ADAM_2.12: Core 1.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package ds
  Definition Classes
    adam
-  package feature
  Definition Classes
    ds
-  package fragment
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    ds
-  package read
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    ds
-  package sequence
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    ds
-  package variant
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    ds
- ADAMContext
- ADAMSaveAnyArgs
- AvroGenomicDataset
- AvroReadGroupGenomicDataset
- DatasetBoundGenericGenomicDataset
- DatasetBoundGenomicDataset
- FullOuterShuffleRegionJoin
- GenericConverter
- GenericGenomicDataset
- GenomeBins
- GenomicBroadcast
- GenomicDataset
- GenomicDatasetConversion
- GenomicDatasetWithLineage
- GenomicPositionPartitioner
- GenomicRegionPartitioner
- InFormatter
- InFormatterCompanion
- InnerShuffleRegionJoin
- InnerShuffleRegionJoinAndGroupByLeft
- InnerTreeRegionJoin
- InnerTreeRegionJoinAndGroupByRight
- LeftOuterShuffleRegionJoin
- LeftOuterShuffleRegionJoinAndGroupByLeft
- MultisampleAvroGenomicDataset
- MultisampleGenomicDataset
- OutFormatter
- RDDBoundGenericGenomicDataset
- ReferencePartitioner
- RegionJoin
- RightOuterShuffleRegionJoinAndGroupByLeft
- RightOuterTreeRegionJoin
- RightOuterTreeRegionJoinAndGroupByRight
- ShuffleRegionJoin
- SortedIntervalPartitionJoinWithVictims
- TreeRegionJoin
- VictimlessSortedIntervalPartitionJoin

c

org.bdgenomics.adam.ds

# InnerShuffleRegionJoin 

###

#### case class InnerShuffleRegionJoin[T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$3: ClassTag[T], evidence$4: ClassTag[U]) extends ShuffleRegionJoin[T, U, T, U] with VictimlessSortedIntervalPartitionJoin[T, U, T, U] with Product with Serializable

Linear Supertypes
Product, Equals, VictimlessSortedIntervalPartitionJoin[T, U, T, U], ShuffleRegionJoin[T, U, T, U], RegionJoin[T, U, T, U], Serializable, Serializable, AnyRef, Any
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Inherited

1. InnerShuffleRegionJoin
2. Product
3. Equals
4. VictimlessSortedIntervalPartitionJoin
5. ShuffleRegionJoin
6. RegionJoin
7. Serializable
8. Serializable
9. AnyRef
10. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new InnerShuffleRegionJoin(leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit arg0: ClassTag[T], arg1: ClassTag[U])

### 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.  def advanceCache(cache: SetTheoryCache[U, T, U], right: BufferedIterator[(ReferenceRegion, U)], until: ReferenceRegion): Unit

   Adds elements from right to cache based on the next region encountered.

   Adds elements from right to cache based on the next region encountered.

   cache

     The cache for this partition.

   right

     The right iterator.

   until

     The next region to join with.

   Attributes
     protected
   Definition Classes
     VictimlessSortedIntervalPartitionJoin → ShuffleRegionJoin
5.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
6.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native()
7.  def compute(): RDD[(T, U)]

   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.  def emptyFn(left: Iterator[(ReferenceRegion, T)], right: Iterator[(ReferenceRegion, U)]): Iterator[(T, U)]

   Handles the case where either the left or the right iterator were empty.

   Handles the case where either the left or the right iterator were empty. In the case of inner join, we return an empty iterator.

   left

     The left iterator.

   right

     The right iterator.

   returns

     An empty iterator.

   Attributes
     protected
   Definition Classes
     InnerShuffleRegionJoin → ShuffleRegionJoin
9.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
10.  def finalize(): Unit
    Attributes
      protected[lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
11.  def finalizeHits(cache: SetTheoryCache[U, T, U], right: BufferedIterator[(ReferenceRegion, U)]): Iterable[(T, U)]

    Computes all victims for the partition.

    Computes all victims for the partition. NOTE: These are victimless joins so we have no victims.

    cache

      The cache for this partition.

    right

      The right iterator.

    returns

      An empty iterator.

    Attributes
      protected
    Definition Classes
      VictimlessSortedIntervalPartitionJoin → ShuffleRegionJoin
12.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
13.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
14.  val leftRdd: RDD[(ReferenceRegion, T)]
    Definition Classes
      InnerShuffleRegionJoin → ShuffleRegionJoin
15.  def makeIterator(leftIter: Iterator[(ReferenceRegion, T)], rightIter: Iterator[(ReferenceRegion, U)]): Iterator[(T, U)]
    Attributes
      protected
    Definition Classes
      ShuffleRegionJoin
16.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
17.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
18.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
19.  def partitionAndJoin(left: RDD[(ReferenceRegion, T)], right: RDD[(ReferenceRegion, U)]): RDD[(T, U)]

    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
20.  def postProcessHits(iter: Iterable[U], currentLeft: T): Iterable[(T, U)]

    Computes post processing required to complete the join and properly format hits.

    Computes post processing required to complete the join and properly format hits.

    iter

      The iterable of hits.

    currentLeft

      The current value from the left iterator.

    returns

      The post processed iterable.

    Attributes
      protected
    Definition Classes
      InnerShuffleRegionJoin → ShuffleRegionJoin
21.  def processHits(cache: SetTheoryCache[U, T, U], currentLeft: T, currentLeftRegion: ReferenceRegion): Iterable[(T, U)]

    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
22.  def pruneCache(cache: SetTheoryCache[U, T, U], to: ReferenceRegion): Unit

    Removes elements from cache in place that do not meet the condition for the next region.

    Removes elements from cache in place that do not meet the condition for the next region.

    cache

      The cache for this partition.

    to

      The next region in the left iterator.

    Attributes
      protected
    Definition Classes
      VictimlessSortedIntervalPartitionJoin → ShuffleRegionJoin
    Note

      At one point these were all variables and we built new collections and reassigned the pointers every time. We fixed this by using trimStart() and ++=() to improve performance. Overall, we see roughly 25% improvement in runtime by doing things this way.

23.  val rightRdd: RDD[(ReferenceRegion, U)]
    Definition Classes
      InnerShuffleRegionJoin → ShuffleRegionJoin
24.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
25.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
26.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
27.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()

### Inherited from Product

### Inherited from Equals

### Inherited from VictimlessSortedIntervalPartitionJoin[T, U, T, U]

### Inherited from ShuffleRegionJoin[T, U, T, U]

### Inherited from RegionJoin[T, U, T, U]

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped