Class FQZParam

java.lang.Object
htsjdk.samtools.cram.compression.fqzcomp.FQZParam
public class FQZParam extends Object
A single parameter block for the FQZComp quality score codec. Defines the context model used to compress quality scores, including the number of context bits allocated to quality history, position within read, running delta, and selector. Also holds optional lookup tables (qtab, ptab, dtab) and quality maps for remapping sparse quality value alphabets.

The 16-bit context for each quality score is assembled from:

  • qbits bits of quality history at bit position qloc
  • Position context from ptab[] at bit position ploc
  • Delta context from dtab[] at bit position dloc
  • Selector bits at bit position sloc
See Also:

  • Constructor Details

    • FQZParam

      public FQZParam(ByteBuffer inBuffer, int numberOfSymbols)

  • Method Details

    • getContext

      public int getContext()

    • isDoDedup

      public boolean isDoDedup()

    • getFixedLen

      public int getFixedLen()

    • isDoSel

      public boolean isDoSel()

    • isDoQmap

      public boolean isDoQmap()

    • isDoPos

      public boolean isDoPos()

    • isDoDelta

      public boolean isDoDelta()

    • isDoQtab

      public boolean isDoQtab()

    • getMaxSymbols

      public int getMaxSymbols()

    • getQualityContextBits

      public int getQualityContextBits()

    • getQualityContextShift

      public int getQualityContextShift()

    • getQualityContextLocation

      public int getQualityContextLocation()

    • getSelectorContextLocation

      public int getSelectorContextLocation()

    • getPositionContextLocation

      public int getPositionContextLocation()

    • getDeltaContextLocation

      public int getDeltaContextLocation()

    • getQualityMap

      public int[] getQualityMap()

    • getQualityContextTable

      public int[] getQualityContextTable()

    • getPositionContextTable

      public int[] getPositionContextTable()

    • getDeltaContextTable

      public int[] getDeltaContextTable()

    • setFixedLen

      public void setFixedLen(int fixedLen)