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

Example 1 with Target

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

the class HDF5PCACoveragePoN method renderPoNTargets.

private static List<Target> renderPoNTargets(final String[][] values, final List<String> targetNamesToRender, final HDF5File reader) {
    if (values.length != targetNamesToRender.size()) {
        throw new GATKException(String.format("Wrong number of elements in the targets recovered " + "from file '%s': number of targets found in file (%d) != number of target names (%d)", reader.getFile(), values.length, targetNamesToRender.size()));
    }
    final int numTargetCols = (int) reader.readDouble(NUM_TARGET_COLUMNS_PATH);
    final List<Target> result = new ArrayList<>(values.length);
    for (int i = 0; i < values.length; i++) {
        if (values[i].length != numTargetCols) {
            throw new GATKException(String.format("Wrong number of column elements in the targets recovered " + "from file '%s': number of columns found in file (%d) != number of target columns (%d)", reader.getFile(), values[i].length, numTargetCols));
        }
        result.add(new Target(targetNamesToRender.get(i), new SimpleInterval(values[i][0], Integer.parseInt(values[i][1]), Integer.parseInt(values[i][2]))));
    }
    return result;
}

Example 2 with Target

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

the class HDF5PCACoveragePoN method writeTargets.

private void writeTargets(final String fullPath, List<Target> targets) {
    final String[][] targetValues = new String[targets.size()][NUM_TARGET_COLUMNS];
    for (int i = 0; i < targets.size(); i++) {
        final Target target = targets.get(i);
        targetValues[i][targetColumnToPoNIndex.get(TargetTableColumn.CONTIG)] = target.getContig();
        targetValues[i][targetColumnToPoNIndex.get(TargetTableColumn.START)] = String.valueOf(target.getStart());
        targetValues[i][targetColumnToPoNIndex.get(TargetTableColumn.END)] = String.valueOf(target.getEnd());
    }
    file.makeStringMatrix(fullPath, targetValues, NUM_TARGET_COLUMNS_PATH);
}

Example 3 with Target

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method simpleEigensampleData.

@DataProvider(name = "singleEigensample")
public Object[][] simpleEigensampleData() {
    final List<Object[]> result = new ArrayList<>();
    final int NUM_TARGETS = 10;
    final int NUM_SAMPLES = 5;
    final List<Target> targets = IntStream.range(0, NUM_TARGETS).boxed().map(i -> new Target("target_" + i, new SimpleInterval("1", 100 * i + 1, 100 * i + 5))).collect(Collectors.toList());
    final List<String> columnNames = IntStream.range(0, NUM_SAMPLES).boxed().map(i -> "sample_" + i).collect(Collectors.toList());
    double[][] countsArray = new double[NUM_TARGETS][NUM_SAMPLES];
    final RealMatrix counts = new Array2DRowRealMatrix(countsArray);
    // All row data is the same (0,1,2,3,4...)
    final double[] rowData = IntStream.range(0, NUM_SAMPLES).boxed().mapToDouble(i -> i).toArray();
    for (int i = 0; i < NUM_TARGETS; i++) {
        counts.setRow(i, rowData);
    }
    new ReadCountCollection(targets, columnNames, counts);
    result.add(new Object[] { new ReadCountCollection(targets, columnNames, counts) });
    return result.toArray(new Object[result.size()][]);
}

Example 4 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk 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 5 with Target

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

the class CoverageModelParameters method read.

/**
     * Reads the model from disk.
     *
     * @param modelPath input model path
     * @return an instance of {@link CoverageModelParameters}
     */
public static CoverageModelParameters read(@Nonnull final String modelPath) {
    final File modelPathFile = new File(Utils.nonNull(modelPath, "The input model path must be non-null"));
    Utils.validateArg(modelPathFile.exists(), "The model path does not exist: " + modelPathFile.getAbsolutePath());
    final File targetListFile = new File(modelPath, CoverageModelGlobalConstants.TARGET_LIST_OUTPUT_FILE);
    final List<Target> targetList;
    try (final Reader reader = new FileReader(targetListFile)) {
        targetList = TargetTableReader.readTargetFromReader(targetListFile.getAbsolutePath(), reader);
    } catch (final IOException ex) {
        throw new UserException.CouldNotCreateOutputFile(targetListFile, "Could not read targets interval list");
    }
    /* all models must provide mean log bias and target-specific unexplained variance */
    final File targetMeanLogBiasFile = new File(modelPath, CoverageModelGlobalConstants.TARGET_MEAN_LOG_BIAS_OUTPUT_FILE);
    final INDArray targetMeanLogBias = Nd4jIOUtils.readNDArrayMatrixFromTextFile(targetMeanLogBiasFile).transpose();
    final File targetUnexplainedVarianceFile = new File(modelPath, CoverageModelGlobalConstants.TARGET_UNEXPLAINED_VARIANCE_OUTPUT_FILE);
    final INDArray targetUnexplainedVariance = Nd4jIOUtils.readNDArrayMatrixFromTextFile(targetUnexplainedVarianceFile).transpose();
    /* if the bias covariates file is found, then the model has bias covariates enabled */
    final File meanBiasCovariatesFile = new File(modelPath, CoverageModelGlobalConstants.MEAN_BIAS_COVARIATES_OUTPUT_FILE);
    final INDArray meanBiasCovariates, biasCovariatesARDCoefficients;
    if (meanBiasCovariatesFile.exists()) {
        meanBiasCovariates = Nd4jIOUtils.readNDArrayMatrixFromTextFile(meanBiasCovariatesFile);
        /* check to see if we have ARD coefficients */
        final File biasCovariatesARDCoefficientsFile = new File(modelPath, CoverageModelGlobalConstants.BIAS_COVARIATES_ARD_COEFFICIENTS_OUTPUT_FILE);
        if (biasCovariatesARDCoefficientsFile.exists()) {
            /* ARD enabled */
            biasCovariatesARDCoefficients = Nd4jIOUtils.readNDArrayMatrixFromTextFile(biasCovariatesARDCoefficientsFile);
        } else {
            biasCovariatesARDCoefficients = null;
        }
    } else {
        meanBiasCovariates = null;
        biasCovariatesARDCoefficients = null;
    }
    return new CoverageModelParameters(targetList, targetMeanLogBias, targetUnexplainedVariance, meanBiasCovariates, biasCovariatesARDCoefficients);
}