Trait

org.bdgenomics.adam.rdd

SortedIntervalPartitionJoinWithVictims

Related Doc: package rdd

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

Linear Supertypes
ShuffleRegionJoin[T, U, RT, RU], RegionJoin[T, U, RT, RU], Serializable, Serializable, AnyRef, Any
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Inherited
  1. SortedIntervalPartitionJoinWithVictims
  2. ShuffleRegionJoin
  3. RegionJoin
  4. Serializable
  5. Serializable
  6. AnyRef
  7. Any
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Abstract Value Members

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

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    Attributes
    protected
    Definition Classes
    ShuffleRegionJoin
  2. abstract val leftRdd: RDD[(ReferenceRegion, T)]

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    Attributes
    protected
    Definition Classes
    ShuffleRegionJoin
  3. abstract def postProcessHits(iter: Iterable[U], currentLeft: T): Iterable[(RT, RU)]

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    Attributes
    protected
    Definition Classes
    ShuffleRegionJoin
  4. abstract def postProcessPruned(pruned: U): (RT, RU)

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

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    Attributes
    protected
    Definition Classes
    ShuffleRegionJoin

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

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    Definition Classes
    AnyRef → Any
  4. def advanceCache(cache: SetTheoryCache[U, RT, RU], 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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    Definition Classes
    Any
  6. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  7. 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.

    Definition Classes
    ShuffleRegionJoin
  8. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  9. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  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, RT, RU], right: BufferedIterator[(ReferenceRegion, U)]): Iterable[(RT, RU)]

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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
    AnyRef → Any
  13. def hashCode(): Int

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

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

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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[(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
  20. 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
    Definition Classes
    ShuffleRegionJoin
  21. def pruneCache(cache: SetTheoryCache[U, RT, RU], 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
  22. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  23. def toString(): String

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    Definition Classes
    AnyRef → Any
  24. final def wait(): Unit

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped