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

Example 66 with HDF5File

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

the class HDF5PCACoveragePoNCreationUtilsUnitTest method testCalculateVarianceCalculation.

@Test
public void testCalculateVarianceCalculation() {
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    try (final HDF5File ponHDF5File = new HDF5File(TEST_FULL_PON_FILE)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponHDF5File);
        final PCATangentNormalizationResult tnWithSpark = pon.normalizeNormalsInPoN(ctx);
        final double[] variances = MatrixSummaryUtils.getRowVariances(tnWithSpark.getTangentNormalized().counts());
        final double[] targetVariances = pon.getTargetVariances();
        PoNTestUtils.assertEqualsDoubleArrays(targetVariances, variances);
    }
}

Example 67 with HDF5File

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

the class HDF5PCACoveragePoNUnitTest method testTargetNameReading.

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

Example 68 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk-protected 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 69 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk-protected 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 70 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk-protected 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);
}