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

Example 11 with ArgumentsBuilder

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

the class MeanQualityByCycleIntegrationTest method test.

@Test(dataProvider = "filenames", groups = { "R" })
public void test(final String inputFile, final String referenceName) throws IOException {
    final File input = new File(TEST_DATA_DIR, inputFile);
    final File expectedFile = new File(TEST_DATA_DIR, "meanqualbycycle.txt");
    final File outfile = BaseTest.createTempFile("testMeanQualityByCycle", ".metrics");
    final File pdf = BaseTest.createTempFile("testMeanQualityByCycle", ".pdf");
    outfile.deleteOnExit();
    pdf.deleteOnExit();
    final ArgumentsBuilder args = new ArgumentsBuilder();
    args.add("--input");
    args.add(input.getAbsolutePath());
    args.add("--output");
    args.add(outfile.getAbsolutePath());
    args.add("--CHART");
    args.add(pdf.getAbsolutePath());
    args.add("--PRODUCE_PLOT");
    args.add("true");
    if (null != referenceName) {
        final File REF = new File(referenceName);
        args.add("-R");
        args.add(REF.getAbsolutePath());
    }
    runCommandLine(args.getArgsArray());
    try (final FileReader actualReader = new FileReader(outfile)) {
        final MetricsFile<?, Integer> output = new MetricsFile<>();
        output.read(actualReader);
        Assert.assertEquals(output.getAllHistograms().size(), 1);
        Assert.assertEquals(output.getHistogram().size(), 202);
    }
    Assert.assertTrue(pdf.exists(), "exists");
    Assert.assertTrue(pdf.length() > 0, "length");
    IntegrationTestSpec.assertEqualTextFiles(outfile, expectedFile, "#");
}

Example 12 with ArgumentsBuilder

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

the class QualityScoreDistributionIntegrationTest method test.

@Test(dataProvider = "QualityScoreDistribution", groups = { "R" })
public void test(final String unsortedBamName, final String expectedFileName, final String referenceName, final boolean makePdf, final boolean pfReadsOnly, final boolean alignedReadsOnly) throws IOException {
    final File unsortedBam = new File(TEST_DATA_DIR, unsortedBamName);
    final File expectedFile = new File(TEST_DATA_DIR, expectedFileName);
    //Note we compare to non-spark outputs
    final File outfile = BaseTest.createTempFile("test", ".metrics");
    final File pdf = BaseTest.createTempFile("test", ".pdf");
    ArgumentsBuilder args = new ArgumentsBuilder();
    args.add("--" + "input");
    args.add(unsortedBam.getCanonicalPath());
    args.add("--" + "output");
    args.add(outfile.getCanonicalPath());
    if (null != referenceName) {
        final File REF = new File(referenceName);
        args.add("-R");
        args.add(REF.getAbsolutePath());
    }
    args.add("--" + "CHART_OUTPUT");
    args.add(pdf.getCanonicalPath());
    args.add("--" + "PRODUCE_PLOT");
    args.add(makePdf);
    args.add("--" + "PF_READS_ONLY");
    args.add(pfReadsOnly);
    args.add("--" + "ALIGNED_READS_ONLY");
    args.add(alignedReadsOnly);
    this.runCommandLine(args.getArgsArray());
    IntegrationTestSpec.assertEqualTextFiles(outfile, expectedFile, "#");
}

Example 13 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 14 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 15 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);
    }
}