Enum SAMFlag

    • Enum Constant Detail

      • READ_PAIRED

        public static final SAMFlag READ_PAIRED
      • PROPER_PAIR

        public static final SAMFlag PROPER_PAIR
      • READ_UNMAPPED

        public static final SAMFlag READ_UNMAPPED
      • MATE_UNMAPPED

        public static final SAMFlag MATE_UNMAPPED
      • READ_REVERSE_STRAND

        public static final SAMFlag READ_REVERSE_STRAND
      • MATE_REVERSE_STRAND

        public static final SAMFlag MATE_REVERSE_STRAND
      • FIRST_OF_PAIR

        public static final SAMFlag FIRST_OF_PAIR
      • SECOND_OF_PAIR

        public static final SAMFlag SECOND_OF_PAIR
      • SECONDARY_ALIGNMENT

        public static final SAMFlag SECONDARY_ALIGNMENT
      • READ_FAILS_VENDOR_QUALITY_CHECK

        public static final SAMFlag READ_FAILS_VENDOR_QUALITY_CHECK
      • DUPLICATE_READ

        public static final SAMFlag DUPLICATE_READ
      • SUPPLEMENTARY_ALIGNMENT

        public static final SAMFlag SUPPLEMENTARY_ALIGNMENT
    • Method Detail

      • values

        public static SAMFlag[] 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 (SAMFlag c : SAMFlag.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static SAMFlag 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
      • intValue

        public int intValue()
        Returns:
        this flag as an int
      • getLabel

        public String getLabel()
        Returns:
        a human label for this SAMFlag
      • getDescription

        public String getDescription()
        Returns:
        a human description for this SAMFlag
      • valueOf

        public static SAMFlag valueOf​(int flag)
        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:
        flag - 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
      • findByName

        public static SAMFlag findByName​(String flag)
        Returns:
        find SAMFlag the flag by name, or null if it was not found
      • isSet

        public boolean isSet​(int flag)
      • isUnset

        public boolean isUnset​(int flag)
      • getFlags

        public static Set<SAMFlag> getFlags​(int flag)