Class FQZState

java.lang.Object
htsjdk.samtools.cram.compression.fqzcomp.FQZState
public class FQZState extends Object
Mutable state tracked during FQZComp encoding and decoding. Updated per quality score as the context model evolves, and reset at each record boundary. Tracks quality context history, position within read, running delta, and per-record metadata (lengths, reversal flags).

  • Constructor Details

    • FQZState

      public FQZState()

  • Method Details

    • getContext

      public int getContext()

    • setContext

      public void setContext(int context)

    • getQualityContext

      public int getQualityContext()

    • setQualityContext

      public void setQualityContext(int qualityContext)

    • getPreviousQuality

      public int getPreviousQuality()

    • setPreviousQuality

      public void setPreviousQuality(int previousQuality)

    • getDelta

      public int getDelta()

    • setDelta

      public void setDelta(int delta)

    • getBases

      public int getBases()

    • setBases

      public void setBases(int bases)

    • getSelector

      public int getSelector()

    • setSelector

      public void setSelector(int selector)

    • getSelectorTable

      public int getSelectorTable()

    • setSelectorTable

      public void setSelectorTable(int selectorTable)

    • getRecordLength

      public int getRecordLength()

    • setRecordLength

      public void setRecordLength(int recordLength)

    • getIsDuplicate

      public boolean getIsDuplicate()

    • setIsDuplicate

      public void setIsDuplicate(boolean isDuplicate)

    • getReadOrdinal

      public int getReadOrdinal()

    • setReadOrdinal

      public void setReadOrdinal(int readOrdinal)

    • getQualityLengthArray

      public int[] getQualityLengthArray()

    • getReverseArray

      public boolean[] getReverseArray()