org.broadinstitute.hellbender.tools.copynumber.utils

Class HDF5Utils

java.lang.Object

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

public final class HDF5Utils
extends java.lang.Object

TODO move into hdf5-java-bindings

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CHUNK_INDEX_PATH_SUFFIX
static java.lang.String	INTERVAL_CONTIG_NAMES_SUB_PATH
static java.lang.String	INTERVAL_MATRIX_SUB_PATH
static int	MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX
static java.lang.String	NUMBER_OF_CHUNKS_SUB_PATH
static java.lang.String	NUMBER_OF_COLUMNS_SUB_PATH
static java.lang.String	NUMBER_OF_ROWS_SUB_PATH

Method Summary

Modifier and Type	Method and Description
static double[][]	readChunkedDoubleMatrix(org.broadinstitute.hdf5.HDF5File file, java.lang.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 java.util.List<SimpleInterval>	readIntervals(org.broadinstitute.hdf5.HDF5File file, java.lang.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, java.lang.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_NUM_VALUES_PER_HDF5_MATRIX.
static <T extends SimpleInterval> void	writeIntervals(org.broadinstitute.hdf5.HDF5File file, java.lang.String path, java.util.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 Detail

INTERVAL_CONTIG_NAMES_SUB_PATH

public static final java.lang.String INTERVAL_CONTIG_NAMES_SUB_PATH

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Constant Field Values

INTERVAL_MATRIX_SUB_PATH

public static final java.lang.String INTERVAL_MATRIX_SUB_PATH

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Constant Field Values

MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX

public static final int MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX

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Constant Field Values

NUMBER_OF_ROWS_SUB_PATH

public static final java.lang.String NUMBER_OF_ROWS_SUB_PATH

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Constant Field Values

NUMBER_OF_COLUMNS_SUB_PATH

public static final java.lang.String NUMBER_OF_COLUMNS_SUB_PATH

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Constant Field Values

NUMBER_OF_CHUNKS_SUB_PATH

public static final java.lang.String NUMBER_OF_CHUNKS_SUB_PATH

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Constant Field Values

CHUNK_INDEX_PATH_SUFFIX

public static final java.lang.String CHUNK_INDEX_PATH_SUFFIX

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Constant Field Values

Method Detail

readIntervals

public static java.util.List<SimpleInterval> readIntervals(org.broadinstitute.hdf5.HDF5File file,
                                                           java.lang.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,
                                                             java.lang.String path,
                                                             java.util.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,
                                                 java.lang.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,
                                            java.lang.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_NUM_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.