Examples with Target org.broadinstitute.hellbender.tools.exome.Target used on opensource projects

Example 16 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk-protected by broadinstitute.

the class SparkGenomeReadCountsIntegrationTest method testSparkGenomeReadCountsBigBins.

@Test
public void testSparkGenomeReadCountsBigBins() throws IOException {
    final File outputFile = createTempFile(BAM_FILE.getName(), ".cov");
    final String[] arguments = { "--disableSequenceDictionaryValidation", "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REFERENCE_FILE.getAbsolutePath(), "-" + StandardArgumentDefinitions.INPUT_SHORT_NAME, BAM_FILE.getAbsolutePath(), "-" + SparkGenomeReadCounts.OUTPUT_FILE_SHORT_NAME, outputFile.getAbsolutePath(), "-" + SparkGenomeReadCounts.BINSIZE_SHORT_NAME, "16000" };
    runCommandLine(arguments);
    Assert.assertTrue(outputFile.exists());
    Assert.assertTrue(outputFile.length() > 0);
    final ReadCountCollection coverage = ReadCountCollectionUtils.parse(outputFile);
    final File targetsFile = new File(outputFile.getAbsolutePath() + ".targets.tsv");
    Assert.assertTrue(targetsFile.exists());
    Assert.assertTrue(targetsFile.length() > 0);
    final List<Target> targets = TargetTableReader.readTargetFile(targetsFile);
    Assert.assertEquals(targets.size(), 4);
    Assert.assertEquals(targets.get(1).getEnd(), 16000);
    Assert.assertEquals(targets.get(2).getName(), "target_3_1_16000");
    Assert.assertEquals(coverage.targets().size(), targets.size());
}

Example 17 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk-protected by broadinstitute.

the class SparkGenomeReadCountsIntegrationTest method testSparkGenomeReadCountsSubContig.

@Test
public void testSparkGenomeReadCountsSubContig() {
    final File outputFile = createTempFile(BAM_FILE.getName(), ".cov");
    final String[] arguments = { "--disableSequenceDictionaryValidation", "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REFERENCE_FILE.getAbsolutePath(), "-" + StandardArgumentDefinitions.INPUT_SHORT_NAME, BAM_FILE.getAbsolutePath(), "-" + SparkGenomeReadCounts.OUTPUT_FILE_SHORT_NAME, outputFile.getAbsolutePath(), "-" + SparkGenomeReadCounts.BINSIZE_SHORT_NAME, "100", "-L", "1:1-500" };
    runCommandLine(arguments);
    final File targetsFile = new File(outputFile.getAbsolutePath() + ".targets.tsv");
    final List<Target> targets = TargetTableReader.readTargetFile(targetsFile);
    Assert.assertTrue(targets.stream().allMatch(t -> t.getContig().equals("1")));
    Assert.assertEquals(targets.size(), 5);
    for (int i = 0; i < targets.size(); i++) {
        Assert.assertEquals(targets.get(i).getStart(), i * 100 + 1);
        Assert.assertEquals(targets.get(i).getEnd(), (i + 1) * 100);
    }
}

Example 18 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class GermlineCNVCallerIntegrationTest method reportCopyNumberSummaryStatistics.

