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 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