Class

org.bdgenomics.adam.rdd

RightOuterBroadcastRegionJoin

Related Doc: package rdd

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case class RightOuterBroadcastRegionJoin[T, U]() extends BroadcastRegionJoin[T, U, Option[T]] with Product with Serializable

Extends the BroadcastRegionJoin trait to implement a right outer join.

Linear Supertypes
Serializable, Serializable, Product, Equals, BroadcastRegionJoin[T, U, Option[T]], RegionJoin[T, U, Option[T], U], AnyRef, Any
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  1. RightOuterBroadcastRegionJoin
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. BroadcastRegionJoin
  7. RegionJoin
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Instance Constructors

  1. new RightOuterBroadcastRegionJoin()

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Value Members

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

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    AnyRef → Any
  2. final def ##(): Int

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    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

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    Any
  5. def clone(): AnyRef

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    protected[java.lang]
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    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean

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    AnyRef
  7. def finalize(): Unit

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    protected[java.lang]
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    AnyRef
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    @throws( classOf[java.lang.Throwable] )
  8. final def getClass(): Class[_]

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  9. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  10. def joinAndFilterFn(tRdd: RDD[(ReferenceRegion, (ReferenceRegion, T))], uRdd: RDD[(ReferenceRegion, (ReferenceRegion, U))]): RDD[(Option[T], U)]

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    Attributes
    protected
    Definition Classes
    RightOuterBroadcastRegionJoinBroadcastRegionJoin
  11. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  12. final def notify(): Unit

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    Definition Classes
    AnyRef
  13. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  14. def partitionAndJoin(baseRDD: RDD[(ReferenceRegion, T)], joinedRDD: RDD[(ReferenceRegion, U)])(implicit tManifest: ClassTag[T], uManifest: ClassTag[U]): RDD[(Option[T], U)]

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    Performs a region join between two RDDs (broadcast join).

    Performs a region join between two RDDs (broadcast join).

    This implementation first _collects_ the left-side RDD; therefore, if the left-side RDD is large or otherwise idiosyncratic in a spatial sense (i.e. contains a set of regions whose unions overlap a significant fraction of the genome) then the performance of this implementation will likely be quite bad.

    Once the left-side RDD is collected, its elements are reduced to their distinct unions; these can then be used to define the partitions over which the region-join will be computed.

    The regions in the left-side are keyed by their corresponding partition (each such region should have exactly one partition). The regions in the right-side are also keyed by their corresponding partitions (here there can be more than one partition for a region, since a region may cross the boundaries of the partitions defined by the left-side).

    Finally, within each separate partition, we essentially perform a cartesian-product-and-filter operation. The result is the region-join.

    baseRDD

    The 'left' side of the join

    joinedRDD

    The 'right' side of the join

    tManifest

    implicit type of baseRDD

    uManifest

    implicit type of joinedRDD

    returns

    An RDD of pairs (x, y), where x is from baseRDD, y is from joinedRDD, and the region corresponding to x overlaps the region corresponding to y.

    Definition Classes
    BroadcastRegionJoinRegionJoin
  15. def regionsFor(u: (ReferenceRegion, U), regions: Broadcast[MultiContigNonoverlappingRegions]): Iterable[ReferenceRegion]

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    Attributes
    protected
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    RightOuterBroadcastRegionJoinBroadcastRegionJoin
  16. final def synchronized[T0](arg0: ⇒ T0): T0

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  17. final def wait(): Unit

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    @throws( ... )
  18. final def wait(arg0: Long, arg1: Int): Unit

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    @throws( ... )
  19. final def wait(arg0: Long): Unit

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Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from BroadcastRegionJoin[T, U, Option[T]]

Inherited from RegionJoin[T, U, Option[T], U]

Inherited from AnyRef

Inherited from Any

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