Enum Class CigarOperator

java.lang.Object
java.lang.Enum<CigarOperator>
htsjdk.samtools.CigarOperator
All Implemented Interfaces:
Serializable, Comparable<CigarOperator>, Constable

public enum CigarOperator extends Enum<CigarOperator>
The operators that can appear in a cigar string, and information about their disk representations.
  • Enum Constant Details

  • Field Details

  • Method Details

    • values

      public static CigarOperator[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared
    • valueOf

      public static CigarOperator valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class 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
    • toString

      public String toString()
      Returns the cigar operator as it would be seen in a SAM file.
      Overrides:
      toString in class Enum<CigarOperator>