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 <: AvroGenomicRDD[T, U]] extends ADAMRDDFunctions[T] with GenomicRDD[T, U]

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

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

   An abstract class describing a GenomicRDD where:

5. #### case class FullOuterShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit evidence$9: ClassTag[T], evidence$10: ClassTag[U]) extends ShuffleRegionJoin[T, U, Option[T], Option[U]] with Product with Serializable

   Extends the ShuffleRegionJoin trait to implement a full outer join.

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

   Partition a genome into a set of bins.

7. #### 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.

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

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

9. #### 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.

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

    Formats data going into a pipe to an invoked process.

11. #### 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.

12. #### case class InnerShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit evidence$3: ClassTag[T], evidence$4: ClassTag[U]) extends ShuffleRegionJoin[T, U, T, U] with Product with Serializable

    Extends the ShuffleRegionJoin trait to implement an inner join.

13. #### case class InnerShuffleRegionJoinAndGroupByLeft[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit evidence$11: ClassTag[T], evidence$12: ClassTag[U]) 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.

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

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

15. #### 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] with Product with Serializable

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

16. #### case class LeftOuterShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit evidence$5: ClassTag[T], evidence$6: ClassTag[U]) 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]

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

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

    A trait describing a GenomicRDD with data from multiple samples.

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. #### 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.

22. #### case class RightOuterShuffleRegionJoin[T, U](sd: SequenceDictionary, partitionSize: Long, sc: SparkContext)(implicit evidence$7: ClassTag[T], evidence$8: ClassTag[U]) extends ShuffleRegionJoin[T, U, Option[T], U] with Product with Serializable

    Extends the ShuffleRegionJoin trait to implement a right outer join.

23. #### 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

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

24. #### 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] with Product with Serializable

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

25. #### 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] with Product with Serializable

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

26. #### 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.

27. #### trait TreeRegionJoin[T, U] extends AnyRef

    Implements a shuffle free (broadcast) region join.

28. #### trait Unaligned extends AnyRef

    A trait for genomic data that is not aligned to a reference (e.

### 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 FileMerger extends Logging

   Helper object to merge sharded files together.

3. #### object GenomicPositionPartitioner extends Serializable

   Helper for creating genomic position partitioners.

4. #### object GenomicRegionPartitioner extends Serializable

   Helper object for creating GenomicRegionPartitioners.

5. #### package contig

6. #### package feature

7. #### package fragment

8. #### package read

9. #### package variant

### Ungrouped