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

Example 51 with HDF5File

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

the class HDF5PCACoveragePoNUnitTest method testLogNormalizedMatrixReading.

@Test(dependsOnMethods = { "testTargetNameReading", "testLogNormalizedSampleNameReading" })
public void testLogNormalizedMatrixReading() 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.getLogNormalizedCounts();
    Assert.assertNotNull(actual);
    Assert.assertEquals(actual.getRowDimension(), targets.size());
    Assert.assertEquals(actual.getColumnDimension(), samples.size());
    final RealMatrix expected = readDoubleMatrix(TEST_PON_LOG_NORMALS);
    MathObjectAsserts.assertRealMatrixEquals(actual, expected);
}

Example 52 with HDF5File

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

the class PCATangentNormalizationUtilsUnitTest method testSparkNormalizeNormalsSomePoN.

@Test
public void testSparkNormalizeNormalsSomePoN() {
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    try (final HDF5File ponHDF5File = new HDF5File(TEST_SOME_PON)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponHDF5File);
        final RealMatrix gtTNedNormals = PoNTestUtils.readTsvIntoMatrix(TEST_SOME_NORMALS_TN_FILE);
        final PCATangentNormalizationResult tnWithSpark = pon.normalizeNormalsInPoN(ctx);
        PoNTestUtils.assertEqualsMatrix(tnWithSpark.getTangentNormalized().counts(), gtTNedNormals, false);
    }
}

Example 53 with HDF5File

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

the class PCATangentNormalizationUtilsUnitTest method testSparkNormalizeNormalsFullPoN.

@Test
public void testSparkNormalizeNormalsFullPoN() {
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    try (final HDF5File ponHDF5File = new HDF5File(TEST_FULL_PON)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponHDF5File);
        final RealMatrix gtTNedNormals = PoNTestUtils.readTsvIntoMatrix(TEST_FULL_NORMALS_TN_FILE);
        final PCATangentNormalizationResult tnWithSpark = pon.normalizeNormalsInPoN(ctx);
        PoNTestUtils.assertEqualsMatrix(tnWithSpark.getTangentNormalized().counts(), gtTNedNormals, false);
    }
}

Example 54 with HDF5File

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

the class PCATangentNormalizationUtilsUnitTest method testSparkTangentNormalizeSparkVsNoSpark.

@Test
public void testSparkTangentNormalizeSparkVsNoSpark() {
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    final File ponFile = PoNTestUtils.createDummyHDF5FilePoN(TEST_PCOV_FILE, 20);
    try (final HDF5File ponHDF5File = new HDF5File(ponFile)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponHDF5File);
        final PCATangentNormalizationResult tnWithSpark = pon.normalizeNormalsInPoN(ctx);
        final PCATangentNormalizationResult tnWithoutSpark = pon.normalizeNormalsInPoN();
        PoNTestUtils.assertEqualsMatrix(tnWithSpark.getTangentNormalized().counts(), tnWithoutSpark.getTangentNormalized().counts(), false);
        PoNTestUtils.assertEqualsMatrix(tnWithSpark.getPreTangentNormalized().counts(), tnWithoutSpark.getPreTangentNormalized().counts(), false);
        PoNTestUtils.assertEqualsMatrix(tnWithSpark.getTangentBetaHats(), tnWithoutSpark.getTangentBetaHats(), false);
    }
}

Example 55 with HDF5File

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

the class RamPCACoveragePoNUnitTest method testCopiesReturnedOfMatrices.

@Test
public void testCopiesReturnedOfMatrices() {
    final PCACoveragePoN filePoN = new HDF5PCACoveragePoN(new HDF5File(PoNTestUtils.createDummyHDF5FilePoN(TEST_PCOV_FILE, 20), HDF5File.OpenMode.READ_ONLY));
    final PCACoveragePoN ramPoN = new RamPCACoveragePoN(filePoN);
    assertNormalizedCounts(filePoN, ramPoN);
    assertLogNormalizedCounts(filePoN, ramPoN);
    assertLogNormalizedPinvCounts(filePoN, ramPoN);
    assertReducedPanelCounts(filePoN, ramPoN);
    assertLogNormalizedPinvCounts(filePoN, ramPoN);
    assertReducedPanelPInverseCounts(filePoN, ramPoN);
    PoNTestUtils.assertEquivalentPoN(ramPoN, filePoN);
}