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

Example 71 with HDF5File

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

the class HDF5PCACoveragePoNUnitTest method testLogNormalizedPInvMatrixReading.

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

Example 72 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk-protected 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 73 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk-protected 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 74 with HDF5File

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

Example 75 with HDF5File

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

the class HDF5LibraryUnitTest method testMakeDoubleMatrix.

@Test()
public void testMakeDoubleMatrix() throws IOException {
    final File testFile = File.createTempFile("hdf5", ".hd5");
    HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE);
    file.makeGroup("test-group/double-group");
    final double[][] testValues = new double[][] { new double[] { 1.1, -2.2, Double.POSITIVE_INFINITY, Double.NEGATIVE_INFINITY, 0.0111e10 - 10 }, new double[] { -1.1, 2.2, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, -0.01111e10 - 10 } };
    Assert.assertTrue(file.makeDoubleMatrix("test-group/double-group/my-double", testValues));
    System.err.println(testFile);
    file.close();
    final long time = System.currentTimeMillis();
    Assert.assertTrue(testFile.length() > 0);
    Assert.assertTrue(testFile.lastModified() <= time);
    file = new HDF5File(testFile, HDF5File.OpenMode.READ_ONLY);
    final double[][] theDoubles = file.readDoubleMatrix("test-group/double-group/my-double");
    Assert.assertTrue(Arrays.deepEquals(theDoubles, testValues.clone()));
    file.close();
}