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

Example 21 with ArgumentsBuilder

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

the class CollectInsertSizeMetricsIntegrationTest method test.

@Test(dataProvider = "metricsfiles")
public void test(final String fileName, final String referenceName, final boolean allLevels, final String expectedResultsFile) throws IOException {
    final File input = new File(TEST_DATA_DIR, fileName);
    final File outfile = BaseTest.createTempFile("test", ".insert_size_metrics");
    final File pdf = BaseTest.createTempFile("test", ".pdf");
    final ArgumentsBuilder args = new ArgumentsBuilder();
    args.add("--input");
    args.add(input.getAbsolutePath());
    args.add("--output");
    args.add(outfile.getAbsolutePath());
    if (null != referenceName) {
        final File REF = new File(referenceName);
        args.add("-R");
        args.add(REF.getAbsolutePath());
    }
    if (allLevels) {
        // accumulation level options (all included for better test coverage)
        args.add("-" + "LEVEL");
        args.add(MetricAccumulationLevel.ALL_READS.toString());
        args.add("-" + "LEVEL");
        args.add(MetricAccumulationLevel.SAMPLE.toString());
        args.add("-" + "LEVEL");
        args.add(MetricAccumulationLevel.LIBRARY.toString());
        args.add("-" + "LEVEL");
        args.add(MetricAccumulationLevel.READ_GROUP.toString());
    }
    args.add("--producePlot");
    args.add("--histogramPlotFile");
    args.add(pdf.getAbsolutePath());
    runCommandLine(args.getArgsArray());
    IntegrationTestSpec.assertEqualTextFiles(outfile, new File(TEST_DATA_DIR, expectedResultsFile), "#");
}

Example 22 with ArgumentsBuilder

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

the class CollectQualityYieldMetricsIntegrationTest method test.

@Test(dataProvider = "CollectQualityYieldMetrics")
public void test(final String inName, final String outName, final String referenceName, final boolean useOQ) throws IOException {
    final File input = new File(TEST_DATA_DIR, inName);
    //file created using picard 1.130
    final File expectedFile = new File(TEST_DATA_DIR, outName);
    final File outfile = BaseTest.createTempFile("testCollectQualityYield", ".metrics");
    ArgumentsBuilder args = new ArgumentsBuilder();
    args.add("--I");
    args.add(input.getCanonicalPath());
    args.add("--O");
    args.add(outfile.getCanonicalPath());
    if (null != referenceName) {
        final File REF = new File(referenceName);
        args.add("--R");
        args.add(REF.getAbsolutePath());
    }
    args.add("-OQ");
    args.add(String.valueOf(useOQ));
    runCommandLine(args.getArgsList());
    IntegrationTestSpec.assertEqualTextFiles(outfile, expectedFile, "#");
}

Example 23 with ArgumentsBuilder

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

the class GenomicsDBImportIntegrationTest method testSampleMappingFileInsteadOfVCFs.

@Test
public void testSampleMappingFileInsteadOfVCFs() throws IOException {
    final File sampleNameFile = createTempSampleMapFile();
    final String workspace = createTempDir("gendbtest").getAbsolutePath() + "/workspace";
    final ArgumentsBuilder args = new ArgumentsBuilder().addArgument(GenomicsDBImport.SAMPLE_NAME_MAP_LONG_NAME, sampleNameFile.getAbsolutePath()).addArgument("L", IntervalUtils.locatableToString(INTERVAL)).addArgument(GenomicsDBImport.WORKSPACE_ARG_NAME, workspace);
    runCommandLine(args);
    checkJSONFilesAreWritten(workspace);
    checkGenomicsDBAgainstExpected(workspace, INTERVAL, COMBINED);
}

Example 24 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 25 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, "#");
}