Class DnaQualityCoder

  • All Implemented Interfaces:
    java.io.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:
    Serialized Form
    • Method Detail

      • 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: