Trait

org.bdgenomics.adam.rdd

ShuffleRegionJoin

Related Doc: package rdd

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sealed trait ShuffleRegionJoin[T, U, RT, RU] extends RegionJoin[T, U, RT, RU]

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RegionJoin[T, U, RT, RU], AnyRef, Any
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Abstract Value Members

  1. abstract def emptyFn(left: Iterator[((ReferenceRegion, Int), T)], right: Iterator[((ReferenceRegion, Int), U)]): Iterator[(RT, RU)]

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    protected
  2. abstract def makeIterator(region: ReferenceRegion, left: BufferedIterator[((ReferenceRegion, Int), T)], right: BufferedIterator[((ReferenceRegion, Int), U)]): Iterator[(RT, RU)]

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  3. abstract val partitionSize: Long

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  4. abstract val sc: SparkContext

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  5. abstract val sd: SequenceDictionary

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Concrete Value Members

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

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  2. final def ##(): Int

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

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  4. final def asInstanceOf[T0]: T0

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  5. val bins: Broadcast[GenomeBins]

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  6. def clone(): AnyRef

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

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  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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

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  11. def hashCode(): Int

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  12. final def isInstanceOf[T0]: Boolean

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

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  14. final def notify(): Unit

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  15. final def notifyAll(): Unit

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

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    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.

    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
    ShuffleRegionJoinRegionJoin
  17. val seqLengths: Map[String, Long]

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  18. def sweep(leftIter: Iterator[((ReferenceRegion, Int), T)], rightIter: Iterator[((ReferenceRegion, Int), U)]): Iterator[(RT, RU)]

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

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  20. def toString(): String

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  21. final def wait(): Unit

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

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

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Inherited from RegionJoin[T, U, RT, RU]

Inherited from AnyRef

Inherited from Any

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