org.bdgenomics.adam

# rdd

#### package rdd

Visibility

1. Public
2. All

### Type Members

1. #### class ADAMContext extends Serializable with Logging

   The ADAMContext provides functions on top of a SparkContext for loading genomic data.

2. #### trait ADAMSaveAnyArgs extends SaveArgs

   Argument configuration for saving any output format.

3. #### abstract class AvroGenomicRDD [T, U <: Product, V <: AvroGenomicRDD[T, U, V]] extends ADAMRDDFunctions[T] with GenomicDataset[T, U, V]

   An abstract class that extends GenomicRDD and where the underlying data are Avro IndexedRecords.

4. #### abstract class AvroRecordGroupGenomicRDD [T, U <: Product, V <: AvroRecordGroupGenomicRDD[T, U, V]] extends AvroGenomicRDD[T, U, V] with GenomicRDDWithLineage[T, V]

   An abstract class describing a GenomicRDD where:

5. #### case class FullOuterShuffleRegionJoin [T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$11: ClassTag[T], evidence$12: ClassTag[U]) extends ShuffleRegionJoin[T, U, Option[T], Option[U]] with SortedIntervalPartitionJoinWithVictims[T, U, Option[T], Option[U]] with Product with Serializable

6. #### case class GenericGenomicRDD [T](rdd: RDD[T], sequences: SequenceDictionary, regionFn: (T) ⇒ Seq[ReferenceRegion], optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = scala.None)(implicit tTag: ClassTag[T]) extends GenomicRDD[T, GenericGenomicRDD[T]] with Product with Serializable

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

   Partition a genome into a set of bins.

8. #### trait GenomicDataset [T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicRDD[T, V]

   A trait describing a GenomicRDD that also supports the Spark SQL APIs.

9. #### trait GenomicDatasetConversion [T <: Product, U <: GenomicDataset[_, T, U], X <: Product, Y <: GenomicDataset[_, X, Y]] extends Function2[U, Dataset[X], Y]

10. #### 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.

11. #### trait GenomicRDD [T, U <: GenomicRDD[T, U]] extends Logging

    A trait that wraps an RDD of genomic data with helpful metadata.

12. #### trait GenomicRDDWithLineage [T, U <: GenomicRDDWithLineage[T, U]] extends GenomicRDD[T, U]

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

    A partitioner for ReferenceRegion-keyed data.

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

    Formats data going into a pipe to an invoked process.

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

    A trait for singleton objects that build an InFormatter from a GenomicRDD.

16. #### 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

17. #### case class InnerShuffleRegionJoinAndGroupByLeft [T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$5: ClassTag[T], evidence$6: ClassTag[U]) extends ShuffleRegionJoin[T, U, T, Iterable[U]] with VictimlessSortedIntervalPartitionJoin[T, U, T, Iterable[U]] with Product with Serializable

18. #### case class InnerTreeRegionJoin [T, U]()(implicit evidence$1: ClassTag[T], evidence$2: ClassTag[U]) extends RegionJoin[T, U, T, U] with TreeRegionJoin[T, U, T, U] with Product with Serializable

    Implements an inner region join where the left side of the join is broadcast.

19. #### case class InnerTreeRegionJoinAndGroupByRight [T, U]()(implicit evidence$5: ClassTag[T], evidence$6: ClassTag[U]) extends RegionJoin[T, U, Iterable[T], U] with TreeRegionJoin[T, U, Iterable[T], U] with Product with Serializable

    Performs an inner region join, followed logically by grouping by the right value.

20. #### case class LeftOuterShuffleRegionJoin [T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$7: ClassTag[T], evidence$8: ClassTag[U]) extends ShuffleRegionJoin[T, U, T, Option[U]] with VictimlessSortedIntervalPartitionJoin[T, U, T, Option[U]] with Product with Serializable

21. #### case class LeftOuterShuffleRegionJoinAndGroupByLeft [T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$9: ClassTag[T], evidence$10: ClassTag[U]) extends ShuffleRegionJoin[T, U, T, Iterable[U]] with VictimlessSortedIntervalPartitionJoin[T, U, T, Iterable[U]] with Product with Serializable

22. #### abstract class MultisampleAvroGenomicRDD [T, U <: Product, V <: MultisampleAvroGenomicRDD[T, U, V]] extends AvroGenomicRDD[T, U, V] with MultisampleGenomicRDD[T, V]

    An abstract class that extends the MultisampleGenomicRDD trait, where the data are Avro IndexedRecords.

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

    A trait describing a GenomicRDD with data from multiple samples.

24. #### trait OutFormatter [T] extends Serializable

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

25. #### 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.

26. #### abstract class RegionJoin [T, U, RT, RU] extends Serializable

    A trait describing a join in the genomic coordinate space between two RDDs where the values are keyed by a ReferenceRegion.

27. #### case class RightOuterShuffleRegionJoinAndGroupByLeft [T, U](leftRdd: RDD[(ReferenceRegion, T)], rightRdd: RDD[(ReferenceRegion, U)])(implicit evidence$13: ClassTag[T], evidence$14: ClassTag[U]) extends ShuffleRegionJoin[T, U, Option[T], Iterable[U]] with SortedIntervalPartitionJoinWithVictims[T, U, Option[T], Iterable[U]] with Product with Serializable

28. #### case class RightOuterTreeRegionJoin [T, U]()(implicit evidence$3: ClassTag[T], evidence$4: ClassTag[U]) extends RegionJoin[T, U, Option[T], U] with TreeRegionJoin[T, U, Option[T], U] with Product with Serializable

    Implements a right outer region join where the left side of the join is broadcast.

29. #### case class RightOuterTreeRegionJoinAndGroupByRight [T, U]()(implicit evidence$7: ClassTag[T], evidence$8: ClassTag[U]) extends RegionJoin[T, U, Iterable[T], U] with TreeRegionJoin[T, U, Iterable[T], U] with Product with Serializable

    Performs a right outer region join, followed logically by grouping by the right value.

30. #### 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.

31. #### sealed trait SortedIntervalPartitionJoinWithVictims [T, U, RT, RU] extends ShuffleRegionJoin[T, U, RT, RU]

32. #### trait TreeRegionJoin [T, U, RT, RU] extends RegionJoin[T, U, RT, RU]

    Implements a shuffle free (broadcast) region join.

33. #### sealed trait VictimlessSortedIntervalPartitionJoin [T, U, RT, RU] extends ShuffleRegionJoin[T, U, RT, RU]

### Value Members

1. #### object ADAMContext extends Serializable

   This singleton provides an implicit conversion from a SparkContext to the ADAMContext, as well as implicit functions for the Pipe API.

2. #### object GenomicPositionPartitioner extends Serializable

   Helper for creating genomic position partitioners.

3. #### object GenomicRegionPartitioner extends Serializable

   Helper object for creating GenomicRegionPartitioners.

4. #### package contig

5. #### package feature

6. #### package fragment

7. #### package read

8. #### package variant

### Ungrouped