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

Class SliceBlocksReadStreams

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

SliceBlocksReadStreams

Method Details

getCoreBlockInputStream

getExternalInputStream