ShuffleRegionJoin

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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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13. final def notify(): Unit

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14. final def notifyAll(): Unit

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15. def partitionAndJoin[T, U](leftRDD: RDD[(ReferenceRegion, T)], rightRDD: RDD[(ReferenceRegion, U)])(implicit tManifest: ClassTag[T], uManifest: ClassTag[U]): RDD[(T, U)]

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

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

    This implementation is shuffle-based, so does not require collecting one side into memory like BroadcastRegionJoin. It basically performs a global sort of each RDD by genome position and then does a sort-merge join, similar to the chromsweep implementation in bedtools. More specifically, it first defines a set of bins across the genome, then assigns each object in the RDDs to each bin that they overlap (replicating if necessary), performs the shuffle, and sorts the object in each bin. Finally, each bin independently performs a chromsweep sort-merge join.

    T

    type of leftRDD

    U

    type of rightRDD

    leftRDD

    The 'left' side of the join

    rightRDD

    The 'right' side of the join

    tManifest

    implicit type of leftRDD

    uManifest

    implicit type of rightRDD

    returns

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

    Definition Classes

    ShuffleRegionJoin → RegionJoin

16. val partitionSize: Long

17. val sd: SequenceDictionary

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

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19. final def wait(): Unit

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

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