Package htsjdk.samtools.cram.structure

Class SliceBlocksReadStreams

java.lang.Object

htsjdk.samtools.cram.structure.SliceBlocksReadStreams

public class SliceBlocksReadStreams
extends Object

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

Constructor Summary

Constructors

Constructor	Description
SliceBlocksReadStreams(SliceBlocks sliceBlocks, CompressorCache compressorCache)

Method Summary

Modifier and Type	Method	Description
BitInputStream	getCoreBlockInputStream()	Get the BitInputStream for this SliceBlocks core block
ByteArrayInputStream	getExternalInputStream(Integer contentID)	Get the ByteArrayInputStream for the given contentID.

Methods inherited from class java.lang.Object

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

Constructor Details

SliceBlocksReadStreams

public SliceBlocksReadStreams(SliceBlocks sliceBlocks,
 CompressorCache compressorCache)

Parameters:

sliceBlocks - SliceBlocks that have been populated from a CRAM stream

Method Details

getCoreBlockInputStream

public BitInputStream getCoreBlockInputStream()

Get the BitInputStream for this SliceBlocks core block

Returns:

BitInputStream for the core block

getExternalInputStream

public ByteArrayInputStream getExternalInputStream(Integer contentID)

Get the ByteArrayInputStream for the given contentID.

Parameters:

contentID -

Returns:

ByteArrayInputStream for contentID