/* Shame on me for using {@link ReadCountCollection} to store copy numbers! */
private void reportCopyNumberSummaryStatistics(@Nonnull final File posteriorsOutputPath, @Nonnull final File truthCopyNumberFile, @Nonnull final List<Target> targets, @Nonnull final SexGenotypeDataCollection sexGenotypeDataCollection) {
    final ReadCountCollection truthCopyNumberCollection = loadTruthCopyNumberTable(truthCopyNumberFile, targets);
    final RealMatrix calledCopyNumberMatrix = Nd4jApacheAdapterUtils.convertINDArrayToApacheMatrix(Nd4jIOUtils.readNDArrayMatrixFromTextFile(new File(posteriorsOutputPath, CoverageModelGlobalConstants.COPY_RATIO_VITERBI_FILENAME)));
    final ReadCountCollection calledCopyNumberCollection = new ReadCountCollection(targets, truthCopyNumberCollection.columnNames(), calledCopyNumberMatrix);
    final int numSamples = calledCopyNumberCollection.columnNames().size();
    final List<String> sampleSexGenotypes = truthCopyNumberCollection.columnNames().stream().map(sampleName -> sexGenotypeDataCollection.getSampleSexGenotypeData(sampleName).getSexGenotype()).collect(Collectors.toList());
    final List<SampleCopyNumberSummaryStatistics> sampleSummaryStatisticsList = IntStream.range(0, numSamples).mapToObj(si -> calculateSampleCopyNumberConcordance(truthCopyNumberCollection, calledCopyNumberCollection, si, sampleSexGenotypes.get(si))).collect(Collectors.toList());
    /* calculation various summary statistics */
    final AbstractUnivariateStatistic calculator = new Mean();
    final ConfusionRates homDelMedianRates = ConfusionMatrix.getConfusionRates(sampleSummaryStatisticsList.stream().map(ss -> ss.homozygousDeletionConfusionMatrix).collect(Collectors.toList()), calculator);
    final ConfusionRates hetDelMedianRates = ConfusionMatrix.getConfusionRates(sampleSummaryStatisticsList.stream().map(ss -> ss.heterozygousDeletionConfusionMatrix).collect(Collectors.toList()), calculator);
    final ConfusionRates dupMedianRates = ConfusionMatrix.getConfusionRates(sampleSummaryStatisticsList.stream().map(ss -> ss.duplicationConfusionMatrix).collect(Collectors.toList()), calculator);
    final double absoluteConcordance = Concordance.getCollectionConcordance(sampleSummaryStatisticsList.stream().map(ss -> ss.absoluteCopyNumberConcordance).collect(Collectors.toList()), calculator);
    /* log */
    logger.info("Homozygous deletion statistics: " + homDelMedianRates.toString());
    logger.info("Heterozygous deletion statistics: " + hetDelMedianRates.toString());
    logger.info("Duplication statistics: " + dupMedianRates.toString());
    logger.info(String.format("Absolute copy number calling concordance: %f", absoluteConcordance));
}

Example 19 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class GermlineCNVCallerIntegrationTest method runLearningAndCallingTest.

private void runLearningAndCallingTest(final String... extraArgs) {
    runCommandLine(getLearningArgs(extraArgs));
    final List<Target> modelledTargets = TargetTableReader.readTargetFile(new File(LEARNING_MODEL_OUTPUT_PATH, CoverageModelGlobalConstants.TARGET_LIST_OUTPUT_FILE));
    reportCopyNumberSummaryStatistics(LEARNING_POSTERIORS_OUTPUT_PATH, TEST_LEARNING_COMBINED_COPY_NUMBER_FILE, modelledTargets, LEARNING_SEX_GENOTYPES_DATA);
    logger.info("Copy number concordance test passed for simultaneous learning and calling");
}

Example 20 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class GermlineCNVCallerIntegrationTest method runCaseSampleCallingTestOnExactModelParams.

private void runCaseSampleCallingTestOnExactModelParams(final String... extraArgs) {
    runCommandLine(getCallingOnExactModelArgs(ArrayUtils.addAll(new String[] { "--" + GermlineCNVCaller.INPUT_MODEL_PATH_LONG_NAME, TEST_TRUTH_SIM_MODEL.getAbsolutePath() }, extraArgs)));
    final List<Target> callingTargets = TargetTableReader.readTargetFile(new File(CALLING_POSTERIORS_OUTPUT_PATH, CoverageModelGlobalConstants.TARGET_LIST_OUTPUT_FILE));
    reportCopyNumberSummaryStatistics(CALLING_POSTERIORS_OUTPUT_PATH, TEST_CALLING_COMBINED_COPY_NUMBER_FILE, callingTargets, CALLING_SEX_GENOTYPES_DATA);
    logger.info("Copy number concordance test passed for case sample calling");
}