htsjdk.samtools.cram.structure

Class SliceBlocksWriteStreams

java.lang.Object

htsjdk.samtools.cram.structure.SliceBlocksWriteStreams

public class SliceBlocksWriteStreams
extends java.lang.Object

Provides a layer over a SliceBlocks object and acts as a bridge between the DataSeries codecs and their underlying blocks when writing a CRAM stream by presenting a bit (core) or byte (external) stream for each block.

Constructor Summary

Constructors

Constructor and Description
SliceBlocksWriteStreams(CompressionHeader compressionHeader)

Method Summary

Modifier and Type	Method and Description
SliceBlocks	flushStreamsToBlocks() Compress and write each each stream to a corresponding Block (note that this does not write the blocks themselves to a container output stream - that can't happen until the slice is aggregated into a container.
BitOutputStream	getCoreOutputStream()
java.io.ByteArrayOutputStream	getExternalOutputStream(java.lang.Integer contentID) Get the ByteArrayOutputStream corresponding to the requested contentID

Methods inherited from class java.lang.Object

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

Constructor Detail

SliceBlocksWriteStreams

public SliceBlocksWriteStreams(CompressionHeader compressionHeader)

Parameters:

compressionHeader - CompressionHeader for the container containing the slice

Method Detail

getCoreOutputStream

public BitOutputStream getCoreOutputStream()

Returns:

the BitOutputStream for the core block

getExternalOutputStream

public java.io.ByteArrayOutputStream getExternalOutputStream(java.lang.Integer contentID)

Get the ByteArrayOutputStream corresponding to the requested contentID

Parameters:

contentID - ID of content being requested

Returns:

ByteArrayOutputStream for contentID

flushStreamsToBlocks

public SliceBlocks flushStreamsToBlocks()

Compress and write each each stream to a corresponding Block (note that this does not write the blocks themselves to a container output stream - that can't happen until the slice is aggregated into a container.