htsjdk.samtools.cram.encoding

Class CRAMEncoding<T>

java.lang.Object

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

Type Parameters:

T - the (source) data eries value type for this encoding. There is no way to express the type constraint on this type using Java type bounds, since the legitimate values are drawn from a set of Java types that correspond to the allowable types defined by DataSeriesType, but logically it must be a type that corresponds to one of the DataSeriesType "types", i.e., it must one of be Byte, Integer, Long or byte[].

Direct Known Subclasses:

BetaIntegerEncoding, ByteArrayLenEncoding, ByteArrayStopEncoding, CanonicalHuffmanByteEncoding, CanonicalHuffmanIntegerEncoding, ExternalEncoding, GammaIntegerEncoding, GolombIntegerEncoding, GolombLongEncoding, GolombRiceIntegerEncoding, SubexponentialIntegerEncoding

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

A base class for the various CRAM encodings. This class serves as a (typed) bridge between an EncodingDescriptor, which only describes an encoding, and the various CRAMCodec classes, which can be used to read and write typed values to a stream. Has methods to serialize/deserialize its parameters to/from a byte array and a method to construct a read or write CRAMCodec instance.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
abstract CRAMCodec<T>	buildCodec(SliceBlocksReadStreams sliceBlocksReadStreams, SliceBlocksWriteStreams sliceBlocksWriteStreams) Instantiate the codec represented by this encoding by supplying it with the appropriate streams
CRAMCodec<T>	buildReadCodec(SliceBlocksReadStreams sliceBlocksReadStreams) Convenience initializer method for read codecs
CRAMCodec<T>	buildWriteCodec(SliceBlocksWriteStreams sliceBlocksWriteStreams) Convenience initializer method for write codecs
EncodingID	id()
EncodingDescriptor	toEncodingDescriptor()
abstract byte[]	toSerializedEncodingParams() Serialize encoding parameters to an ITF8-encoded byte array.

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMEncoding

protected CRAMEncoding(EncodingID encodingId)

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

Parameters:

encodingId - the EncodingID associated with the concrete implementation

Method Detail

id

public EncodingID id()

toEncodingDescriptor

public EncodingDescriptor toEncodingDescriptor()

toSerializedEncodingParams

public abstract byte[] toSerializedEncodingParams()

Serialize encoding parameters to an ITF8-encoded byte array. By convention, each subclass should have a corresponding and symmetric "fromSerializedEncodingParams" that returns a new instance of that encoding populated with values from the serialized encoding params.

Returns:

a byte array containing the encoding's parameter values encoded as an ITF8 stream.

buildCodec

public abstract CRAMCodec<T> buildCodec(SliceBlocksReadStreams sliceBlocksReadStreams,
                                        SliceBlocksWriteStreams sliceBlocksWriteStreams)

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

Parameters:

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

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

Returns:

a newly instantiated codec

buildReadCodec

public CRAMCodec<T> buildReadCodec(SliceBlocksReadStreams sliceBlocksReadStreams)

Convenience initializer method for read codecs

Parameters:

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

Returns:

buildWriteCodec

public CRAMCodec<T> buildWriteCodec(SliceBlocksWriteStreams sliceBlocksWriteStreams)

Convenience initializer method for write codecs

Parameters:

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

Returns: