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

Example 36 with HDF5File

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

Example 37 with HDF5File

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

the class CreatePanelOfNormalsIntegrationTest method assertBasicPoNAssumptions.

private void assertBasicPoNAssumptions(final File ponFile, final File initialTargetsFileUsedToCreatePoN) {
    try (final HDF5File ponHDF5File = new HDF5File(ponFile)) {
        final HDF5PCACoveragePoN pon = new HDF5PCACoveragePoN(ponHDF5File);
        Assert.assertTrue(pon.getTargets().size() >= pon.getPanelTargets().size());
        Assert.assertTrue(pon.getRawTargets().size() > pon.getTargets().size());
        Assert.assertTrue(pon.getTargetNames().size() == pon.getTargets().size());
        Assert.assertTrue(pon.getPanelTargetNames().size() == pon.getPanelTargetNames().size());
        Assert.assertTrue(pon.getRawTargetNames().size() == pon.getRawTargetNames().size());
        if (initialTargetsFileUsedToCreatePoN != null) {
            final TargetCollection<Target> tc = TargetArgumentCollection.readTargetCollection(initialTargetsFileUsedToCreatePoN);
            Assert.assertEquals(pon.getRawTargets().size(), tc.targetCount());
            // Check that the raw targets are the same
            Assert.assertTrue(IntStream.of(new IntRange(0, pon.getRawTargets().size() - 1).toArray()).boxed().map(i -> pon.getRawTargets().get(i).equals(tc.target(i))).allMatch(t -> t));
        }
    }
}

Example 38 with HDF5File

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

the class HDF5LibraryUnitTest method testOpenReadOnly.

@Test
public void testOpenReadOnly() {
    final HDF5File reader = new HDF5File(TEST_PON);
    reader.close();
}

Example 39 with HDF5File

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

the class HDF5LibraryUnitTest method testCreateLargeMatrix.

@Test
public void testCreateLargeMatrix() {
    // Creates a large PoN of junk values and simply tests that these can be written and read.
    // Make a big, fake set of read counts.
    final int numRows = 2500000;
    final int numCols = 10;
    final double mean = 3e-7;
    final double sigma = 1e-9;
    final RealMatrix bigCounts = createMatrixOfGaussianValues(numRows, numCols, mean, sigma);
    final File tempOutputHD5 = IOUtils.createTempFile("big-ol-", ".hd5");
    final HDF5File hdf5File = new HDF5File(tempOutputHD5, HDF5File.OpenMode.CREATE);
    final String hdf5Path = "/test/m";
    hdf5File.makeDoubleMatrix(hdf5Path, bigCounts.getData());
    hdf5File.close();
    final HDF5File hdf5FileForReading = new HDF5File(tempOutputHD5, HDF5File.OpenMode.READ_ONLY);
    final double[][] result = hdf5FileForReading.readDoubleMatrix(hdf5Path);
    final RealMatrix resultAsRealMatrix = new Array2DRowRealMatrix(result);
    Assert.assertTrue(resultAsRealMatrix.getRowDimension() == numRows);
    Assert.assertTrue(resultAsRealMatrix.getColumnDimension() == numCols);
    final RealMatrix readMatrix = new Array2DRowRealMatrix(result);
    PoNTestUtils.assertEqualsMatrix(readMatrix, bigCounts, false);
}

Example 40 with HDF5File

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

the class HDF5LibraryUnitTest method testMakeDouble.

@Test()
public void testMakeDouble() throws IOException {
    final File testFile = File.createTempFile("hdf5", ".hd5");
    HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE);
    file.makeGroup("test-group/double-group");
    Assert.assertTrue(file.makeDouble("test-group/double-group/my-double", 1.1));
    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 theDouble = file.readDouble("test-group/double-group/my-double");
    Assert.assertEquals(theDouble, 1.1);
    file.close();
}