htsjdk.samtools.cram.build

Class CompressionHeaderFactory

java.lang.Object

htsjdk.samtools.cram.build.CompressionHeaderFactory

public final class CompressionHeaderFactory
extends java.lang.Object

Factory for creating CRAM compression headers for containers when writing to a CRAM stream. The fixed data series are generally the same for every container in the stream (this is not required by the spec, but reflects the current htsjdk implementation), however, the tag data series and encodings can vary across containers based on which tags are present in the actual records for that container, and the best compressor to use based on the actual data. This class delegates to a CRAMEncodingStrategy object to determine which encodings to use for the fixed CRAM data series, and dynamically chooses the best encoding for tag data series.

Field Summary

Fields

Modifier and Type	Field and Description
static int	ALL_BYTES_USED
static int	BYTE_SPACE_SIZE

Constructor Summary

Constructors

Constructor and Description
CompressionHeaderFactory(CRAMEncodingStrategy encodingStrategy) Create a CompressionHeaderFactory using the provided CRAMEncodingStrategy.

Method Summary

Modifier and Type	Method and Description
CompressionHeader	createCompressionHeader(java.util.List<CRAMCompressionRecord> containerCRAMCompressionRecords, boolean coordinateSorted) Creates a compression header for the provided list of CRAMCompressionRecord objects.
ExternalCompressor	getBestExternalCompressor(byte[] data) Get the best external compressor to use for the given byte array.
static htsjdk.samtools.cram.build.CompressionHeaderFactory.ByteSizeRange	getByteSizeRangeOfTagValues(java.util.List<CRAMCompressionRecord> records, int tagID)
CRAMEncodingStrategy	getEncodingStrategy()

Methods inherited from class java.lang.Object

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

Field Detail

BYTE_SPACE_SIZE

public static final int BYTE_SPACE_SIZE

See Also:

Constant Field Values

ALL_BYTES_USED

public static final int ALL_BYTES_USED

See Also:

Constant Field Values

Constructor Detail

CompressionHeaderFactory

public CompressionHeaderFactory(CRAMEncodingStrategy encodingStrategy)

Create a CompressionHeaderFactory using the provided CRAMEncodingStrategy.

Parameters:

encodingStrategy - CRAMEncodingStrategy to use, may not be null

Method Detail

createCompressionHeader

public CompressionHeader createCompressionHeader(java.util.List<CRAMCompressionRecord> containerCRAMCompressionRecords,
                                                 boolean coordinateSorted)

Creates a compression header for the provided list of CRAMCompressionRecord objects. Resets any internal state (i.e. the tag encoding map state) as preparation for starting the next compression header.

Parameters:

containerCRAMCompressionRecords - all CRAMRecords that will be stored in the container

coordinateSorted - if true the records are assumed to be sorted by alignment position

Returns:

CompressionHeader for the container for containerCRAMRecords

getEncodingStrategy

public CRAMEncodingStrategy getEncodingStrategy()

getBestExternalCompressor

public ExternalCompressor getBestExternalCompressor(byte[] data)

Get the best external compressor to use for the given byte array.

Parameters:

data - byte array to compress

Returns:

best compressor to use for the data

getByteSizeRangeOfTagValues

public static htsjdk.samtools.cram.build.CompressionHeaderFactory.ByteSizeRange getByteSizeRangeOfTagValues(java.util.List<CRAMCompressionRecord> records,
                                                                                                            int tagID)