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

Example 26 with ArgumentsBuilder

use of org.broadinstitute.hellbender.utils.test.ArgumentsBuilder 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 27 with ArgumentsBuilder

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

the class CountBasesSparkIntegrationTest method testNoNPRWhenOutputIsUnspecified.

@Test(groups = "spark")
public void testNoNPRWhenOutputIsUnspecified() {
    ArgumentsBuilder args = new ArgumentsBuilder();
    args.addInput(new File(getTestDataDir(), "count_bases.bam"));
    this.runCommandLine(args.getArgsArray());
}

Example 28 with ArgumentsBuilder

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

the class CountReadsSparkIntegrationTest method testCountReadsWithIntervals.

@Test(dataProvider = "intervals", groups = "spark")
public void testCountReadsWithIntervals(final String interval_args, final long expectedCount) throws Exception {
    final File ORIG_BAM = new File(getTestDataDir(), "count_reads_sorted.bam");
    final File outputFile = createTempFile("count_reads_spark", "count");
    ArgumentsBuilder args = new ArgumentsBuilder();
    args.addInput(ORIG_BAM);
    args.add(interval_args);
    args.addOutput(outputFile);
    this.runCommandLine(args.getArgsArray());
    try (XReadLines output = new XReadLines(outputFile)) {
        Assert.assertEquals((long) Long.valueOf(output.next()), expectedCount);
    }
}

Example 29 with ArgumentsBuilder

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

the class CountReadsSparkIntegrationTest method testCountReads.

@Test(dataProvider = "filenames", groups = "spark")
public void testCountReads(final String fileIn, final String referenceName, final long expectedCount) throws Exception {
    final File ORIG_BAM = new File(getTestDataDir(), fileIn);
    final File outputTxt = createTempFile("count_reads", ".txt");
    final ArgumentsBuilder args = new ArgumentsBuilder();
    args.addInput(ORIG_BAM);
    args.addOutput(outputTxt);
    if (null != referenceName) {
        final File REF = new File(getTestDataDir(), referenceName);
        args.addReference(REF);
    }
    this.runCommandLine(args.getArgsArray());
    final String readIn = FileUtils.readFileToString(outputTxt.getAbsoluteFile());
    Assert.assertEquals((long) Long.valueOf(readIn), expectedCount);
}

Example 30 with ArgumentsBuilder

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

the class CountReadsSparkIntegrationTest method testNoNPRWhenOutputIsUnspecified.

@Test(groups = "spark")
public void testNoNPRWhenOutputIsUnspecified() {
    ArgumentsBuilder args = new ArgumentsBuilder();
    args.addInput(new File(getTestDataDir(), "count_reads.bam"));
    this.runCommandLine(args.getArgsArray());
}