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

Example 76 with HDF5File

use of org.broadinstitute.hdf5.HDF5File in project gatk 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 77 with HDF5File

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

the class HDF5LibraryUnitTest method testOpenReadOnly.

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

Example 78 with HDF5File

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

Example 79 with HDF5File

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

the class HDF5LibraryUnitTest method testOpenReadOnlyOnBadFile.

@Test(expectedExceptions = HDF5LibException.class)
public void testOpenReadOnlyOnBadFile() {
    final HDF5File reader = new HDF5File(new File("/tmp/no-file"));
    reader.close();
}

Example 80 with HDF5File

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

the class AllelicPanelOfNormals method read.

/**
     * Reads an allelic panel of normals from an HDF5 or tab-separated file (file type is automatically detected).
     * Tab-separated files should have global hyperparameter values alpha and beta specified by comment lines
     * denoted by {@code GLOBAL_ALPHA_COMMENT_STRING} and {@code GLOBAL_BETA_COMMENT_STRING}:
     * <p>
     *     #GLOBAL_ALPHA=...<br>
     *     #GLOBAL_BETA=...
     * </p>
     * followed by lines specifying hyperparameter values at each site,
     * with column headers as in {@link AllelicPanelOfNormalsTableColumn}:
     * <p>
     *     CONTIG \t POSITION \t ALPHA \t BETA
     * </p>
     *
     * Note that we opt for a static read method as opposed to a constructor that takes a file parameter because
     * the former allows us to return the static {@code EMPTY_PON} if the allelic panel of normals is not present in
     * an HDF5 file.
     * @param inputFile    HDF5 file containing a coverage panel of normals created by {@link CreatePanelOfNormals}
     *                     and an allelic panel of normals created and set by {@link CreateAllelicPanelOfNormals}
     *                     ({@code EMPTY_PON} is returned if the latter was never set), or a
     *                     tab-separated file that contains global hyperparameters in comment lines and lines specifying hyperparameter values at each site
     */
public static AllelicPanelOfNormals read(final File inputFile) {
    IOUtils.canReadFile(inputFile);
    if (isHDF5File(inputFile)) {
        //construct from HDF5 file
        try (final HDF5File hdf5File = new HDF5File(inputFile)) {
            final AllelicPanelOfNormals allelicPoN = HDF5AllelicPoNUtils.read(hdf5File);
            logger.info(String.format("Loaded allelic panel of normals from HDF5 file: %s.", inputFile));
            return allelicPoN;
        }
    } else {
        //construct from TSV file
        try (final AllelicPanelOfNormalsReader reader = new AllelicPanelOfNormalsReader(inputFile)) {
            //parse comment lines for global hyperparameter values
            final AllelicPanelOfNormals.HyperparameterValues globalHyperparameterValues = parseGlobalHyperparameterValues(inputFile);
            //parse data lines for local hyperparameter values
            final Map<SimpleInterval, HyperparameterValues> siteToHyperparameterValuesMap = new HashMap<>();
            reader.stream().forEach(s -> siteToHyperparameterValuesMap.put(s.getKey(), s.getValue()));
            final AllelicPanelOfNormals allelicPoN = new AllelicPanelOfNormals(globalHyperparameterValues, siteToHyperparameterValuesMap);
            logger.info(String.format("Loaded allelic panel of normals from TSV file: %s.", inputFile));
            return allelicPoN;
        } catch (final IOException | UncheckedIOException ex) {
            throw new UserException.CouldNotReadInputFile(inputFile, ex);
        }
    }
}