htsjdk.samtools.cram.structure

Class CompressionHeader

java.lang.Object

htsjdk.samtools.cram.structure.CompressionHeader

public class CompressionHeader
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
boolean	APDelta
byte[][][]	dictionary
java.util.Map<DataSeries,EncodingParams>	encodingMap
java.util.Map<java.lang.Integer,ExternalCompressor>	externalCompressors
java.util.List<java.lang.Integer>	externalIds
boolean	readNamesIncluded
SubstitutionMatrix	substitutionMatrix
java.util.Map<java.lang.Integer,EncodingParams>	tMap

Constructor Summary

Constructors

Constructor and Description
CompressionHeader()

Method Summary

Modifier and Type	Method and Description
byte[][]	getTagIds(int id)
static CompressionHeader	read(int cramVersion, java.io.InputStream blockStream) Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader We do this instead of reading the InputStream directly because the Block content may be compressed
void	write(Version cramVersion, java.io.OutputStream blockStream) Write this CompressionHeader out to an internal OutputStream, wrap it in a Block, and write that Block out to the passed-in OutputStream.

Methods inherited from class java.lang.Object

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

Field Detail

readNamesIncluded

public boolean readNamesIncluded

APDelta

public boolean APDelta

encodingMap

public java.util.Map<DataSeries,EncodingParams> encodingMap

tMap

public java.util.Map<java.lang.Integer,EncodingParams> tMap

externalCompressors

public final java.util.Map<java.lang.Integer,ExternalCompressor> externalCompressors

substitutionMatrix

public SubstitutionMatrix substitutionMatrix

externalIds

public java.util.List<java.lang.Integer> externalIds

dictionary

public byte[][][] dictionary

Constructor Detail

CompressionHeader

public CompressionHeader()

Method Detail

getTagIds

public byte[][] getTagIds(int id)

write

public void write(Version cramVersion,
                  java.io.OutputStream blockStream)

Write this CompressionHeader out to an internal OutputStream, wrap it in a Block, and write that Block out to the passed-in OutputStream.

Parameters:

cramVersion - the CRAM major version number

blockStream - the stream to write to

read

public static CompressionHeader read(int cramVersion,
                                     java.io.InputStream blockStream)

Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader We do this instead of reading the InputStream directly because the Block content may be compressed

Parameters:

cramVersion - the CRAM version

blockStream - the stream to read from

Returns:

a new CompressionHeader from the input