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

Example 71 with ReadCountCollection

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method testSubsetTargetToUsableOnes.

@Test(dataProvider = "readCountAndPercentileData")
public void testSubsetTargetToUsableOnes(final ReadCountCollection readCount, final double percentile) {
    final Median median = new Median();
    final RealMatrix counts = readCount.counts();
    final double[] targetMedians = IntStream.range(0, counts.getRowDimension()).mapToDouble(i -> median.evaluate(counts.getRow(i))).toArray();
    final double threshold = new Percentile(percentile).evaluate(targetMedians);
    final Boolean[] toBeKept = DoubleStream.of(targetMedians).mapToObj(d -> d >= threshold).toArray(Boolean[]::new);
    final int toBeKeptCount = (int) Stream.of(toBeKept).filter(b -> b).count();
    final Pair<ReadCountCollection, double[]> result = HDF5PCACoveragePoNCreationUtils.subsetReadCountsToUsableTargets(readCount, percentile, NULL_LOGGER);
    Assert.assertEquals(result.getLeft().targets().size(), toBeKeptCount);
    Assert.assertEquals(result.getRight().length, toBeKeptCount);
    int nextIndex = 0;
    for (int i = 0; i < toBeKept.length; i++) {
        if (toBeKept[i]) {
            int index = result.getLeft().targets().indexOf(readCount.targets().get(i));
            Assert.assertEquals(index, nextIndex++);
            Assert.assertEquals(counts.getRow(i), result.getLeft().counts().getRow(index));
            Assert.assertEquals(result.getRight()[index], targetMedians[i]);
        } else {
            Assert.assertEquals(result.getLeft().targets().indexOf(readCount.targets().get(i)), -1);
        }
    }
}

Example 72 with ReadCountCollection

use of org.broadinstitute.hellbender.tools.exome.ReadCountCollection in project gatk 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()][]);
}

Example 73 with ReadCountCollection

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

the class PCATangentNormalizationUtilsUnitTest method normalizeReadCountByTargetFactorsData.

@DataProvider(name = "normalizeReadCountByTargetFactorsData")
public Object[][] normalizeReadCountByTargetFactorsData() {
    final List<Object[]> result = new ArrayList<>(1);
    @SuppressWarnings("serial") final List<Target> targets = new ArrayList<Target>() {

        {
            add(new Target("A"));
            add(new Target("B"));
            add(new Target("C"));
        }
    };
    @SuppressWarnings("serial") final List<String> columnNames = new ArrayList<String>() {

        {
            add("1");
            add("2");
            add("3");
        }
    };
    result.add(new Object[] { new ReadCountCollection(targets, columnNames, new Array2DRowRealMatrix(new double[][] { new double[] { 1.1, 2.2, 3.3 }, new double[] { 0.1, 0.2, 0.3 }, new double[] { 11.1, 22.2, 33.3 } }, false)), new double[] { 100.0, 200.0, 300.0 } });
    return result.toArray(new Object[1][]);
}

Example 74 with ReadCountCollection

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

the class TitanFileConverter method convertCRToTitanCovFile.

/**
     * Create a target file that is compatible with TITAN.
     *
     * @param tnFile Readable file from {@link org.broadinstitute.hellbender.tools.exome.NormalizeSomaticReadCounts}
     * @param outputFile Not {@code null}
     */
public static void convertCRToTitanCovFile(final File tnFile, final File outputFile) {
    IOUtils.canReadFile(tnFile);
    try {
        final ReadCountCollection rcc = ReadCountCollectionUtils.parse(tnFile);
        final TitanCopyRatioEstimateWriter titanCopyRatioEstimateWriter = new TitanCopyRatioEstimateWriter(outputFile);
        titanCopyRatioEstimateWriter.writeAllRecords(rcc.records());
        titanCopyRatioEstimateWriter.close();
    } catch (final IOException ioe) {
        throw new UserException.BadInput("Bad output file: " + outputFile);
    }
}