VariantContextRDDFunctions

Value Members

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

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

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3. final def ##(): Int

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

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

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6. 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

7. final def asInstanceOf[T0]: T0

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8. def clone(): AnyRef

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

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10. def equals(arg0: Any): Boolean

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11. def finalize(): Unit

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12. def getCallsetSamples(): List[String]

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

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14. 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

15. def hashCode(): Int

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16. final def isInstanceOf[T0]: Boolean

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17. def isTraceEnabled(): Boolean

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

    Left outer join database variant annotations

19. def log: Logger

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

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21. def logDebug(msg: ⇒ String): Unit

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

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23. def logError(msg: ⇒ String): Unit

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

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25. def logInfo(msg: ⇒ String): Unit

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26. def logName: String

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

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28. def logTrace(msg: ⇒ String): Unit

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

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

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

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32. final def notify(): Unit

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33. final def notifyAll(): Unit

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34. def saveAsVcf(filePath: String, dict: Option[SequenceDictionary] = None, sortOnSave: Boolean = false, coalesceTo: Option[Int] = None): RDD[VariantContext]

    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    filePath

    The filepath to save to.

    dict

    An optional sequence dictionary. Default is none.

    sortOnSave

    Whether to sort before saving. Sort is run after coalescing. Default is false (no sort).

    coalesceTo

    Optionally coalesces the RDD down to _n_ partitions. Default is none.

35. lazy val sc: SparkContext

    Definition Classes

    ADAMSequenceDictionaryRDDAggregator

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

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37. def toString(): String

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38. final def wait(): Unit

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

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

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