htsjdk.samtools.cram.structure

Class CompressionHeaderEncodingMap

java.lang.Object

htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap

public class CompressionHeaderEncodingMap
extends java.lang.Object

Maintains a map of DataSeries to EncodingDescriptor, and a second map that contains the compressor to use for each EncodingDescriptor that represents an EXTERNAL encoding. There are two constructors; one populates the map from scratch using the default encodings chosen by this (htsjdk) implementation, used when writing a new CRAM; one populates the map from a serialized CRAM stream resulting in encodings chosen by the implementation that wrote that CRAM. Although the CRAM spec defines a fixed list of data series, individual CRAM implementations may choose to use only a subset of these. Therefore, the actual set of encodings that are instantiated can vary depending on the source. Notes on the htsjdk CRAM write implementation: This implementation encodes ALL DataSeries to external blocks, (although some of the external encodings split the data between core and external; see ByteArrayLenEncoding, and does not use the 'BB' or 'QQ' DataSeries when writing CRAM at all. Relies heavily on GZIP and RANS for compression. See EncodingFactory for details on how an EncodingDescriptor is mapped to the codec that actually transfers data to and from underlying Slice blocks.

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Set<DataSeries>	DATASERIES_NOT_READ_BY_HTSJDK

Constructor Summary

Constructors

Constructor and Description
CompressionHeaderEncodingMap(CRAMEncodingStrategy encodingStrategy) Constructor used to create the default encoding map for writing CRAMs.
CompressionHeaderEncodingMap(java.io.InputStream inputStream) Constructor used to discover an encoding map from a serialized CRAM stream.

Method Summary

Modifier and Type	Method and Description
Block	createCompressedBlockForStream(java.lang.Integer contentId, java.io.ByteArrayOutputStream outputStream) Given a content ID, return a Block for that ID by obtaining the contents of the stream, compressing it using the compressor for that contentID, and converting the result to a Block.
boolean	equals(java.lang.Object o)
ExternalCompressor	getBestExternalCompressor(byte[] data, CRAMEncodingStrategy encodingStrategy) Return the best external compressor to use for the provided byte array (compressor that results in the smallest compressed size).
EncodingDescriptor	getEncodingDescriptorForDataSeries(DataSeries dataSeries) Get the encoding params that should be used for a given DataSeries.
java.util.List<java.lang.Integer>	getExternalIDs() Get a list of all external IDs for this encoding map
int	hashCode()
void	putExternalEncoding(DataSeries dataSeries, EncodingDescriptor encodingDescriptor, ExternalCompressor compressor)
void	putTagBlockCompression(int tagId, ExternalCompressor compressor) Add an external compressor for a tag block
void	write(java.io.OutputStream outputStream) Write the encoding map out to a CRAM Stream

Methods inherited from class java.lang.Object

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

Field Detail

DATASERIES_NOT_READ_BY_HTSJDK

public static final java.util.Set<DataSeries> DATASERIES_NOT_READ_BY_HTSJDK

Constructor Detail

CompressionHeaderEncodingMap

public CompressionHeaderEncodingMap(CRAMEncodingStrategy encodingStrategy)

Constructor used to create the default encoding map for writing CRAMs. The encoding strategy parameter values are used to set compression levels, etc, but any encoding map embedded is ignored since this uses the default strategy.

Parameters:

encodingStrategy - CRAMEncodingStrategy containing parameter values to use when creating the encoding map

CompressionHeaderEncodingMap

public CompressionHeaderEncodingMap(java.io.InputStream inputStream)

Constructor used to discover an encoding map from a serialized CRAM stream.

Parameters:

inputStream - the CRAM input stream to be consumed

Method Detail

putTagBlockCompression

public void putTagBlockCompression(int tagId,
                                   ExternalCompressor compressor)

Add an external compressor for a tag block

Parameters:

tagId - the tag as a content ID

compressor - compressor to be used for this tag block

getEncodingDescriptorForDataSeries

public EncodingDescriptor getEncodingDescriptorForDataSeries(DataSeries dataSeries)

Get the encoding params that should be used for a given DataSeries.

Parameters:

dataSeries -

Returns:

EncodingDescriptor for the DataSeries

getExternalIDs

public java.util.List<java.lang.Integer> getExternalIDs()

Get a list of all external IDs for this encoding map

Returns:

list of all external IDs for this encoding map

createCompressedBlockForStream

public Block createCompressedBlockForStream(java.lang.Integer contentId,
                                            java.io.ByteArrayOutputStream outputStream)

Given a content ID, return a Block for that ID by obtaining the contents of the stream, compressing it using the compressor for that contentID, and converting the result to a Block.

Parameters:

contentId - contentID to use

outputStream - stream to compress

Returns:

Block containing the compressed contends of the stream

write

public void write(java.io.OutputStream outputStream)
           throws java.io.IOException

Write the encoding map out to a CRAM Stream

Parameters:

outputStream - stream to write

Throws:

java.io.IOException

getBestExternalCompressor

public ExternalCompressor getBestExternalCompressor(byte[] data,
                                                    CRAMEncodingStrategy encodingStrategy)

Return the best external compressor to use for the provided byte array (compressor that results in the smallest compressed size). Note that this does not necessarily mean this is the best compression to use for the source data series, as it does not consider the size of the alphabet (2 byte int, 4 byte int) since its only choosing from EXTERNAL compressors.

Parameters:

data - byte array to compress

encodingStrategy - encoding strategy parameters to use

Returns:

the best ExternalCompressor to use for this data

putExternalEncoding

public void putExternalEncoding(DataSeries dataSeries,
                                EncodingDescriptor encodingDescriptor,
                                ExternalCompressor compressor)

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object