Class

org.bdgenomics.adam.rdd

ShuffleRegionJoin

Related Doc: package rdd

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sealed abstract class ShuffleRegionJoin[T, U, RT, RU] extends RegionJoin[T, U, RT, RU]

A trait describing join implementations that are based on a sort-merge join.

T

The type of the left RDD.

U

The type of the right RDD.

RT

The type of data yielded by the left RDD at the output of the join. This may not match T if the join is an outer join, etc.

RU

The type of data yielded by the right RDD at the output of the join.

Linear Supertypes
RegionJoin[T, U, RT, RU], Serializable, Serializable, AnyRef, Any
Known Subclasses
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Inherited
  1. ShuffleRegionJoin
  2. RegionJoin
  3. Serializable
  4. Serializable
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Visibility
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Abstract Value Members

  1. abstract def advanceCache(cache: SetTheoryCache[U, RT, RU], right: BufferedIterator[(ReferenceRegion, U)], until: ReferenceRegion): Unit

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    Attributes
    protected
  2. abstract def emptyFn(left: Iterator[(ReferenceRegion, T)], right: Iterator[(ReferenceRegion, U)]): Iterator[(RT, RU)]

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    protected
  3. abstract def finalizeHits(cache: SetTheoryCache[U, RT, RU], right: BufferedIterator[(ReferenceRegion, U)]): Iterable[(RT, RU)]

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    protected
  4. abstract val leftRdd: RDD[(ReferenceRegion, T)]

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    protected
  5. abstract def postProcessHits(iter: Iterable[U], currentLeft: T): Iterable[(RT, RU)]

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    protected
  6. abstract def pruneCache(cache: SetTheoryCache[U, RT, RU], to: ReferenceRegion): Unit

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    protected
  7. abstract val rightRdd: RDD[(ReferenceRegion, U)]

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    protected

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

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    Any
  5. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. def compute(): 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). 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.

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

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    AnyRef
  8. def equals(arg0: Any): Boolean

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    AnyRef → Any
  9. def finalize(): Unit

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

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    AnyRef → Any
  11. def hashCode(): Int

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

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    Definition Classes
    Any
  13. def makeIterator(leftIter: Iterator[(ReferenceRegion, T)], rightIter: Iterator[(ReferenceRegion, U)]): Iterator[(RT, RU)]

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    protected
  14. final def ne(arg0: AnyRef): Boolean

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

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

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    Definition Classes
    AnyRef
  17. def partitionAndJoin(left: RDD[(ReferenceRegion, T)], right: RDD[(ReferenceRegion, U)]): RDD[(RT, RU)]

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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
  18. def processHits(cache: SetTheoryCache[U, RT, RU], currentLeft: T, currentLeftRegion: ReferenceRegion): Iterable[(RT, RU)]

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

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    Definition Classes
    AnyRef
  20. def toString(): String

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    AnyRef → Any
  21. final def wait(): Unit

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

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

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    @throws( ... )

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

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped