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.

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

    

    Extends the BroadcastRegionJoin trait to implement an inner join.

12. 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.

13. 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.

14. 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.

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

    

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

    

17. 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.

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

    

19. 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.

20. 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.

21. 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.

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

    

23. trait Unaligned extends AnyRef