Class

org.bdgenomics.adam.rdd.contig

RDDBoundNucleotideContigFragmentRDD

Related Doc: package contig

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case class RDDBoundNucleotideContigFragmentRDD extends NucleotideContigFragmentRDD with Product with Serializable

A wrapper class for RDD[NucleotideContigFragment].

Linear Supertypes
Serializable, Serializable, Product, Equals, NucleotideContigFragmentRDD, AvroGenomicDataset[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD], GenomicDataset[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD], Logging, AnyRef, Any
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  1. RDDBoundNucleotideContigFragmentRDD
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. NucleotideContigFragmentRDD
  7. AvroGenomicDataset
  8. GenomicDataset
  9. Logging
  10. AnyRef
  11. Any
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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. def addSequence(sequenceToAdd: SequenceRecord): NucleotideContigFragmentRDD

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    Appends metadata for a single sequence to the current RDD.

    Appends metadata for a single sequence to the current RDD.

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicDataset with this sequence appended.

    Definition Classes
    GenomicDataset
  5. def addSequences(sequencesToAdd: SequenceDictionary): NucleotideContigFragmentRDD

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    Appends sequence metadata to the current RDD.

    Appends sequence metadata to the current RDD.

    sequencesToAdd

    The new sequences to append.

    returns

    Returns a new GenomicDataset with the sequences appended.

    Definition Classes
    GenomicDataset
  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  7. def broadcast()(implicit tTag: ClassTag[NucleotideContigFragment]): GenomicBroadcast[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

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    Definition Classes
    GenomicDataset
  8. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], txTag: ClassTag[(NucleotideContigFragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Y)]): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

  9. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], txTag: ClassTag[(NucleotideContigFragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Y)]): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

  10. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. Python/Java friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  11. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. SparkR friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  12. def broadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, NucleotideContigFragment)]): GenericGenomicDataset[(X, NucleotideContigFragment), (Y, NucleotideContigFragment)]

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    Performs a broadcast inner join between this RDD and data that has been broadcast.

    Performs a broadcast inner join between this RDD and data that has been broadcast.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    broadcastRegionJoin

  13. def broadcastRegionJoinAgainstAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], NucleotideContigFragment)]): GenericGenomicDataset[(Iterable[X], NucleotideContigFragment), (Seq[Y], NucleotideContigFragment)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    broadcastRegionJoinAndGroupByRight

  14. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[NucleotideContigFragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  15. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[NucleotideContigFragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

    Permalink

    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  16. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  17. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

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    Performs a broadcast inner join between this RDD and another RDD.

    Performs a broadcast inner join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  18. def buildTree(rdd: RDD[(ReferenceRegion, NucleotideContigFragment)])(implicit tTag: ClassTag[NucleotideContigFragment]): IntervalArray[ReferenceRegion, NucleotideContigFragment]

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    Attributes
    protected
    Definition Classes
    NucleotideContigFragmentRDDGenomicDataset
  19. def cache(): NucleotideContigFragmentRDD

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    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

    Cached GenomicDataset.

    Definition Classes
    GenomicDataset
  20. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  21. def countKmers(kmerLength: Integer): JavaRDD[(String, Long)]

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    Counts the k-mers contained in a FASTA contig.

    Counts the k-mers contained in a FASTA contig.

    Java friendly variant.

    kmerLength

    The length of k-mers to count.

    returns

    Returns an RDD containing k-mer/count pairs.

    Definition Classes
    NucleotideContigFragmentRDD
  22. def countKmers(kmerLength: Int): RDD[(String, Long)]

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    Counts the k-mers contained in a FASTA contig.

    Counts the k-mers contained in a FASTA contig.

    kmerLength

    The length of k-mers to count.

    returns

    Returns an RDD containing k-mer/count pairs.

    Definition Classes
    NucleotideContigFragmentRDD
  23. lazy val dataset: Dataset[NucleotideContigFragment]

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    A SQL Dataset of contig fragments.

    A SQL Dataset of contig fragments.

    Definition Classes
    RDDBoundNucleotideContigFragmentRDDGenomicDataset
  24. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  25. def extract(region: ReferenceRegion): String

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    From a set of contigs, returns the base sequence that corresponds to a region of the reference.

    From a set of contigs, returns the base sequence that corresponds to a region of the reference.

    region

    Reference region over which to get sequence.

    returns

    String of bases corresponding to reference sequence.

    Definition Classes
    NucleotideContigFragmentRDD
    Exceptions thrown

    UnsupportedOperationException Throws exception if query region is not found.

  26. def extractRegions(regions: Iterable[ReferenceRegion]): RDD[(ReferenceRegion, String)]

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    From a set of contigs, returns a list of sequences based on reference regions provided

    From a set of contigs, returns a list of sequences based on reference regions provided

    regions

    List of Reference regions over which to get sequences

    returns

    RDD[(ReferenceRegion, String)] of region -> sequence pairs.

