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