Class DnaSequenceByte


  • public class DnaSequenceByte
    extends java.lang.Object
    Binary packed DNA sequence. Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'bytes; - Most significant bits are the first bases in the sequence (makes comparison easier)
    Author:
    pcingola
    • Field Detail

      • MASK

        public static final byte[] MASK
      • BASES

        public static final char[] BASES
      • BASE2CODE

        public static final byte[] BASE2CODE
    • Constructor Detail

      • DnaSequenceByte

        public DnaSequenceByte​(int length,
                               byte[] codes)
      • DnaSequenceByte

        public DnaSequenceByte​(java.lang.String seqStr)
    • Method Detail

      • getBase

        public char getBase​(int index)
      • getCodes

        public byte[] getCodes()
      • getLength

        public int getLength()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
      • length

        public int length()
        Sequence lenth
        Returns:
      • set

        public void set​(java.lang.String seqStr)
        Set sequence
        Parameters:
        seqStr -
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object