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

Example 6 with Target

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method readCountAndPercentileData.

// this is duplicated from ReadCountCollectionUtilsUnitTest
@DataProvider(name = "readCountAndPercentileData")
public Object[][] readCountAndPercentileData() {
    final double[] percentiles = new double[] { 1.0, 2.5, 5.0, 10.0, 25.0 };
    final List<Object[]> result = new ArrayList<>();
    final Random rdn = new Random(13);
    final int columnCount = 100;
    final int targetCount = 100;
    final List<String> columnNames = IntStream.range(0, columnCount).mapToObj(i -> "sample_" + (i + 1)).collect(Collectors.toList());
    final List<Target> targets = IntStream.range(0, targetCount).mapToObj(i -> new Target("target_" + (i + 1))).collect(Collectors.toList());
    for (final double percentile : percentiles) {
        final double[][] counts = new double[columnCount][targetCount];
        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, percentile });
    }
    return result.toArray(new Object[result.size()][]);
}

Example 7 with Target

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method readCountOnlyData.

@DataProvider(name = "readCountOnlyData")
public Object[][] readCountOnlyData() {
    final int repeats = 4;
    final List<Object[]> result = new ArrayList<>(repeats);
    final Random rdn = new Random(13);
    final int columnCount = 100;
    final int targetCount = 100;
    final List<String> columnNames = IntStream.range(0, columnCount).mapToObj(i -> "sample_" + (i + 1)).collect(Collectors.toList());
    final List<Target> targets = IntStream.range(0, targetCount).mapToObj(i -> new Target("target_" + (i + 1))).collect(Collectors.toList());
    for (int k = 0; k < repeats; k++) {
        final double[][] counts = new double[columnCount][targetCount];
        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()][]);
}

Example 8 with Target

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

the class CoverageModelParameters method write.

/**
     * Writes the model to disk.
     *
     * @param outputPath model output path
     */
public static void write(@Nonnull CoverageModelParameters model, @Nonnull final String outputPath) {
    /* create output directory if it doesn't exist */
    createOutputPath(Utils.nonNull(outputPath, "The output path string must be non-null"));
    /* write targets list */
    final File targetListFile = new File(outputPath, CoverageModelGlobalConstants.TARGET_LIST_OUTPUT_FILE);
    TargetWriter.writeTargetsToFile(targetListFile, model.getTargetList());
    final List<String> targetNames = model.getTargetList().stream().map(Target::getName).collect(Collectors.toList());
    /* write target mean bias to file */
    final File targetMeanBiasFile = new File(outputPath, CoverageModelGlobalConstants.TARGET_MEAN_LOG_BIAS_OUTPUT_FILE);
    Nd4jIOUtils.writeNDArrayMatrixToTextFile(model.getTargetMeanLogBias().transpose(), targetMeanBiasFile, MEAN_LOG_BIAS_MATRIX_NAME, targetNames, null);
    /* write target unexplained variance to file */
    final File targetUnexplainedVarianceFile = new File(outputPath, CoverageModelGlobalConstants.TARGET_UNEXPLAINED_VARIANCE_OUTPUT_FILE);
    Nd4jIOUtils.writeNDArrayMatrixToTextFile(model.getTargetUnexplainedVariance().transpose(), targetUnexplainedVarianceFile, TARGET_UNEXPLAINED_VARIANCE_MATRIX_NAME, targetNames, null);
    if (model.isBiasCovariatesEnabled()) {
        /* write mean bias covariates to file */
        final List<String> meanBiasCovariatesNames = IntStream.range(0, model.getNumLatents()).mapToObj(li -> String.format(BIAS_COVARIATE_COLUMN_NAME_FORMAT, li)).collect(Collectors.toList());
        final File meanBiasCovariatesFile = new File(outputPath, CoverageModelGlobalConstants.MEAN_BIAS_COVARIATES_OUTPUT_FILE);
        Nd4jIOUtils.writeNDArrayMatrixToTextFile(model.getMeanBiasCovariates(), meanBiasCovariatesFile, MEAN_BIAS_COVARIATES_MATRIX_NAME, targetNames, meanBiasCovariatesNames);
        /* write norm_2 of mean bias covariates to file */
        final INDArray WTW = model.getMeanBiasCovariates().transpose().mmul(model.getMeanBiasCovariates());
        final double[] biasCovariatesNorm2 = IntStream.range(0, model.getNumLatents()).mapToDouble(li -> WTW.getDouble(li, li)).toArray();
        final File biasCovariatesNorm2File = new File(outputPath, CoverageModelGlobalConstants.MEAN_BIAS_COVARIATES_NORM2_OUTPUT_FILE);
        Nd4jIOUtils.writeNDArrayMatrixToTextFile(Nd4j.create(biasCovariatesNorm2, new int[] { 1, model.getNumLatents() }), biasCovariatesNorm2File, MEAN_BIAS_COVARIATES_NORM_2_MATRIX_NAME, null, meanBiasCovariatesNames);
        /* if ARD is enabled, write the ARD coefficients and covariance of W as well */
        if (model.isARDEnabled()) {
            final File biasCovariatesARDCoefficientsFile = new File(outputPath, CoverageModelGlobalConstants.BIAS_COVARIATES_ARD_COEFFICIENTS_OUTPUT_FILE);
            Nd4jIOUtils.writeNDArrayMatrixToTextFile(model.getBiasCovariateARDCoefficients(), biasCovariatesARDCoefficientsFile, BIAS_COVARIATES_ARD_COEFFICIENTS_MATRIX_NAME, null, meanBiasCovariatesNames);
        }
    }
}

