class BwaMemArgs extends ReadGroupArgs

Bwa mem function arguments.

Linear Supertypes
ReadGroupArgs, Args4jBase, AnyRef, Any
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Inherited
  1. BwaMemArgs
  2. ReadGroupArgs
  3. Args4jBase
  4. AnyRef
  5. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new BwaMemArgs()

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. var addFiles: Boolean
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  7. def createReadGroup(): ReadGroup

    Create a read group from the arguments in this class.

    Create a read group from the arguments in this class.

    returns

    a read group created from the arguments in this class.

    Definition Classes
    ReadGroupArgs
  8. var doPrintUsage: Boolean
    Definition Classes
    Args4jBase
  9. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  10. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  11. var executable: String
  12. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  13. var flowOrder: String
    Definition Classes
    ReadGroupArgs
  14. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  15. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  16. var image: String
  17. var indexPath: String
  18. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  19. var keySequence: String
    Definition Classes
    ReadGroupArgs
  20. var library: String
    Definition Classes
    ReadGroupArgs
  21. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  22. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  23. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  24. var platform: String
    Definition Classes
    ReadGroupArgs
  25. var platformModel: String
    Definition Classes
    ReadGroupArgs
  26. var platformUnit: String
    Definition Classes
    ReadGroupArgs
  27. var predictedMedianInsertSize: Integer
    Definition Classes
    ReadGroupArgs
  28. var readGroup: ReadGroup

    Read group, to specify directly.

    Read group, to specify directly.

    Definition Classes
    ReadGroupArgs
  29. var readGroupId: String
    Definition Classes
    ReadGroupArgs
  30. var runDate: Long
    Definition Classes
    ReadGroupArgs
  31. var sampleId: String
    Definition Classes
    ReadGroupArgs
  32. var sequencingCenter: String
    Definition Classes
    ReadGroupArgs
  33. var sudo: Boolean
  34. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  35. def toString(): String
    Definition Classes
    AnyRef → Any
  36. var useDocker: Boolean
  37. var useSingularity: Boolean
  38. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  39. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  40. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()

Inherited from ReadGroupArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped