VariantContextRDDFunctions

Value Members

1. final def !=(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

2. final def !=(arg0: Any): Boolean

   Definition Classes

   Any

3. final def ##(): Int

   Definition Classes

   AnyRef → Any

4. final def ==(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

5. final def ==(arg0: Any): Boolean

   Definition Classes

   Any

6. def adamGetSequenceDictionary(): 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

7. def adamVCFSave(filePath: String, dict: Option[SequenceDictionary] = None): RDD[VariantContext]

8. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

9. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

10. final def eq(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

11. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

12. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

13. def getCallsetSamples(): List[String]

14. final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

15. def getSequenceRecordsFromElement(elem: VariantContext): Set[SequenceRecord]

    For a single variant context, returns sequence record elements.

    For a single variant context, returns sequence record elements.

    elem

    Element from which to extract sequence records.

    returns

    A seq of sequence records.

    Definition Classes

    VariantContextRDDFunctions → ADAMSequenceDictionaryRDDAggregator

16. def hashCode(): Int

    Definition Classes

    AnyRef → Any

17. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

18. def isTraceEnabled(): Boolean

    Attributes

    protected

    Definition Classes

    Logging

19. def joinDatabaseVariantAnnotation(ann: RDD[DatabaseVariantAnnotation]): RDD[VariantContext]

    Left outer join database variant annotations

20. def log: Logger

    Attributes

    protected

    Definition Classes

    Logging

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

    Attributes

    protected

    Definition Classes

    Logging

22. def logDebug(msg: ⇒ String): Unit

    Attributes

    protected

    Definition Classes

    Logging

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

    Attributes

    protected

    Definition Classes

    Logging

24. def logError(msg: ⇒ String): Unit

    Attributes

    protected

    Definition Classes

    Logging

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

    Attributes

    protected

    Definition Classes

    Logging

26. def logInfo(msg: ⇒ String): Unit

    Attributes

    protected

    Definition Classes

    Logging

27. def logName: String

    Attributes

    protected

    Definition Classes

    Logging

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

    Attributes

    protected

    Definition Classes

    Logging

29. def logTrace(msg: ⇒ String): Unit

    Attributes

    protected

    Definition Classes

    Logging

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

    Attributes

    protected

    Definition Classes

    Logging

31. def logWarning(msg: ⇒ String): Unit

    Attributes

    protected

    Definition Classes

    Logging

32. final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

33. final def notify(): Unit

    Definition Classes

    AnyRef

34. final def notifyAll(): Unit

    Definition Classes

    AnyRef

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

    Definition Classes

    AnyRef

36. def toString(): String

    Definition Classes

    AnyRef → Any

37. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

39. final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )