Class

org.bdgenomics.adam.rdd

RightOuterShuffleRegionJoinAndGroupByLeft

Related Doc: package rdd

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case class RightOuterShuffleRegionJoinAndGroupByLeft[T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$13: ClassTag[T], evidence$14: ClassTag[U]) extends ShuffleRegionJoin[T, U, Option[T], Iterable[U]] with SortedIntervalPartitionJoinWithVictims[T, U, Option[T], Iterable[U]] with Product with Serializable

Linear Supertypes
Product, Equals, SortedIntervalPartitionJoinWithVictims[T, U, Option[T], Iterable[U]], ShuffleRegionJoin[T, U, Option[T], Iterable[U]], RegionJoin[T, U, Option[T], Iterable[U]], Serializable, Serializable, AnyRef, Any
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Inherited
  1. RightOuterShuffleRegionJoinAndGroupByLeft
  2. Product
  3. Equals
  4. SortedIntervalPartitionJoinWithVictims
  5. ShuffleRegionJoin
  6. RegionJoin
  7. Serializable
  8. Serializable
  9. AnyRef
  10. Any
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Visibility
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Instance Constructors

  1. new RightOuterShuffleRegionJoinAndGroupByLeft(leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit arg0: ClassTag[T], arg1: ClassTag[U])

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Value Members

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

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

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

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    Definition Classes
    AnyRef → Any
  4. def advanceCache(cache: SetTheoryCache[U, Option[T], Iterable[U]], right: BufferedIterator[(ReferenceRegion, U)], until: ReferenceRegion): Unit

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    Adds elements from right to victimCache based on the next region encountered.

    Adds elements from right to victimCache based on the next region encountered.

    cache

    The cache for this partition.

    right

    The right iterator.

    until

    The next value on the left to perform the join.

    Attributes
    protected
    Definition Classes
    SortedIntervalPartitionJoinWithVictimsShuffleRegionJoin
  5. final def asInstanceOf[T0]: T0

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    Any
  6. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  7. def compute(): RDD[(Option[T], Iterable[U])]

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

    Performs a region join between two RDDs (shuffle join). All data should be pre-shuffled and copartitioned.

    returns

    An RDD of joins (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
  8. def emptyFn(left: Iterator[(ReferenceRegion, T)], right: Iterator[(ReferenceRegion, U)]): Iterator[(Option[T], Iterable[U])]

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    Handles the case where one of the iterators contains no data.

    Handles the case where one of the iterators contains no data.

    left

    The left iterator.

    right

    The right iterator.

    returns

    The iterator containing properly formatted tuples.

    Attributes
    protected
    Definition Classes
    RightOuterShuffleRegionJoinAndGroupByLeftShuffleRegionJoin
  9. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  10. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  11. def finalizeHits(cache: SetTheoryCache[U, Option[T], Iterable[U]], right: BufferedIterator[(ReferenceRegion, U)]): Iterable[(Option[T], Iterable[U])]

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    Computes all victims for the partition.

    Computes all victims for the partition. If there are any remaining values in the right iterator, those are considered victims.

    cache

    The cache for this partition.

    right

    The right iterator containing unmatched regions.

    returns

    An iterable containing all pruned hits.

    Attributes
    protected
    Definition Classes
    SortedIntervalPartitionJoinWithVictimsShuffleRegionJoin
  12. final def getClass(): Class[_]

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    Definition Classes
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  13. final def isInstanceOf[T0]: Boolean

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    Any
  14. val leftRdd: RDD[(ReferenceRegion, T)]

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  15. def makeIterator(leftIter: Iterator[(ReferenceRegion, T)], rightIter: Iterator[(ReferenceRegion, U)]): Iterator[(Option[T], Iterable[U])]

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    Attributes
    protected
    Definition Classes
    ShuffleRegionJoin
  16. final def ne(arg0: AnyRef): Boolean

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

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

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    Definition Classes
    AnyRef
  19. def partitionAndJoin(left: RDD[(ReferenceRegion, T)], right: RDD[(ReferenceRegion, U)]): RDD[(Option[T], Iterable[U])]

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    Performs a region join between two RDDs.

    Performs a region join between two RDDs.

    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
    ShuffleRegionJoinRegionJoin
  20. def postProcessHits(iter: Iterable[U], currentLeft: T): Iterable[(Option[T], Iterable[U])]

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    Computes post processing required to complete the join and properly format hits.

    Computes post processing required to complete the join and properly format hits.

    iter

    The iterator of all hits

    currentLeft

    The current left value.

    returns

    The post processed iterator.

    Attributes
    protected
    Definition Classes
    RightOuterShuffleRegionJoinAndGroupByLeftShuffleRegionJoin
  21. def postProcessPruned(pruned: U): (Option[T], Iterable[U])

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    Properly formats right values that did not join with a region on the left.

    Properly formats right values that did not join with a region on the left.

    pruned

    The right value that did not join.

    returns

    A tuple with the postProcessed right value.

    Attributes
    protected
    Definition Classes
    RightOuterShuffleRegionJoinAndGroupByLeftSortedIntervalPartitionJoinWithVictims
  22. def processHits(cache: SetTheoryCache[U, Option[T], Iterable[U]], currentLeft: T, currentLeftRegion: ReferenceRegion): Iterable[(Option[T], Iterable[U])]

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    Process hits for a given object in left.

    Process hits for a given object in left.

    cache

    The cache containing potential hits.

    currentLeft

    The current object from the left

    currentLeftRegion

    The ReferenceRegion of currentLeft.

    returns

    An iterator containing all hits, formatted by postProcessHits.

    Attributes
    protected
    Definition Classes
    ShuffleRegionJoin
  23. def pruneCache(cache: SetTheoryCache[U, Option[T], Iterable[U]], to: ReferenceRegion): Unit

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    Removes elements from cache in place that do not meet the condition for join.

    Removes elements from cache in place that do not meet the condition for join. Also adds the elements that are not hits to the list of pruned.

    cache

    The cache for this partition.

    to

    The next region in the left iterator.

    Attributes
    protected
    Definition Classes
    SortedIntervalPartitionJoinWithVictimsShuffleRegionJoin
  24. val rightRdd: RDD[(ReferenceRegion, U)]

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

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    Definition Classes
    AnyRef
  26. final def wait(): Unit

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    Definition Classes
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    Annotations
    @throws( ... )
  27. final def wait(arg0: Long, arg1: Int): Unit

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

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    Definition Classes
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    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from SortedIntervalPartitionJoinWithVictims[T, U, Option[T], Iterable[U]]

Inherited from ShuffleRegionJoin[T, U, Option[T], Iterable[U]]

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

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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