htsjdk.samtools.cram.encoding

Class ByteArrayLenEncoding

java.lang.Object

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

htsjdk.samtools.cram.encoding.ByteArrayLenEncoding

public class ByteArrayLenEncoding
extends CRAMEncoding<byte[]>

NOTE: this encoding can be a hybrid encoding in that it ALLOWS for the possibility to split it's data between the core block and an external block (i.e., if lenEncoding is CORE and byteEncoding is EXTERNAL) This has implications for data access, since some of it's data is interleaved with other data in the core block.

Constructor Summary

Constructors

Constructor and Description
ByteArrayLenEncoding(CRAMEncoding<java.lang.Integer> lenEncoding, CRAMEncoding<byte[]> byteEncoding) Note: depending on the sub-encodings, this encoding can wind up being a core/external hybrid.

Method Summary

Modifier and Type	Method and Description
CRAMCodec<byte[]>	buildCodec(SliceBlocksReadStreams sliceBlocksReadStreams, SliceBlocksWriteStreams sliceBlocksWriteStreams) Instantiate the codec represented by this encoding by supplying it with the appropriate streams
static ByteArrayLenEncoding	fromSerializedEncodingParams(byte[] serializedParams) Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
byte[]	toSerializedEncodingParams() Serialize encoding parameters to an ITF8-encoded byte array.
java.lang.String	toString()

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

buildReadCodec, buildWriteCodec, id, toEncodingDescriptor

Methods inherited from class java.lang.Object

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

Constructor Detail

ByteArrayLenEncoding

public ByteArrayLenEncoding(CRAMEncoding<java.lang.Integer> lenEncoding,
                            CRAMEncoding<byte[]> byteEncoding)

Note: depending on the sub-encodings, this encoding can wind up being a core/external hybrid. See https://github.com/samtools/hts-specs/issues/426).

Method Detail

fromSerializedEncodingParams

public static ByteArrayLenEncoding fromSerializedEncodingParams(byte[] serializedParams)

Create a new instance of this encoding using the (ITF8 encoded) serializedParams.

Parameters:

serializedParams -

Returns:

ByteArrayLenEncoding with parameters populated from serializedParams

toSerializedEncodingParams

public byte[] toSerializedEncodingParams()

Description copied from class: CRAMEncoding

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.

Specified by:

toSerializedEncodingParams in class CRAMEncoding<byte[]>

Returns:

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

buildCodec

public CRAMCodec<byte[]> buildCodec(SliceBlocksReadStreams sliceBlocksReadStreams,
                                    SliceBlocksWriteStreams sliceBlocksWriteStreams)

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:

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object