org.bdgenomics.adam

# rdd

#### package rdd

Visibility

1. Public
2. All

### Type Members

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

2. #### class ADAMRDDFunctions[T] extends Serializable with Logging

3. #### trait ADAMSaveAnyArgs extends SaveArgs

4. #### abstract class ADAMSequenceDictionaryRDDAggregator[T] extends Serializable with Logging

   A class that provides functions to recover a sequence dictionary from a generic RDD of records.

5. #### class ADAMSpecificRecordSequenceDictionaryRDDAggregator[T] extends ADAMSequenceDictionaryRDDAggregator[T]

   A class that provides functions to recover a sequence dictionary from a generic RDD of records that are defined in Avro.

6. #### class Coverage extends Serializable

   A base is 'covered' by a region set if any region in the set contains the base itself.

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] extends AnyRef

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

11. #### class InstrumentedADAMAvroParquetOutputFormat extends InstrumentedOutputFormat[Void, IndexedRecord]

12. #### class PairingRDD[T] extends Serializable

    PairingRDD provides some simple helper methods, allowing us take an RDD (presumably an RDD whose values are in some reasonable or intelligible order within and across partitions) and get paired or windowed views on that list of items.

13. #### 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.

14. #### trait RegionJoin extends AnyRef

15. #### case class ShuffleRegionJoin(sd: SequenceDictionary, partitionSize: Long) extends RegionJoin with Product with Serializable

16. #### trait Unaligned extends AnyRef

### Value Members

1. #### object ADAMContext extends Serializable

2. #### object BroadcastRegionJoin extends RegionJoin

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

3. #### object GenomicPositionPartitioner extends Serializable

4. #### object GenomicRegionPartitioner extends Serializable

5. #### object PairingRDD extends Serializable

6. #### package contig

7. #### package features

8. #### package fragment

9. #### package read

10. #### package variation

### Ungrouped