    Definition Classes
    NucleotideContigFragmentRDD
  27. def filterByOverlappingRegion(query: ReferenceRegion): NucleotideContigFragmentRDD

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    Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.

    Runs a filter that selects data in the underlying RDD that overlaps a single genomic region.

    query

    The region to query for.

    returns

    Returns a new GenomicDataset containing only data that overlaps the query region.

    Definition Classes
    GenomicDataset
  28. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): NucleotideContigFragmentRDD

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    Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.

    Runs a filter that selects data in the underlying RDD that overlaps several genomic regions. Java friendly version.

    querys

    The regions to query for.

    returns

    Returns a new GenomicRDD containing only data that overlaps the querys region.

    Definition Classes
    GenomicDataset
  29. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): NucleotideContigFragmentRDD

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    Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.

    Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.

    querys

    The regions to query for.

    returns

    Returns a new GenomicDataset containing only data that overlaps the querys region.

    Definition Classes
    GenomicDataset
  30. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  31. def flankAdjacentFragments(flankLength: Int): NucleotideContigFragmentRDD

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    For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.

    For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.

    flankLength

    The length to extend adjacent records by.

    returns

    Returns the RDD, with all adjacent fragments extended with flanking sequence.

    Definition Classes
    NucleotideContigFragmentRDD
  32. def flankAdjacentFragments(flankLength: Integer): NucleotideContigFragmentRDD

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    For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.

    For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.

    Java friendly variant.

    flankLength

    The length to extend adjacent records by.

    returns

    Returns the RDD, with all adjacent fragments extended with flanking sequence.

    Definition Classes
    NucleotideContigFragmentRDD
  33. def flattenRddByRegions(): RDD[(ReferenceRegion, NucleotideContigFragment)]

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    Attributes
    protected
    Definition Classes
    GenomicDataset
  34. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otoxTag: ClassTag[(Option[NucleotideContigFragment], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Option[Y])]): GenericGenomicDataset[(Option[NucleotideContigFragment], Option[X]), (Option[NucleotideContigFragment], Option[Y])]

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    Performs a sort-merge full outer join between this RDD and another RDD.

    Performs a sort-merge full outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either RDD does not overlap any values in the other RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a None.

    Definition Classes
    GenomicDataset
  35. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otoxTag: ClassTag[(Option[NucleotideContigFragment], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Option[Y])]): GenericGenomicDataset[(Option[NucleotideContigFragment], Option[X]), (Option[NucleotideContigFragment], Option[Y])]

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    Performs a sort-merge full outer join between this RDD and another RDD.

    Performs a sort-merge full outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either RDD does not overlap any values in the other RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a None.

    Definition Classes
    GenomicDataset
  36. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[NucleotideContigFragment], Option[X]), (Option[NucleotideContigFragment], Option[Y])]

    Permalink

    Performs a sort-merge full outer join between this RDD and another RDD.

    Performs a sort-merge full outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either RDD does not overlap any values in the other RDD, it will be paired with a None in the product of the join. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a None.

    Definition Classes
    GenomicDataset
  37. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[NucleotideContigFragment], Option[X]), (Option[NucleotideContigFragment], Option[Y])]

    Permalink

    Performs a sort-merge full outer join between this RDD and another RDD.

    Performs a sort-merge full outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a full outer join, if a value from either RDD does not overlap any values in the other RDD, it will be paired with a None in the product of the join. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and values that did not overlap will be paired with a None.

    Definition Classes
    GenomicDataset
  38. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  39. def getReferenceRegions(elem: NucleotideContigFragment): Seq[ReferenceRegion]

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    elem

    Fragment to extract a region from.

    returns

    If a fragment is aligned to a reference location, returns a single reference region. If the fragment start position and name is not defined, returns no regions.

    Attributes
    protected
    Definition Classes
    NucleotideContigFragmentRDDGenomicDataset
  40. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  41. def isSorted: Boolean

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    Definition Classes
    GenomicDataset
  42. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  43. lazy val jrdd: JavaRDD[NucleotideContigFragment]

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    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicDataset
  44. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], toxTag: ClassTag[(NucleotideContigFragment, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Option[Y])]): GenericGenomicDataset[(NucleotideContigFragment, Option[X]), (NucleotideContigFragment, Option[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD.

    Performs a sort-merge left outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  45. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], toxTag: ClassTag[(NucleotideContigFragment, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Option[Y])]): GenericGenomicDataset[(NucleotideContigFragment, Option[X]), (NucleotideContigFragment, Option[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD.

    Performs a sort-merge left outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  46. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(NucleotideContigFragment, Option[X]), (NucleotideContigFragment, Option[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD.

