RightOuterShuffleRegionJoinAndGroupByLeft

Instance Constructors

new RightOuterShuffleRegionJoinAndGroupByLeft(sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit arg0: ClassTag[T], arg1: ClassTag[U])

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

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

Definition Classes
AnyRef → Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
val bins: Broadcast[GenomeBins]

Attributes
protected
Definition Classes
ShuffleRegionJoin
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def emptyFn(left: Iterator[((ReferenceRegion, Int), T)], right: Iterator[((ReferenceRegion, Int), U)]): Iterator[(Option[T], Iterable[U])]

Attributes
protected
Definition Classes
RightOuterShuffleRegionJoinAndGroupByLeft → ShuffleRegionJoin
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

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

Definition Classes
Any
def makeIterator(region: ReferenceRegion, left: BufferedIterator[((ReferenceRegion, Int), T)], right: BufferedIterator[((ReferenceRegion, Int), U)]): Iterator[(Option[T], Iterable[U])]

Attributes
protected
Definition Classes
RightOuterShuffleRegionJoinAndGroupByLeft → ShuffleRegionJoin
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def partitionAndJoin(leftRDD: RDD[(ReferenceRegion, T)], rightRDD: RDD[(ReferenceRegion, U)]): RDD[(Option[T], Iterable[U])]

Performs a region join between two RDDs (shuffle join).
Performs a region join between two RDDs (shuffle join).
This implementation is shuffle-based, so does not require collecting one side into memory like BroadcastRegionJoin. It basically performs a global sort of each RDD by genome position and then does a sort-merge join, similar to the chromsweep implementation in bedtools. More specifically, it first defines a set of bins across the genome, then assigns each object in the RDDs to each bin that they overlap (replicating if necessary), performs the shuffle, and sorts the object in each bin. Finally, each bin independently performs a chromsweep sort-merge join.
leftRDD
The 'left' side of the join
rightRDD
The 'right' side of the join
returns
An RDD of pairs (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 → RegionJoin
val partitionSize: Long

Definition Classes
RightOuterShuffleRegionJoinAndGroupByLeft → ShuffleRegionJoin
val sc: SparkContext

Definition Classes
RightOuterShuffleRegionJoinAndGroupByLeft → ShuffleRegionJoin
val sd: SequenceDictionary

Definition Classes
RightOuterShuffleRegionJoinAndGroupByLeft → ShuffleRegionJoin
val seqLengths: Map[String, Long]

Attributes
protected
Definition Classes
ShuffleRegionJoin
def sweep(leftIter: Iterator[((ReferenceRegion, Int), T)], rightIter: Iterator[((ReferenceRegion, Int), U)]): Iterator[(Option[T], Iterable[U])]

Definition Classes
ShuffleRegionJoin
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
final def wait(): Unit

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

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

Definition Classes
AnyRef
Annotations
@throws( ... )

Related Doc: package rdd

case class RightOuterShuffleRegionJoinAndGroupByLeft[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit evidence$13: ClassTag[T], evidence$14: ClassTag[U]) extends ShuffleRegionJoin[T, U, Option[T], Iterable[U]] with Product with Serializable

Instance Constructors

new RightOuterShuffleRegionJoinAndGroupByLeft(sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit arg0: ClassTag[T], arg1: ClassTag[U])

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

val bins: Broadcast[GenomeBins]

def clone(): AnyRef

def emptyFn(left: Iterator[((ReferenceRegion, Int), T)], right: Iterator[((ReferenceRegion, Int), U)]): Iterator[(Option[T], Iterable[U])]

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

final def getClass(): Class[_]

final def isInstanceOf[T0]: Boolean

def makeIterator(region: ReferenceRegion, left: BufferedIterator[((ReferenceRegion, Int), T)], right: BufferedIterator[((ReferenceRegion, Int), U)]): Iterator[(Option[T], Iterable[U])]

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def partitionAndJoin(leftRDD: RDD[(ReferenceRegion, T)], rightRDD: RDD[(ReferenceRegion, U)]): RDD[(Option[T], Iterable[U])]

val partitionSize: Long

val sc: SparkContext

val sd: SequenceDictionary

val seqLengths: Map[String, Long]

def sweep(leftIter: Iterator[((ReferenceRegion, Int), T)], rightIter: Iterator[((ReferenceRegion, Int), U)]): Iterator[(Option[T], Iterable[U])]

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

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from Product

Inherited from Equals

Inherited from ShuffleRegionJoin[T, U, Option[T], Iterable[U]]

Inherited from RegionJoin[T, U, Option[T], Iterable[U]]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped