rdd

Type Members

1. class ADAMContext extends Serializable with Logging

2. trait ADAMSaveAnyArgs extends SaveArgs

3. abstract class AvroGenomicRDD[T, U <: AvroGenomicRDD[T, U]] extends ADAMRDDFunctions[T] with GenomicRDD[T, U]

4. abstract class AvroReadGroupGenomicRDD[T, U <: AvroReadGroupGenomicRDD[T, U]] extends AvroGenomicRDD[T, U]

5. sealed trait BroadcastRegionJoin[T, U, RT] extends RegionJoin[T, U, RT, U]

   Contains multiple implementations of a 'region join', an operation that joins two sets of regions based on the spatial overlap between the regions.

6. case class FullOuterShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext) extends ShuffleRegionJoin[T, U, Option[T], Option[U]] with Product with Serializable

   Extends the ShuffleRegionJoin trait to implement a full outer join.

7. case class GenomeBins(binSize: Long, seqLengths: Map[String, Long]) extends Serializable with Product

   Partition a genome into a set of bins.

8. case class GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Long]) extends Partitioner with Logging with Product with Serializable

   GenomicPositionPartitioner partitions ReferencePosition objects into separate, spatially-coherent regions of the genome.

9. trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends AnyRef

10. case class GenomicRegionPartitioner(partitionSize: Long, seqLengths: Map[String, Long], start: Boolean = true) extends Partitioner with Logging with Product with Serializable

11. trait InFormatter[T, U <: GenomicRDD[T, U], V <: InFormatter[T, U, V]] extends Serializable

    Formats data going into a pipe to an invoked process.

12. trait InFormatterCompanion[T, U <: GenomicRDD[T, U], V <: InFormatter[T, U, V]] extends AnyRef

13. case class InnerBroadcastRegionJoin[T, U]() extends BroadcastRegionJoin[T, U, T] with Product with Serializable

    Extends the BroadcastRegionJoin trait to implement an inner join.

14. case class InnerShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext) extends ShuffleRegionJoin[T, U, T, U] with Product with Serializable

    Extends the ShuffleRegionJoin trait to implement an inner join.

15. case class InnerShuffleRegionJoinAndGroupByLeft[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext) extends ShuffleRegionJoin[T, U, T, Iterable[U]] with Product with Serializable

    Extends the ShuffleRegionJoin trait to implement an inner join followed by grouping by the left value.

16. case class LeftOuterShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext) extends ShuffleRegionJoin[T, U, T, Option[U]] with Product with Serializable

    Extends the ShuffleRegionJoin trait to implement a left outer join.

17. abstract class MultisampleAvroGenomicRDD[T, U <: MultisampleAvroGenomicRDD[T, U]] extends AvroGenomicRDD[T, U] with MultisampleGenomicRDD[T, U]

18. trait MultisampleGenomicRDD[T, U <: MultisampleGenomicRDD[T, U]] extends GenomicRDD[T, U]

19. trait OutFormatter[T] extends Serializable

    Deserializes data coming out of a pipe from an invoked process.

20. case class ReferencePartitioner(sd: SequenceDictionary) extends Partitioner with Product with Serializable

    Repartitions objects that are keyed by a ReferencePosition or ReferenceRegion into a single partition per contig.

21. trait RegionJoin[T, U, RT, RU] extends AnyRef

22. case class RightOuterBroadcastRegionJoin[T, U]() extends BroadcastRegionJoin[T, U, Option[T]] with Product with Serializable

    Extends the BroadcastRegionJoin trait to implement a right outer join.

23. case class RightOuterShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext) extends ShuffleRegionJoin[T, U, Option[T], U] with Product with Serializable

    Extends the ShuffleRegionJoin trait to implement a right outer join.

24. case class RightOuterShuffleRegionJoinAndGroupByLeft[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext) extends ShuffleRegionJoin[T, U, Option[T], Iterable[U]] with Product with Serializable

    Extends the ShuffleRegionJoin trait to implement a right outer join followed by grouping by all non-null left values.

25. sealed trait ShuffleRegionJoin[T, U, RT, RU] extends RegionJoin[T, U, RT, RU]

26. trait Unaligned extends AnyRef