org.bdgenomics.adam

# rdd

#### package rdd

Visibility

1. Public
2. All

### 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.

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

   Different implementations will have different performance characteristics -- and new implementations will likely be added in the future, see the notes to each individual method for more details.

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.

   Partition a genome into a set of bins.

   Note that this class will not tolerate invalid input, so filter in advance if you use it.

   binSize

     The size of each bin in nucleotides

   seqLengths

     A map containing the length of each contig

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.

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

   This can be used to organize genomic data for computation that is spatially distributed (e.g. GATK and Queue's "scatter-and-gather" for locus-parallelizable walkers).

   numParts

     The number of equally-sized regions into which the total genomic space is partitioned; the total number of partitions is numParts + 1, with the "+1" resulting from one extra partition that is used to capture null or UNMAPPED values of the ReferencePosition type.

   seqLengths

     a map relating sequence-name to length and indicating the set and length of all extant sequences in 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.

    Formats data going into a pipe to an invoked process.

    T

      The type of records being formatted.

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.

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

    T

      The type of records being formatted.

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

### Value Members

1. #### object ADAMContext extends Serializable

2. #### object FileMerger extends Logging

   Helper object to merge sharded files together.

3. #### object GenomicPositionPartitioner extends Serializable

4. #### object GenomicRegionPartitioner extends Serializable

5. #### package contig

6. #### package features

7. #### package fragment

8. #### package read

9. #### package variation

### Ungrouped