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<EncodingKey,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)
void	read(byte[] data)
byte[]	toByteArray()

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<EncodingKey,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)

read

public void read(byte[] data)

toByteArray

public byte[] toByteArray()
                   throws java.io.IOException

Throws:

java.io.IOException