ADAM_2.12: Core 0.33.0 API < Back
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# Packages

-  package root
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    root
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    bdgenomics
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    adam
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- ADAMContext
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- AvroReadGroupGenomicDataset
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- FullOuterShuffleRegionJoin
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- MultisampleAvroGenomicDataset
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- RightOuterTreeRegionJoin
- RightOuterTreeRegionJoinAndGroupByRight
- ShuffleRegionJoin
- SortedIntervalPartitionJoinWithVictims
- TreeRegionJoin
- VictimlessSortedIntervalPartitionJoin

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
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Inherited

1. ShuffleRegionJoin
2. RegionJoin
3. Serializable
4. Serializable
5. AnyRef
6. Any

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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
   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 AnyRef

### Inherited from Any

### Ungrouped