Enum CigarOperator

    • Method Detail

      • values

        public static CigarOperator[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (CigarOperator c : CigarOperator.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static CigarOperator valueOf​(String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        Parameters:
        name - the name of the enum constant to be returned.
        Returns:
        the enum constant with the specified name
        Throws:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null
      • consumesReadBases

        public boolean consumesReadBases()
        If true, represents that this cigar operator "consumes" bases from the read bases.
      • consumesReferenceBases

        public boolean consumesReferenceBases()
        If true, represents that this cigar operator "consumes" bases from the reference sequence.
      • characterToEnum

        public static CigarOperator characterToEnum​(int b)
        Parameters:
        b - CIGAR operator in character form as appears in a text CIGAR string
        Returns:
        CigarOperator enum value corresponding to the given character.
      • binaryToEnum

        public static CigarOperator binaryToEnum​(int i)
        Parameters:
        i - CIGAR operator in binary form as appears in a BAMRecord.
        Returns:
        CigarOperator enum value corresponding to the given int value.
      • enumToBinary

        public static int enumToBinary​(CigarOperator e)
        Parameters:
        e - CigarOperator enum value.
        Returns:
        CIGAR operator corresponding to the enum value in binary form as appears in a BAMRecord.
      • enumToCharacter

        public static byte enumToCharacter​(CigarOperator e)
        Returns the character that should be used within a SAM file.
      • isClipping

        public boolean isClipping()
        Returns true if the operator is a clipped (hard or soft) operator
      • isIndel

        public boolean isIndel()
        Returns true if the operator is a Insertion or Deletion operator
      • isIndelOrSkippedRegion

        public boolean isIndelOrSkippedRegion()
        Returns true if the operator is a Skipped Region Insertion or Deletion operator
      • isAlignment

        public boolean isAlignment()
        Returns true if the operator is a M, a X or a EQ
      • isPadding

        public boolean isPadding()
        Returns true if the operator is a Padding operator