Package org.snpeff.binseq.coder

Class DnaQualityCoder

java.lang.Object
org.snpeff.binseq.coder.Coder
org.snpeff.binseq.coder.DnaCoder
org.snpeff.binseq.coder.DnaQualityCoder
All Implemented Interfaces:
Serializable
public class DnaQualityCoder extends DnaCoder
Class used to encode & decode sequences into binary and vice-versa - Every base is encoded in 8 bits: - Six bits for the base quality [0 , .. , 63] - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3}
Author:
pcingola
See Also:

  • Field Details

  • Method Details

    • get

      public static DnaQualityCoder get()

    • basesPerWord

      public int basesPerWord()
      Description copied from class: Coder
      How many bases can we pack in a word
      Overrides:
      basesPerWord in class DnaCoder
      Returns:

    • baseToBits

      public int baseToBits(char c, int quality)

    • qualityToBits

      public int qualityToBits(int quality)
      WARNING: This implementation transforms the quality to a range [0, ..., 63] (in order to use 6 bits)
      Overrides:
      qualityToBits in class Coder
      Returns:

    • replaceQuality

      public int replaceQuality(byte code, int newQuality)
      Replace quality value in a given code
      Parameters:
      code -
      newQuality -
      Returns:

    • toBase

      public char toBase(int code)
      Decode a base using 2 bits
      Overrides:
      toBase in class DnaCoder
      Parameters:
      c -
      Returns:

    • toQuality

      public int toQuality(int code)
      Description copied from class: Coder
      Decode a quality
      Overrides:
      toQuality in class Coder
      Returns: