org.bdgenomics.adam.rdd.fragment

# FragmentRDDFunctions

#### class FragmentRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[Fragment]

Linear Supertypes
ADAMSequenceDictionaryRDDAggregator[Fragment], Logging, Serializable, Serializable, AnyRef, Any
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1. FragmentRDDFunctions
2. ADAMSequenceDictionaryRDDAggregator
3. Logging
4. Serializable
5. Serializable
6. AnyRef
7. Any

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### Instance Constructors

1. #### new FragmentRDDFunctions(rdd: RDD[Fragment])

### 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 adamGetSequenceDictionary(performLexSort: Boolean = false): SequenceDictionary

   Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.

   Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.

   returns

     A sequence dictionary describing the reference contigs in this dataset.

   Definition Classes
     ADAMSequenceDictionaryRDDAggregator

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

   Definition Classes
     Any

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

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

7. #### final def eq(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

8. #### def equals(arg0: Any): Boolean

   Definition Classes
     AnyRef → Any

9. #### def finalize(): Unit

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

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

    Definition Classes
      AnyRef → Any

11. #### def getSequenceRecordsFromElement(elem: Fragment): Set[SequenceRecord]

    For a single RDD element, returns 0+ sequence record elements.

    For a single RDD element, returns 0+ sequence record elements.

    elem

      Element from which to extract sequence records.

    returns

      A seq of sequence records.

    Definition Classes
      FragmentRDDFunctions → ADAMSequenceDictionaryRDDAggregator

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      Any

14. #### def isTraceEnabled(): Boolean

    Attributes
      protected
    Definition Classes
      Logging

15. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

16. #### def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

17. #### def logDebug(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

18. #### def logError(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

19. #### def logError(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

20. #### def logInfo(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

21. #### def logInfo(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

22. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

23. #### def logTrace(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

24. #### def logTrace(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

25. #### def logWarning(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

26. #### def logWarning(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

30. #### lazy val sc: SparkContext

    Definition Classes
      ADAMSequenceDictionaryRDDAggregator

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

    Definition Classes
      AnyRef

32. #### def toReads: RDD[AlignmentRecord]

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from ADAMSequenceDictionaryRDDAggregator[Fragment]

### Inherited from Logging

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped