Class Utils

java.lang.Object
htsjdk.samtools.cram.compression.rans.Utils
public final class Utils extends Object
Utility methods for rANS encoding and decoding: cumulative frequency lookup, state renormalization, and frequency table normalization.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Utils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    normaliseFrequenciesOrder0(int[] F, int bits)
    Normalize symbol frequencies so they sum to 1 << bits.
    static void
    normaliseFrequenciesOrder0Shift(int[] frequencies, int bits)
    Shift-based frequency normalization: scale frequencies by a power of 2 so they sum to 1 << bits.
    static void
    normaliseFrequenciesOrder1(int[][] F, int shift)
    Normalize Order-1 frequency tables: for each context symbol with non-zero frequency, compute the minimum bit size and normalize that context's frequency table.
    static void
    normaliseFrequenciesOrder1Shift(int[][] F, int shift)
    Shift-based normalization for all Order-1 context rows.
    static long
    RANSDecodeRenormalize4x8(long r, byte[] buf, int[] posHolder)
    4x8 renormalization: reads 1 byte at a time from buf at posHolder[0] until state reaches lower bound.
    static long
    RANSDecodeRenormalizeNx16(long r, byte[] buf, int[] posHolder)
    Nx16 renormalization: reads 2 LE bytes from buf at posHolder[0] if state is below lower bound.
    static int
    RANSGetCumulativeFrequency(long r, int scaleBits)
    Extract the cumulative frequency from a rANS state by masking off the lower scaleBits bits.

    Methods inherited from class Object

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

  • Constructor Details

    • Utils

      public Utils()

  • Method Details

    • RANSGetCumulativeFrequency

      public static int RANSGetCumulativeFrequency(long r, int scaleBits)
      Extract the cumulative frequency from a rANS state by masking off the lower scaleBits bits.
      Parameters:
      r - the current rANS state
      scaleBits - log2 of the total frequency sum
      Returns:
      the cumulative frequency used to look up the decoded symbol

    • RANSDecodeRenormalizeNx16

      public static long RANSDecodeRenormalizeNx16(long r, byte[] buf, int[] posHolder)
      Nx16 renormalization: reads 2 LE bytes from buf at posHolder[0] if state is below lower bound.

    • RANSDecodeRenormalize4x8

      public static long RANSDecodeRenormalize4x8(long r, byte[] buf, int[] posHolder)
      4x8 renormalization: reads 1 byte at a time from buf at posHolder[0] until state reaches lower bound.

    • normaliseFrequenciesOrder0

      public static void normaliseFrequenciesOrder0(int[] F, int bits)
      Normalize symbol frequencies so they sum to 1 << bits. Uses fixed-point arithmetic to scale frequencies proportionally.

    • normaliseFrequenciesOrder1

      public static void normaliseFrequenciesOrder1(int[][] F, int shift)
      Normalize Order-1 frequency tables: for each context symbol with non-zero frequency, compute the minimum bit size and normalize that context's frequency table.

    • normaliseFrequenciesOrder0Shift

      public static void normaliseFrequenciesOrder0Shift(int[] frequencies, int bits)
      Shift-based frequency normalization: scale frequencies by a power of 2 so they sum to 1 << bits.

    • normaliseFrequenciesOrder1Shift

      public static void normaliseFrequenciesOrder1Shift(int[][] F, int shift)
      Shift-based normalization for all Order-1 context rows.