Package org.broadinstitute.hellbender.tools.copynumber.utils

Class HDF5Utils

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils

public final class HDF5Utils
extends Object

TODO move into hdf5-java-bindings

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CHUNK_INDEX_PATH_SUFFIX
static final String	INTERVAL_CONTIG_NAMES_SUB_PATH
static final String	INTERVAL_MATRIX_SUB_PATH
static final int	MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX
static final String	NUMBER_OF_CHUNKS_SUB_PATH
static final String	NUMBER_OF_COLUMNS_SUB_PATH
static final String	NUMBER_OF_ROWS_SUB_PATH

Method Summary

Modifier and Type	Method	Description
static double[][]	readChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File file, String path)	Reads a large matrix stored as a set of chunks (submatrices) using the sub-paths and conventions used by writeChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File, java.lang.String, double[][], int).
static List<SimpleInterval>	readIntervals(org.broadinstitute.hdf5.HDF5File file, String path)	Reads a list of intervals from an HDF5 file using the sub-paths and conventions used by writeIntervals(org.broadinstitute.hdf5.HDF5File, java.lang.String, java.util.List<T>).
static void	writeChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File file, String path, double[][] matrix, int maxChunkSize)	Given a large matrix, chunks the matrix into equally sized subsets of rows (plus a subset containing the remainder, if necessary) and writes these submatrices to indexed sub-paths to avoid a hard limit in Java HDF5 on the number of elements in a matrix given by MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX.
static <T extends SimpleInterval> void	writeIntervals(org.broadinstitute.hdf5.HDF5File file, String path, List<T> intervals)	Given an HDF5 file and an HDF5 path, writes a list of intervals to hard-coded sub-paths.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

INTERVAL_CONTIG_NAMES_SUB_PATH

public static final String INTERVAL_CONTIG_NAMES_SUB_PATH

See Also:

• Constant Field Values

INTERVAL_MATRIX_SUB_PATH

public static final String INTERVAL_MATRIX_SUB_PATH

See Also:

• Constant Field Values

MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX

public static final int MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX

See Also:

• Constant Field Values

NUMBER_OF_ROWS_SUB_PATH

public static final String NUMBER_OF_ROWS_SUB_PATH

See Also:

• Constant Field Values

NUMBER_OF_COLUMNS_SUB_PATH

public static final String NUMBER_OF_COLUMNS_SUB_PATH

See Also:

• Constant Field Values

NUMBER_OF_CHUNKS_SUB_PATH

public static final String NUMBER_OF_CHUNKS_SUB_PATH

See Also:

• Constant Field Values

CHUNK_INDEX_PATH_SUFFIX

public static final String CHUNK_INDEX_PATH_SUFFIX

See Also:

• Constant Field Values

Method Details

readIntervals

public static List<SimpleInterval> readIntervals(org.broadinstitute.hdf5.HDF5File file,
 String path)

Reads a list of intervals from an HDF5 file using the sub-paths and conventions used by writeIntervals(org.broadinstitute.hdf5.HDF5File, java.lang.String, java.util.List<T>).

writeIntervals

public static <T extends SimpleInterval> void writeIntervals(org.broadinstitute.hdf5.HDF5File file,
 String path,
 List<T> intervals)

Given an HDF5 file and an HDF5 path, writes a list of intervals to hard-coded sub-paths. Contig names are represented by a string array, while intervals are represented by a double matrix, in which the contigs are represented by their index in the aforementioned string array.

readChunkedDoubleMatrix

public static double[][] readChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File file,
 String path)

Reads a large matrix stored as a set of chunks (submatrices) using the sub-paths and conventions used by writeChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File, java.lang.String, double[][], int).

writeChunkedDoubleMatrix

public static void writeChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File file,
 String path,
 double[][] matrix,
 int maxChunkSize)

Given a large matrix, chunks the matrix into equally sized subsets of rows (plus a subset containing the remainder, if necessary) and writes these submatrices to indexed sub-paths to avoid a hard limit in Java HDF5 on the number of elements in a matrix given by MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX. The number of chunks is determined by maxChunkSize, which should be set appropriately for the desired number of columns.

Parameters:

maxChunkSize - The maximum number of values in each chunk. Decreasing this number will reduce heap usage when writing chunks, which requires subarrays to be copied. However, since a single row is not allowed to be split across multiple chunks, the number of columns must be less than the maximum number of values in each chunk.