c

org.bdgenomics.adam.rdd

ShuffleRegionJoin

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
FullOuterShuffleRegionJoin, InnerShuffleRegionJoin, InnerShuffleRegionJoinAndGroupByLeft, LeftOuterShuffleRegionJoin, LeftOuterShuffleRegionJoinAndGroupByLeft, RightOuterShuffleRegionJoinAndGroupByLeft, SortedIntervalPartitionJoinWithVictims, VictimlessSortedIntervalPartitionJoin
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. ShuffleRegionJoin
  2. RegionJoin
  3. Serializable
  4. Serializable
  5. AnyRef
  6. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract def advanceCache(cache: SetTheoryCache[U, RT, RU], right: BufferedIterator[(ReferenceRegion, U)], until: ReferenceRegion): Unit
    Attributes
    protected
  2. abstract def emptyFn(left: Iterator[(ReferenceRegion, T)], right: Iterator[(ReferenceRegion, U)]): Iterator[(RT, RU)]
    Attributes
    protected
  3. abstract def finalizeHits(cache: SetTheoryCache[U, RT, RU], right: BufferedIterator[(ReferenceRegion, U)]): Iterable[(RT, RU)]
    Attributes
    protected
  4. abstract val leftRdd: RDD[(ReferenceRegion, T)]
    Attributes
    protected
  5. abstract def postProcessHits(iter: Iterable[U], currentLeft: T): Iterable[(RT, RU)]
    Attributes
    protected
  6. abstract def pruneCache(cache: SetTheoryCache[U, RT, RU], to: ReferenceRegion): Unit
    Attributes
    protected
  7. abstract val rightRdd: RDD[(ReferenceRegion, U)]
    Attributes
    protected

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  6. def compute(): RDD[(RT, RU)]

    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
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  11. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  12. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  13. def makeIterator(leftIter: Iterator[(ReferenceRegion, T)], rightIter: Iterator[(ReferenceRegion, U)]): Iterator[(RT, RU)]
    Attributes
    protected
  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  16. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  17. def partitionAndJoin(left: RDD[(ReferenceRegion, T)], right: RDD[(ReferenceRegion, U)]): RDD[(RT, RU)]

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

    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
    Definition Classes
    AnyRef
  20. def toString(): String
    Definition Classes
    AnyRef → Any
  21. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  23. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )

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

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped