htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode

public class FQZCompDecode extends Object

Decoder for the CRAM 3.1 FQZComp codec, used for compressing quality scores. Allows the use of previous quality values, position within the read sequence, a sum of the quality differences from the previous quality, and a generic model selector to generate a context model. Uses the range (adaptive arithmetic) codec internally for compression.

Constructor Summary

Constructors

Constructor

Description

FQZCompDecode()
Method Summary

Modifier and Type

Method

Description

static void

decodeFQZNewRecord(ByteBuffer inBuffer, RangeCoder rangeCoder, FQZModels model, FQZParams fqzParams, FQZState state)

static int

fqzUpdateContext(FQZParam params, FQZState state, int quality)

static void

reverseQualities(ByteBuffer outBuffer, int outBufferLength, FQZState fqzState)

static ByteBuffer

uncompress(ByteBuffer inBuffer)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- FQZCompDecode
  
  public FQZCompDecode()
Method Details
- uncompress
  
  public static ByteBuffer uncompress(ByteBuffer inBuffer)
- decodeFQZNewRecord
  
  public static void decodeFQZNewRecord(ByteBuffer inBuffer, RangeCoder rangeCoder, FQZModels model, FQZParams fqzParams, FQZState state)
- fqzUpdateContext
  
  public static int fqzUpdateContext(FQZParam params, FQZState state, int quality)
- reverseQualities
  
  public static void reverseQualities(ByteBuffer outBuffer, int outBufferLength, FQZState fqzState)

Class FQZCompDecode

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

FQZCompDecode

Method Details

uncompress

decodeFQZNewRecord

fqzUpdateContext

reverseQualities