Examples with Array2DRowRealMatrix org.apache.commons.math3.linear.Array2DRowRealMatrix used on opensource projects

Example 16 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk-protected 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 17 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk-protected by broadinstitute.

the class CopyRatioSegmenterUnitTest method testSegmentation.

@Test
public void testSegmentation() {
    final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(563));
    final List<Double> trueWeights = Arrays.asList(0.2, 0.5, 0.3);
    final List<Double> trueLog2CopyRatios = Arrays.asList(-2.0, 0.0, 1.4);
    final double trueMemoryLength = 1e5;
    final double trueStandardDeviation = 0.2;
    final CopyRatioHMM trueModel = new CopyRatioHMM(trueLog2CopyRatios, trueWeights, trueMemoryLength, trueStandardDeviation);
    final int chainLength = 10000;
    final List<SimpleInterval> positions = randomPositions("chr1", chainLength, rng, trueMemoryLength / 4);
    final List<Integer> trueStates = trueModel.generateHiddenStateChain(positions);
    final List<Double> trueLog2CopyRatioSequence = trueStates.stream().map(n -> trueLog2CopyRatios.get(n)).collect(Collectors.toList());
    final List<Double> data = trueLog2CopyRatioSequence.stream().map(cr -> generateData(trueStandardDeviation, cr, rng)).collect(Collectors.toList());
    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();
    final double[] segmentCopyRatios = segments.stream().flatMap(s -> Collections.nCopies((int) s.getTargetCount(), s.getSegmentMeanInLog2CRSpace()).stream()).mapToDouble(x -> x).toArray();
    final double averageCopyRatioError = IntStream.range(0, trueLog2CopyRatioSequence.size()).mapToDouble(n -> Math.abs(segmentCopyRatios[n] - trueLog2CopyRatioSequence.get(n))).average().getAsDouble();
    Assert.assertEquals(averageCopyRatioError, 0, 0.025);
}

Example 18 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class ReadCountCollection method subsetColumns.

/**
     * Subsets the count columns in the read-count collection.
     *
     * <p>
     *     Creates a brand-new read-count collection. Changes in the new instance won't affect this one and vice-versa.
     * </p>
     *
     * @param columnsToKeep column names to keep in the result read-count collection.
     * @return never {@code null}.
     */
public ReadCountCollection subsetColumns(final Set<String> columnsToKeep) {
    Utils.nonNull(columnsToKeep, "the set of input columns to keep cannot be null.");
    Utils.nonEmpty(columnsToKeep, "the number of columns to keep must be greater than 0");
    if (!new HashSet<>(columnNames).containsAll(columnsToKeep)) {
        throw unknownColumnToKeepNames(columnsToKeep);
    }
    if (columnsToKeep.size() == columnNames.size()) {
        return new ReadCountCollection(targets, columnNames, counts.copy(), false);
    }
    final int[] columnsToKeepIndices = IntStream.range(0, columnNames.size()).filter(i -> columnsToKeep.contains(columnNames.get(i))).toArray();
    final List<String> resultColumnNames = Arrays.stream(columnsToKeepIndices).mapToObj(columnNames::get).collect(Collectors.toList());
    final RealMatrix resultCountsM = new Array2DRowRealMatrix(counts.getRowDimension(), columnsToKeepIndices.length);
    for (int i = 0; i < columnsToKeepIndices.length; i++) {
        resultCountsM.setColumn(i, counts.getColumn(columnsToKeepIndices[i]));
    }
    return new ReadCountCollection(targets, Collections.unmodifiableList(resultColumnNames), resultCountsM, false);
}

Example 19 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class ReadCountCollection method arrangeTargets.

/**
     * Rearrange the targets so that they are in a particular order.
     * @return a new collection.
     * @throws IllegalArgumentException if any of the following is true:
     * <ul>
     *     <li>{@code targetsInOrder} is {@code null},</li>
     *     <li>is empty,</li>
     *     <li>it contains {@code null},</li>
     *     <li>contains any target not present in this collection.</li>
     * </ul>
     */
public ReadCountCollection arrangeTargets(final List<Target> targetsInOrder) {
    Utils.nonNull(targetsInOrder);
    Utils.nonEmpty(targetsInOrder, "the input targets list cannot be empty");
    final RealMatrix counts = new Array2DRowRealMatrix(targetsInOrder.size(), columnNames.size());
    final Object2IntMap<Target> targetToIndex = new Object2IntOpenHashMap<>(targets.size());
    for (int i = 0; i < targets.size(); i++) {
        targetToIndex.put(targets.get(i), i);
    }
    for (int i = 0; i < targetsInOrder.size(); i++) {
        final Target target = targetsInOrder.get(i);
        Utils.validateArg(targetToIndex.containsKey(target), () -> String.format("target '%s' is not present in the collection", target.getName()));
        counts.setRow(i, this.counts.getRow(targetToIndex.getInt(target)));
    }
    return new ReadCountCollection(new ArrayList<>(targetsInOrder), columnNames, counts, false);
}

Example 20 with Array2DRowRealMatrix

use of org.apache.commons.math3.linear.Array2DRowRealMatrix in project gatk by broadinstitute.

the class ReadCountCollectionUtils method readCounts.

/**
     * Reads the counts section of the file and create the resulting collection.
     *
     * @param sourceName  the source name (used in error messages).
     * @param tableReader the source table-reader.
     * @param columnNames the name of the columns.
     * @return never {@code null}.
     * @throws IOException if there is a low level IO error.
     */
private static ReadCountCollection readCounts(final String sourceName, final TableReader<ReadCountRecord> tableReader, final List<String> columnNames) throws IOException {
    final Buffer buffer = new Buffer();
    ReadCountRecord record;
    while ((record = tableReader.readRecord()) != null) {
        final Target target = record.getTarget();
        final double[] lineCounts = record.getDoubleCounts();
        if (!buffer.add(target, lineCounts)) {
            throw new UserException.BadInput(String.format("duplicated target with name %s in %s", target.getName(), sourceName));
        }
    }
    if (buffer.getTargets().isEmpty()) {
        throw new UserException.BadInput("there is no counts (zero targets) in the input source " + sourceName);
    }
    return new ReadCountCollection(buffer.getTargets(), columnNames, new Array2DRowRealMatrix(buffer.getCounts(), false));
}