Example 9 with Target

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

the class CopyRatioSegmenterUnitTest method testChromosomesOnDifferentSegments.

@Test
public void testChromosomesOnDifferentSegments() {
    final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(563));
    final double[] trueLog2CopyRatios = new double[] { -2.0, 0.0, 1.7 };
    final double trueMemoryLength = 1e5;
    final double trueStandardDeviation = 0.2;
    // randomly set positions
    final int chainLength = 100;
    final List<SimpleInterval> positions = randomPositions("chr1", chainLength, rng, trueMemoryLength / 4);
    positions.addAll(randomPositions("chr2", chainLength, rng, trueMemoryLength / 4));
    positions.addAll(randomPositions("chr3", chainLength, rng, trueMemoryLength / 4));
    //fix everything to the same state 2
    final int trueState = 2;
    final List<Double> data = new ArrayList<>();
    for (int n = 0; n < positions.size(); n++) {
        final double copyRatio = trueLog2CopyRatios[trueState];
        final double observed = generateData(trueStandardDeviation, copyRatio, rng);
        data.add(observed);
    }
    final List<Target> targets = positions.stream().map(Target::new).collect(Collectors.toList());
    final ReadCountCollection rcc = new ReadCountCollection(targets, Arrays.asList("SAMPLE"), new Array2DRowRealMatrix(data.stream().mapToDouble(x -> x).toArray()));
    final CopyRatioSegmenter segmenter = new CopyRatioSegmenter(10, rcc);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    //check that each chromosome has at least one segment
    final int numDifferentContigsInSegments = (int) segments.stream().map(ModeledSegment::getContig).distinct().count();
    Assert.assertEquals(numDifferentContigsInSegments, 3);
}

Example 10 with Target

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method readCountAndPercentileData.

// this is duplicated from ReadCountCollectionUtilsUnitTest
@DataProvider(name = "readCountAndPercentileData")
public Object[][] readCountAndPercentileData() {
    final double[] percentiles = new double[] { 1.0, 2.5, 5.0, 10.0, 25.0 };
    final List<Object[]> result = new ArrayList<>();
    final Random rdn = new Random(13);
    final int columnCount = 100;
    final int targetCount = 100;
    final List<String> columnNames = IntStream.range(0, columnCount).mapToObj(i -> "sample_" + (i + 1)).collect(Collectors.toList());
    final List<Target> targets = IntStream.range(0, targetCount).mapToObj(i -> new Target("target_" + (i + 1))).collect(Collectors.toList());
    for (final double percentile : percentiles) {
        final double[][] counts = new double[columnCount][targetCount];
        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, percentile });
    }
    return result.toArray(new Object[result.size()][]);
}