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

Example 91 with Target

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

the class GermlineCNVCallerIntegrationTest method runCaseSampleCallingTestOnLearnedModelParams.

private void runCaseSampleCallingTestOnLearnedModelParams(final String... extraArgs) {
    runCommandLine(getCallingOnLearnedModelArgs(ArrayUtils.addAll(new String[] { "--" + GermlineCNVCaller.INPUT_MODEL_PATH_LONG_NAME, LEARNING_MODEL_OUTPUT_PATH.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");
}

Example 92 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk-protected 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 93 with Target

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

the class EvaluateCopyNumberTriStateCallsIntegrationTest method checkOutputTargetNumbers.

private void checkOutputTargetNumbers(final File targetsFile, final File vcfOutput) {
    final List<VariantContext> outputVariants = readVCFFile(vcfOutput);
    final TargetCollection<Target> targets = TargetArgumentCollection.readTargetCollection(targetsFile);
    for (final VariantContext context : outputVariants) {
        final List<Target> overlappingTargets = targets.targets(context);
        Assert.assertEquals(context.getAttributeAsInt(XHMMSegmentGenotyper.NUMBER_OF_TARGETS_KEY, -1), overlappingTargets.size());
    }
}

Example 94 with Target

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

the class EvaluateCopyNumberTriStateCalls method doWork.

@Override
protected Object doWork() {
    final TargetCollection<Target> targets = targetArguments.readTargetCollection(false);
    final VCFFileReader truthReader = openVCFReader(truthFile);
    final VCFFileReader callsReader = openVCFReader(callsFile);
    final GenotypeEvaluationRecordWriter caseWriter = openGenotypeEvaluationOutputWriter(caseDetailOutputFile);
    if (samples.isEmpty()) {
        samples = composeSetOfSamplesToEvaluate(callsReader);
    }
    final VariantContextWriter outputWriter = openVCFWriter(outputFile, samples);
    final Map<String, EvaluationSampleSummaryRecord> sampleStats = samples.stream().collect(Collectors.toMap(s -> s, EvaluationSampleSummaryRecord::new));
    final List<SimpleInterval> intervals = composeListOfProcessingIntervalsFromInputs(truthReader, callsReader);
    for (final SimpleInterval interval : intervals) {
        for (final VariantEvaluationContext vc : processInterval(truthReader, callsReader, interval, targets)) {
            outputWriter.add(vc);
            outputCases(caseWriter, vc, targets);
            updateSampleStats(sampleStats, vc);
        }
    }
    truthReader.close();
    callsReader.close();
    outputWriter.close();
    closeCaseRecordWriter(caseWriter);
    writeSampleSummaryFile(sampleSummaryOutputFile, sampleStats);
    return "SUCCESS";
}

Example 95 with Target

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

the class EvaluateCopyNumberTriStateCalls method processInterval.

/**
     * Processes a cluster of truth and called variants that may overlap over a genome region.
     * <p>
     * It returns the list of {@link VariantEvaluationContext} instances to be output for the given interval. These
     * are already sorted by coordinates.
     * </p>
     * @param truthReader reader to the truth variants.
     * @param callsReader reader to the called variants.
     * @param interval the interval to analyze.
     * @return never {@code null}.
     */
private List<VariantEvaluationContext> processInterval(final VCFFileReader truthReader, final VCFFileReader callsReader, final SimpleInterval interval, final TargetCollection<Target> targets) {
    final List<VariantContext> truthVariants = variantQueryToList(truthReader, interval);
    final List<VariantContext> callsVariants = variantQueryToList(callsReader, interval);
    final List<VariantEvaluationContext> evaluatedVariants = new ArrayList<>(truthVariants.size() + callsVariants.size());
    for (final VariantContext truth : truthVariants) {
        // skip truth that does not overlap a single target.
        if (targets.targetCount(truth) == 0) {
            continue;
        }
        final List<VariantContext> overlappingCalls = callsVariants.stream().filter(vc -> IntervalUtils.overlaps(truth, vc)).collect(Collectors.toList());
        evaluatedVariants.add(composeTruthOverlappingVariantContext(truth, overlappingCalls, targets));
    }
    for (final VariantContext call : callsVariants) {
        // skip call that does not overlap a single target (the user might want to call on a smaller set of targets)
        if (targets.targetCount(call) == 0) {
            continue;
        }
        final List<VariantContext> overlappingTruth = truthVariants.stream().filter(vc -> IntervalUtils.overlaps(call, vc)).collect(Collectors.toList());
        if (overlappingTruth.isEmpty()) {
            evaluatedVariants.add(composeNonTruthOverlappingVariantContext(call, targets));
        }
    }
    return evaluatedVariants.stream().sorted(IntervalUtils.LEXICOGRAPHICAL_ORDER_COMPARATOR).map(this::applyVariantContextFilters).collect(Collectors.toList());
}