org.bdgenomics.adam.rdd

FullOuterShuffleRegionJoin

case class FullOuterShuffleRegionJoin[T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$11: ClassTag[T], evidence$12: ClassTag[U]) extends ShuffleRegionJoin[T, U, Option[T], Option[U]] with SortedIntervalPartitionJoinWithVictims[T, U, Option[T], Option[U]] with Product with Serializable

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

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

Value Members

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

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

    Definition Classes
    Any
  3. final def ##(): Int

    Definition Classes
    AnyRef → Any
  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  5. final def ==(arg0: Any): Boolean

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

    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
  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  8. def clone(): AnyRef

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

    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
  10. def emptyFn(left: Iterator[(ReferenceRegion, T)], right: Iterator[(ReferenceRegion, U)]): Iterator[(Option[T], Option[U])]

    Handles the case where the left or the right iterator were empty.

    Handles the case where the left or the right iterator were empty.

    left

    The left iterator.

    right

    The right iterator.

    returns

    The iterator containing properly formatted tuples.

    Attributes
    protected
    Definition Classes
    FullOuterShuffleRegionJoinShuffleRegionJoin
  11. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  12. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any
  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  16. val leftRdd: RDD[(ReferenceRegion, T)]

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

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

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

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

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

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

    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 hits.

    currentLeft

    The current left value for the join.

    returns

    the post processed iterator.

    Attributes
    protected
    Definition Classes
    FullOuterShuffleRegionJoinShuffleRegionJoin
  23. def postProcessPruned(pruned: U): (Option[T], Option[U])

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

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

    pruned

    The right value with no join.

    returns

    The formatted tuple containing the right value.

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

    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
  25. def pruneCache(cache: SetTheoryCache[U, Option[T], Option[U]], to: ReferenceRegion): Unit

    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
  26. val rightRdd: RDD[(ReferenceRegion, U)]

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

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  30. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

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

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

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

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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