Package org.snpeff.binseq.coder

Class Coder

java.lang.Object
org.snpeff.binseq.coder.Coder
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
DnaCoder
public abstract class Coder extends Object implements Serializable
Class used to encode & decode sequences into binary and vice-versa They are usually stored in 'long' words
Author:
pcingola
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    BITS_PER_LONGWORD
     
    static final int
    BYTES_PER_LONGWORD
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    Coder()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    abstract int
    basesPerWord()
    How many bases can we pack in a word
    abstract int
    baseToBits(char c)
    Encode a base using a binary representation
    abstract int
    bitsPerBase()
    How many bits do we need for each base
    abstract int
    decodeWord(long word, int pos)
    Decode bits from a given position in a word
    abstract int
    lastBaseinWord()
    Index of the last base coded in a word
    abstract long
    mask(int baseIndexInWord)
    Bitmask for a base in a word
    int
    qualityToBits(int q)
    Encode a quality using a binary representation
    abstract char
    toBase(int code)
    Decode a base using a binary representation
    abstract char
    toBase(long word, int pos)
    Decode a base from a given position in a word
    int
    toQuality(int code)
    Decode a quality

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

    • Coder

      public Coder()

  • Method Details

    • basesPerWord

      public abstract int basesPerWord()
      How many bases can we pack in a word
      Returns:

    • baseToBits

      public abstract int baseToBits(char c)
      Encode a base using a binary representation
      Parameters:
      c -
      Returns:

    • bitsPerBase

      public abstract int bitsPerBase()
      How many bits do we need for each base
      Returns:

    • decodeWord

      public abstract int decodeWord(long word, int pos)
      Decode bits from a given position in a word
      Parameters:
      word -
      pos -
      Returns:

    • lastBaseinWord

      public abstract int lastBaseinWord()
      Index of the last base coded in a word
      Returns:

    • mask

      public abstract long mask(int baseIndexInWord)
      Bitmask for a base in a word
      Returns:

    • qualityToBits

      public int qualityToBits(int q)
      Encode a quality using a binary representation
      Parameters:
      c -
      Returns:

    • toBase

      public abstract char toBase(int code)
      Decode a base using a binary representation
      Parameters:
      c -
      Returns:

    • toBase

      public abstract char toBase(long word, int pos)
      Decode a base from a given position in a word
      Parameters:
      word -
      pos -
      Returns:

    • toQuality

      public int toQuality(int code)
      Decode a quality
      Parameters:
      c -
      Returns: