Enum Class SAMFlag

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

public enum SAMFlag extends Enum<SAMFlag>
SAM flags as enum, to be used in GUI, menu, etc...
  • Enum Constant Details

    • 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
    • NOT_PRIMARY_ALIGNMENT

      @Deprecated public static final SAMFlag NOT_PRIMARY_ALIGNMENT
      Deprecated.
      use SECONDARY_ALIGNMENT instead.
    • 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 Details

    • values

      public static SAMFlag[] 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 SAMFlag 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
    • 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 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:
      flag - 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
    • 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)