htsjdk.samtools.cram.encoding.external

Class ExternalByteArrayEncoding

java.lang.Object

htsjdk.samtools.cram.encoding.CRAMEncoding<byte[]>

htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding

public class ExternalByteArrayEncoding
extends CRAMEncoding<byte[]>

Constructor Summary

Constructors

Constructor and Description
ExternalByteArrayEncoding(int externalBlockContentId)

Method Summary

Modifier and Type	Method and Description
CRAMCodec<byte[]>	buildCodec(BitInputStream coreBlockInputStream, BitOutputStream coreBlockOutputStream, java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalBlockInputMap, java.util.Map<java.lang.Integer,java.io.ByteArrayOutputStream> externalBlockOutputMap) Instantiate the codec represented by this encoding by supplying it with the appropriate streams
static ExternalByteArrayEncoding	fromParams(byte[] params)
byte[]	toByteArray() Subclasses but have a defined serialization of their parameters

Methods inherited from class htsjdk.samtools.cram.encoding.CRAMEncoding

buildReadCodec, buildWriteCodec, id, toParam

Methods inherited from class java.lang.Object

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

Constructor Detail

ExternalByteArrayEncoding

public ExternalByteArrayEncoding(int externalBlockContentId)

Method Detail

fromParams

public static ExternalByteArrayEncoding fromParams(byte[] params)

toByteArray

public byte[] toByteArray()

Description copied from class: CRAMEncoding

Subclasses but have a defined serialization of their parameters

Specified by:

toByteArray in class CRAMEncoding<byte[]>

Returns:

a byte array representing a specific encoding's parameter values

buildCodec

public CRAMCodec<byte[]> buildCodec(BitInputStream coreBlockInputStream,
                                    BitOutputStream coreBlockOutputStream,
                                    java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalBlockInputMap,
                                    java.util.Map<java.lang.Integer,java.io.ByteArrayOutputStream> externalBlockOutputMap)

Description copied from class: CRAMEncoding

Instantiate the codec represented by this encoding by supplying it with the appropriate streams

Specified by:

buildCodec in class CRAMEncoding<byte[]>

Parameters:

coreBlockInputStream - the core block bit stream a CoreCodec will read from

coreBlockOutputStream - the core block bit stream a CoreCodec will write to

externalBlockInputMap - the external block byte stream a ExternalCodec will read from

externalBlockOutputMap - the external block byte stream a ExternalCodec will write to

Returns:

a newly instantiated codec