Examples with HDF5File org.broadinstitute.hdf5.HDF5File used on opensource projects

Example 21 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk by broadinstitute.

the class NormalizeSomaticReadCountsIntegrationTest method assertBetaHats.

/**
     * Asserts that a collection of beta-hats corresponds to the expected value given
     * the input pre-tangent normalization matrix and the PoN file.
     */
private void assertBetaHats(final ReadCountCollection preTangentNormalized, final RealMatrix actual, final File ponFile) {
    Assert.assertEquals(actual.getColumnDimension(), preTangentNormalized.columnNames().size());
    final double epsilon = PCATangentNormalizationUtils.EPSILON;
    try (final HDF5File ponReader = new HDF5File(ponFile)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponReader);
        final List<String> ponTargets = pon.getPanelTargetNames();
        final RealMatrix inCounts = reorderTargetsToPoNOrder(preTangentNormalized, ponTargets);
        // obtain subset of relevant targets to calculate the beta-hats;
        final int[][] betaHatTargets = new int[inCounts.getColumnDimension()][];
        for (int i = 0; i < inCounts.getColumnDimension(); i++) {
            final List<Integer> relevantTargets = new ArrayList<>();
            for (int j = 0; j < inCounts.getRowDimension(); j++) {
                if (inCounts.getEntry(j, i) > 1 + (Math.log(epsilon) / Math.log(2))) {
                    relevantTargets.add(j);
                }
            }
            betaHatTargets[i] = relevantTargets.stream().mapToInt(Integer::intValue).toArray();
        }
        // calculate beta-hats per column and check with actual values.
        final RealMatrix normalsInv = pon.getReducedPanelPInverseCounts();
        Assert.assertEquals(actual.getRowDimension(), normalsInv.getRowDimension());
        final RealMatrix normalsInvT = normalsInv.transpose();
        for (int i = 0; i < inCounts.getColumnDimension(); i++) {
            final RealMatrix inValues = inCounts.getColumnMatrix(i).transpose().getSubMatrix(new int[] { 0 }, betaHatTargets[i]);
            final RealMatrix normalValues = normalsInvT.getSubMatrix(betaHatTargets[i], IntStream.range(0, normalsInvT.getColumnDimension()).toArray());
            final RealMatrix betaHats = inValues.multiply(normalValues);
            for (int j = 0; j < actual.getRowDimension(); j++) {
                Assert.assertEquals(actual.getEntry(j, i), betaHats.getEntry(0, j), 0.000001, "Col " + i + " row " + j);
            }
        }
    }
}

Example 22 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk by broadinstitute.

the class HDF5PCACoveragePoNUnitTest method testVersionReading.

@Test
public void testVersionReading() {
    final HDF5File reader = new HDF5File(TEST_PON);
    final PCACoveragePoN pon = new HDF5PCACoveragePoN(reader);
    Assert.assertEquals(pon.getVersion(), TEST_PON_VERSION);
    reader.close();
}

Example 23 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk by broadinstitute.

the class HDF5PCACoveragePoNUnitTest method testReducedPoNMatrixReading.

@Test(dependsOnMethods = { "testTargetNameReading", "testLogNormalizedSampleNameReading" })
public void testReducedPoNMatrixReading() throws IOException {
    final HDF5File reader = new HDF5File(TEST_PON);
    final PCACoveragePoN pon = new HDF5PCACoveragePoN(reader);
    final List<String> targets = pon.getTargetNames();
    final List<String> samples = pon.getPanelSampleNames();
    final RealMatrix actual = pon.getReducedPanelCounts();
    Assert.assertNotNull(actual);
    Assert.assertEquals(actual.getRowDimension(), targets.size());
    Assert.assertTrue(actual.getColumnDimension() <= samples.size());
    final RealMatrix expected = readDoubleMatrix(TEST_PON_REDUCED_PON);
    MathObjectAsserts.assertRealMatrixEquals(actual, expected);
}

Example 24 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk by broadinstitute.

the class HDF5PCACoveragePoNUnitTest method testReducedPoNPInvMatrixReading.

@Test(dependsOnMethods = { "testTargetNameReading", "testLogNormalizedSampleNameReading" })
public void testReducedPoNPInvMatrixReading() throws IOException {
    final HDF5File reader = new HDF5File(TEST_PON);
    final PCACoveragePoN pon = new HDF5PCACoveragePoN(reader);
    final List<String> targets = pon.getTargetNames();
    final List<String> samples = pon.getPanelSampleNames();
    final RealMatrix actual = pon.getReducedPanelPInverseCounts();
    Assert.assertNotNull(actual);
    Assert.assertTrue(actual.getRowDimension() <= samples.size());
    Assert.assertEquals(actual.getColumnDimension(), targets.size());
    final RealMatrix expected = readDoubleMatrix(TEST_PON_REDUCED_PON_PINV);
    MathObjectAsserts.assertRealMatrixEquals(actual, expected);
}

Example 25 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk by broadinstitute.

the class HDF5PCACoveragePoNUnitTest method testSampleNameReading.

@Test
public void testSampleNameReading() throws IOException {
    final HDF5File reader = new HDF5File(TEST_PON);
    final PCACoveragePoN pon = new HDF5PCACoveragePoN(reader);
    final List<String> sampleNames = pon.getSampleNames();
    final List<String> expected = readLines(TEST_PON_SAMPLES);
    Assert.assertNotNull(sampleNames);
    Assert.assertEquals(sampleNames, expected);
    reader.close();
}