htsjdk.samtools.cram.encoding

Class CRAMEncoding<T>

java.lang.Object

htsjdk.samtools.cram.encoding.CRAMEncoding<T>

Type Parameters:

T - data series type

Direct Known Subclasses:

BetaIntegerEncoding, ByteArrayLenEncoding, ByteArrayStopEncoding, CanonicalHuffmanByteEncoding, CanonicalHuffmanIntegerEncoding, ExternalByteArrayEncoding, ExternalByteEncoding, ExternalIntegerEncoding, ExternalLongEncoding, GammaIntegerEncoding, GolombIntegerEncoding, GolombLongEncoding, GolombRiceIntegerEncoding, SubexponentialIntegerEncoding

public abstract class CRAMEncoding<T>
extends java.lang.Object

An interface to describe how a data series is encoded. It also has methods to serialize/deserialize its parameters to/from a byte array and a method to construct a CRAMCodec instance.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	CRAMEncoding(EncodingID id) Create a new encoding.

Method Summary

Modifier and Type	Method and Description
abstract CRAMCodec<T>	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
CRAMCodec<T>	buildReadCodec(BitInputStream coreBlockInputStream, java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalBlockInputMap) Convenience initializer method for read codecs
CRAMCodec<T>	buildWriteCodec(BitOutputStream coreBlockOutputStream, java.util.Map<java.lang.Integer,java.io.ByteArrayOutputStream> externalBlockOutputMap) Convenience initializer method for write codecs
EncodingID	id()
abstract byte[]	toByteArray() Subclasses but have a defined serialization of their parameters
EncodingParams	toParam()

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMEncoding

protected CRAMEncoding(EncodingID id)

Create a new encoding. Concrete implementation constructors will specify their parameters

Parameters:

id - the EncodingID associated with the concrete implementation

Method Detail

id

public EncodingID id()

toParam

public EncodingParams toParam()

toByteArray

public abstract byte[] toByteArray()

Subclasses but have a defined serialization of their parameters

Returns:

a byte array representing a specific encoding's parameter values

buildCodec

public abstract CRAMCodec<T> 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

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

buildReadCodec

public CRAMCodec<T> buildReadCodec(BitInputStream coreBlockInputStream,
                                   java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalBlockInputMap)

Convenience initializer method for read codecs

Parameters:

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

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

Returns:

buildWriteCodec

public CRAMCodec<T> buildWriteCodec(BitOutputStream coreBlockOutputStream,
                                    java.util.Map<java.lang.Integer,java.io.ByteArrayOutputStream> externalBlockOutputMap)

Convenience initializer method for write codecs

Parameters:

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

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

Returns: