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

Example 96 with Target

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

the class TargetCoverageSexGenotypeCalculator method getSampleReadDepthFromAutosomalTargets.

/**
     * Estimates read depth per target per homolog for a given sample index in the collection.
     *
     * @param sampleIndex integer index of the sample in the read count collection
     * @return read depth per target per homolog
     */
private double getSampleReadDepthFromAutosomalTargets(final int sampleIndex) {
    final double[] readCounts = processedReadCounts.getColumnOnSpecifiedTargets(sampleIndex, autosomalTargetList, false);
    final double[] readCountsNormalizedByPloidy = IntStream.range(0, readCounts.length).mapToDouble(i -> readCounts[i] / (double) autosomalTargetPloidies[i]).toArray();
    return new Median().evaluate(readCountsNormalizedByPloidy);
}

Example 97 with Target

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

the class TargetCoverageSexGenotypeCalculator method processReadCountsAndTargets.

/**
     * Processes raw read counts and targets:
     * <dl>
     *     <dt> If more than one sample is present in the collection, filters out fully uncovered targets
     *     from read counts and removes the uncovered targets from the target list</dt>
     *
     *     <dt> Otherwise, does nothing and warns the user
     *     </dt>
     * </dl>
     *
     * @param rawReadCounts raw read count collection
     * @param targetList user provided target list
     * @return pair of processed read counts and targets
     */
private ImmutablePair<ReadCountCollection, List<Target>> processReadCountsAndTargets(@Nonnull final ReadCountCollection rawReadCounts, @Nonnull final List<Target> targetList) {
    final ReadCountCollection finalReadCounts;
    final List<Target> finalTargetList;
    /* remove totally uncovered targets */
    if (rawReadCounts.columnNames().size() > 1) {
        finalReadCounts = ReadCountCollectionUtils.removeTotallyUncoveredTargets(rawReadCounts, logger);
        final Set<Target> targetSetFromProcessedReadCounts = new HashSet<>(finalReadCounts.targets());
        finalTargetList = targetList.stream().filter(targetSetFromProcessedReadCounts::contains).collect(Collectors.toList());
    } else {
        final long numUncoveredTargets = rawReadCounts.records().stream().filter(rec -> (int) rec.getDouble(0) == 0).count();
        final long numAllTargets = rawReadCounts.targets().size();
        logger.info("Since only one sample is given for genotyping, the user is responsible for asserting" + " the aptitude of targets. Fully uncovered (irrelevant) targets can not be automatically" + " identified (total targets: " + numAllTargets + ", uncovered targets: " + numUncoveredTargets + ")");
        finalReadCounts = rawReadCounts;
        finalTargetList = targetList;
    }
    return ImmutablePair.of(finalReadCounts, finalTargetList);
}

Example 98 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk 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 99 with Target

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

the class PoNTestUtils method createDummyHDF5FilePoN.

/** Creates a HDF5 PoN (using {@link HDF5PCACoveragePoNCreationUtils} ).  Parameters use the
     * current {@link CreatePanelOfNormals} defaults.
     * @param inputPCovFile regular readable file that could be used to create a PoN.  Must be same format as output of
     *  {@link org.broadinstitute.hellbender.tools.exome.CombineReadCounts}
     * @param numEigensamples number of desired eigensamples in the PoN reduction
     * @return HDF5 File.  Never {@code null}
     */
public static File createDummyHDF5FilePoN(final File inputPCovFile, final int numEigensamples) {
    IOUtils.canReadFile(inputPCovFile);
    ParamUtils.isPositive(numEigensamples, "Number of eigensamples must be greater than zero.");
    final File outputFile = IOUtils.createTempFile("dummy-pon-", ".pon");
    final TargetCollection<Target> targets = TargetArgumentCollection.readTargetCollection(inputPCovFile);
    HDF5PCACoveragePoNCreationUtils.create(null, outputFile, HDF5File.OpenMode.CREATE, inputPCovFile, targets, new ArrayList<>(), CreatePanelOfNormals.DEFAULT_TARGET_FACTOR_THRESHOLD_PERCENTILE, CreatePanelOfNormals.DEFAULT_MAXIMUM_PERCENT_ZEROS_IN_COLUMN, CreatePanelOfNormals.DEFAULT_MAXIMUM_PERCENT_ZEROS_IN_TARGET, CreatePanelOfNormals.DEFAULT_COLUMN_OUTLIER_DROP_THRESHOLD_PERCENTILE, CreatePanelOfNormals.DEFAULT_OUTLIER_TRUNCATE_PERCENTILE_THRESHOLD, OptionalInt.of(numEigensamples), false);
    return outputFile;
}

Example 100 with Target

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method readCountOnlyWithDiverseShapeData.

@DataProvider(name = "readCountOnlyWithDiverseShapeData")
public Object[][] readCountOnlyWithDiverseShapeData() {
    final List<Object[]> result = new ArrayList<>(4);
    final Random rdn = new Random(31);
    final int[] columnCounts = new int[] { 10, 100, 100, 200 };
    final int[] targetCounts = new int[] { 100, 100, 200, 200 };
    for (int k = 0; k < columnCounts.length; k++) {
        final List<String> columnNames = IntStream.range(0, columnCounts[k]).mapToObj(i -> "sample_" + (i + 1)).collect(Collectors.toList());
        final List<Target> targets = IntStream.range(0, targetCounts[k]).mapToObj(i -> new Target("target_" + (i + 1))).collect(Collectors.toList());
        final double[][] counts = new double[targetCounts[k]][columnCounts[k]];
        for (int i = 0; i < counts.length; i++) {
            for (int j = 0; j < counts[0].length; j++) {
                counts[i][j] = rdn.nextDouble();
            }
        }
        final ReadCountCollection readCounts = new ReadCountCollection(targets, columnNames, new Array2DRowRealMatrix(counts, false));
        result.add(new Object[] { readCounts });
    }
    return result.toArray(new Object[result.size()][]);
}