Class RANSEncodingSymbol

java.lang.Object
htsjdk.samtools.cram.compression.rans.RANSEncodingSymbol
public final class RANSEncodingSymbol extends Object
Encoding state for a single symbol in the rANS codec. Fields are package-private to allow the encode loops in RANSNx16Encode and RANS4x8Encode to inline the renormalization and state-update arithmetic directly, avoiding method call overhead in the hot inner loop.

  • Constructor Summary

    Constructors
    Constructor
    Description
    RANSEncodingSymbol()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    long
    putSymbol4x8(long r, byte[] out, int[] posHolder)
    byte[] variant for 4x8 encoding — writes backwards, decrementing posHolder[0].
    long
    putSymbolNx16(long r, byte[] out, int[] posHolder)
    byte[] variant for Nx16 encoding — writes backwards (decrementing posHolder[0]).
    void
    reset()
    Reset all encoding parameters to zero.
    void
    set(int start, int freq, int scaleBits)
    Initialize encoding parameters for a symbol given its position in the frequency table.

    Methods inherited from class Object

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

  • Constructor Details

    • RANSEncodingSymbol

      public RANSEncodingSymbol()

  • Method Details

    • reset

      public void reset()
      Reset all encoding parameters to zero.

    • set

      public void set(int start, int freq, int scaleBits)
      Initialize encoding parameters for a symbol given its position in the frequency table. Computes the reciprocal frequency and bias needed for fast integer division during encoding.
      Parameters:
      start - cumulative frequency of all preceding symbols
      freq - frequency of this symbol (must be > 0)
      scaleBits - log2 of the total frequency sum

    • putSymbolNx16

      public long putSymbolNx16(long r, byte[] out, int[] posHolder)
      byte[] variant for Nx16 encoding — writes backwards (decrementing posHolder[0]). Renormalization bytes are written so the final memory layout is little-endian (LSB at lower address), matching htslib's RansEncPutSymbol output format.

    • putSymbol4x8

      public long putSymbol4x8(long r, byte[] out, int[] posHolder)
      byte[] variant for 4x8 encoding — writes backwards, decrementing posHolder[0].