class Gem extends CannoliFn[FragmentDataset, AlignmentDataset]

GEM-Mapper wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

Linear Supertypes
CannoliFn[FragmentDataset, AlignmentDataset], Logging, (FragmentDataset) ⇒ AlignmentDataset, AnyRef, Any
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Inherited
  1. Gem
  2. CannoliFn
  3. Logging
  4. Function1
  5. AnyRef
  6. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Gem(args: GemArgs, sc: SparkContext)

    args

    GEM-Mapper function arguments.

    sc

    Spark context.

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. def absolute(pathName: String): String
    Definition Classes
    CannoliFn
  5. def andThen[A](g: (AlignmentDataset) ⇒ A): (FragmentDataset) ⇒ A
    Definition Classes
    Function1
    Annotations
    @unspecialized()
  6. def apply(fragments: FragmentDataset): AlignmentDataset
    Definition Classes
    Gem → Function1
  7. val args: GemArgs
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  10. def compose[A](g: (A) ⇒ FragmentDataset): (A) ⇒ AlignmentDataset
    Definition Classes
    Function1
    Annotations
    @unspecialized()
  11. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  12. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  13. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  14. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  16. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  17. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  18. def error(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  19. def files(pathName: String, filter: PathFilter): Seq[String]
    Definition Classes
    CannoliFn
  20. def files(pathName: String): Seq[String]
    Definition Classes
    CannoliFn
  21. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  22. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  23. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  24. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  25. def info(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  26. def isDebugEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  27. def isErrorEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  28. def isInfoEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  29. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  30. def isTraceEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  31. def isWarnEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  32. def logger: Logger
    Attributes
    protected
    Definition Classes
    Logging
  33. def loggerName: String
    Attributes
    protected
    Definition Classes
    Logging
  34. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  35. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  36. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  37. def root(pathName: String): String
    Definition Classes
    CannoliFn
  38. val sc: SparkContext
    Definition Classes
    CannoliFn
  39. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  40. def toString(): String
    Definition Classes
    Function1 → AnyRef → Any
  41. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  42. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  43. def trace(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  44. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  45. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  46. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  47. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  48. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  49. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from CannoliFn[FragmentDataset, AlignmentDataset]

Inherited from Logging

Inherited from (FragmentDataset) ⇒ AlignmentDataset

Inherited from AnyRef

Inherited from Any

Ungrouped