# Gem - Cannoli_2.11: Core 0.8.0 API - org.bdgenomics.cannoli.Gem
Gem - Cannoli 2.11 Core 0.8.0 API - org.bdgenomics.cannoli.Gem
Keywords: Gem Cannoli 2.11 Core 0.8.0 API org.bdgenomics.cannoli.Gem

org.bdgenomics.cannoli

# Gem

###
Related Doc: package cannoli

#### 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
Ordering

1. Alphabetic
2. By Inheritance

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

   GEM-Mapper function arguments.

8. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

9. #### def clone(): AnyRef

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... )

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. #### def finalize(): Unit

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )

22. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

23. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

24. #### def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

25. #### def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

26. #### def info(msg: ⇒ Any): Unit

    Attributes
      protected
    Definition Classes
      Logging

27. #### def isDebugEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

28. #### def isErrorEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

29. #### def isInfoEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

30. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

31. #### def isTraceEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

32. #### def isWarnEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

33. #### def logger: Logger

    Attributes
      protected
    Definition Classes
      Logging

34. #### def loggerName: String

    Attributes
      protected
    Definition Classes
      Logging

35. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

36. #### final def notify(): Unit

    Definition Classes
      AnyRef

37. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

38. #### def root(pathName: String): String

    Definition Classes
      CannoliFn

39. #### val sc: SparkContext

    Spark context.

    Spark context.

    Definition Classes
      CannoliFn

40. #### final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
      AnyRef

41. #### def toString(): String

    Definition Classes
      Function1 → AnyRef → Any

42. #### def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

43. #### def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

44. #### def trace(msg: ⇒ Any): Unit

    Attributes
      protected
    Definition Classes
      Logging

45. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

46. #### final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

47. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

48. #### def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

49. #### def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

50. #### def warn(msg: ⇒ Any): Unit

    Attributes
      protected
    Definition Classes
      Logging

### Inherited from CannoliFn[FragmentDataset, AlignmentDataset]

### Inherited from Logging

### Inherited from (FragmentDataset) ⇒ AlignmentDataset

### Inherited from AnyRef

### Inherited from Any

### Ungrouped