud.
//FIXME: disabled because it fails. https://github.com/broadinstitute/gatk/issues/1119
@Test(dataProvider = "BQSRTest", groups = { "spark", "cloud" }, enabled = false)
public void testBQSRLocal(BQSRTest params) throws IOException {
    ArgumentsBuilder ab = new ArgumentsBuilder().add(params.getCommandLine());
    IntegrationTestSpec spec = new IntegrationTestSpec(ab.getString(), Arrays.asList(params.expectedFileName));
    spec.executeTest("testBQSR-" + params.args, this);
}

Example 5 with IntegrationTestSpec

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

the class PrintReadsSparkIntegrationTest method testReadFiltering_asIntegrationTestSpec.

@Test(groups = "spark")
public void testReadFiltering_asIntegrationTestSpec() throws IOException {
    final File samWithOneMalformedRead = new File(getTestDataDir(), "print_reads_one_malformed_read.sam");
    final IntegrationTestSpec spec = new IntegrationTestSpec(" --" + StandardArgumentDefinitions.INPUT_LONG_NAME + " " + samWithOneMalformedRead.getCanonicalPath() + " --" + StandardArgumentDefinitions.OUTPUT_LONG_NAME + " " + "%s", Arrays.asList(new File(getTestDataDir(), "expected.print_reads_one_malformed_read.bam").getCanonicalPath()));
    spec.executeTest("testReadFiltering_asIntegrationTestSpec", this);
}