org.bdgenomics.adam.rdd

TreeRegionJoin

trait TreeRegionJoin[T, U, RT, RU] extends RegionJoin[T, U, RT, RU]

Implements a shuffle free (broadcast) region join.

The broadcast values are stored in a sorted array. It was going to be an ensemble of interval trees, but, that didn't work out.

Linear Supertypes
RegionJoin[T, U, RT, RU], Serializable, Serializable, AnyRef, Any
Known Subclasses
InnerTreeRegionJoin, InnerTreeRegionJoinAndGroupByRight, RightOuterTreeRegionJoin, RightOuterTreeRegionJoinAndGroupByRight
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  1. TreeRegionJoin
  2. RegionJoin
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Abstract Value Members

  1. abstract def partitionAndJoin(baseRDD: RDD[(ReferenceRegion, T)], joinedRDD: RDD[(ReferenceRegion, U)]): RDD[(RT, RU)]

    Performs a region join between two RDDs.

    Performs a region join between two RDDs.

    baseRDD

    The 'left' side of the join

    joinedRDD

    The 'right' side of the join

    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
    RegionJoin

Concrete Value Members

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

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    AnyRef

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

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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

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  6. final def asInstanceOf[T0]: T0

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  7. def clone(): AnyRef

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    @throws( ... )

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

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  9. def equals(arg0: Any): Boolean

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  10. def finalize(): Unit

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    protected[java.lang]
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    @throws( classOf[java.lang.Throwable] )

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

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  12. def hashCode(): Int

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  13. final def isInstanceOf[T0]: Boolean

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

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  15. final def notify(): Unit

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  16. final def notifyAll(): Unit

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

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  18. def toString(): String

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  19. final def wait(): Unit

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

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

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

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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