    Performs a sort-merge left outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with a None in the product of the join. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  47. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(NucleotideContigFragment, Option[X]), (NucleotideContigFragment, Option[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD.

    Performs a sort-merge left outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with a None in the product of the join. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  48. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], toxTag: ClassTag[(NucleotideContigFragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Seq[Y])]): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with an empty Iterable in the product of the join.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  49. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], toxTag: ClassTag[(NucleotideContigFragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Seq[Y])]): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with an empty Iterable in the product of the join.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  50. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with an empty Iterable in the product of the join. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  51. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

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    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge left outer join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a left outer join, all values in the right RDD that do not overlap a value from the left RDD are dropped. If a value from the left RDD does not overlap any values in the right RDD, it will be paired with an empty Iterable in the product of the join. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the left RDD that did not overlap a key in the right RDD.

    Definition Classes
    GenomicDataset
  52. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging
  53. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  54. def logDebug(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  55. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  56. def logError(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  57. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  58. def logInfo(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  59. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging
  60. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  61. def logTrace(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  62. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  63. def logWarning(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  64. def mergeFragments(): NucleotideContigFragmentRDD

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    Merge fragments by contig name.

    Merge fragments by contig name.

    returns

    Returns a NucleotideContigFragmentRDD containing a single fragment per contig.

    Definition Classes
    NucleotideContigFragmentRDD
  65. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  66. final def notify(): Unit

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    Definition Classes
    AnyRef
  67. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  68. val optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]

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  69. def persist(sl: StorageLevel): NucleotideContigFragmentRDD

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    Persists underlying RDD in memory or disk.

    Persists underlying RDD in memory or disk.

    sl

    new StorageLevel

    returns

    Persisted GenomicDataset.

    Definition Classes
    GenomicDataset
  70. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[NucleotideContigFragmentRDD, RDD[X], Z]): Z

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    Pipes genomic data to a subprocess that runs in parallel using Spark.

    Pipes genomic data to a subprocess that runs in parallel using Spark.

    Java/PySpark friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

    Files to make locally available to the commands being run. Default is empty.

    environment

    A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  71. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[NucleotideContigFragmentRDD, RDD[X], Z]): Z

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    Pipes genomic data to a subprocess that runs in parallel using Spark.

    Pipes genomic data to a subprocess that runs in parallel using Spark.

    SparkR friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

    Files to make locally available to the commands being run. Default is empty.

    environment

    A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  72. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD, W]](cmd: Seq[String], files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0, optTimeout: Option[Int] = None)(implicit tFormatterCompanion: InFormatterCompanion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD, W], xFormatter: OutFormatter[X], convFn: (NucleotideContigFragmentRDD, RDD[X]) ⇒ Z, tManifest: ClassTag[NucleotideContigFragment], xManifest: ClassTag[X]): Z

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    Pipes genomic data to a subprocess that runs in parallel using Spark.

    Pipes genomic data to a subprocess that runs in parallel using Spark.

    Files are substituted in to the command with a $x syntax. E.g., to invoke a command that uses the first file from the files Seq, use $0. To access the path to the directory where the files are copied, use $root.

    Pipes require the presence of an InFormatterCompanion and an OutFormatter as implicit values. The InFormatterCompanion should be a singleton whose apply method builds an InFormatter given a specific type of GenomicDataset. The implicit InFormatterCompanion yields an InFormatter which is used to format the input to the pipe, and the implicit OutFormatter is used to parse the output from the pipe.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

    Files to make locally available to the commands being run. Default is empty.

    environment

    A map containing environment variable/value pairs to set in the environment for the newly created process. Default is empty.

    flankSize

    Number of bases to flank each command invocation by.

    optTimeout

    An optional parameter specifying how long to let a single partition run for, in seconds. If the partition times out, the partial results will be returned, and no exception will be logged. The partition will log that the command timed out.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  73. val productFn: (NucleotideContigFragment) ⇒ NucleotideContigFragment

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    Attributes
    protected
    Definition Classes
    NucleotideContigFragmentRDDGenomicDataset
  74. val rdd: RDD[NucleotideContigFragment]

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    Underlying RDD

    Underlying RDD

    Definition Classes
    RDDBoundNucleotideContigFragmentRDDGenomicDataset
  75. def replaceRdd(newRdd: RDD[NucleotideContigFragment], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): NucleotideContigFragmentRDD

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    Replaces the underlying RDD with a new RDD.

    Replaces the underlying RDD with a new RDD.

    newRdd

    The RDD to use for the new NucleotideContigFragmentRDD.

    returns

    Returns a new NucleotideContigFragmentRDD where the underlying RDD has been replaced.

    Attributes
    protected
    Definition Classes
    NucleotideContigFragmentRDDGenomicDataset
  76. def replaceSequences(newSequences: SequenceDictionary): NucleotideContigFragmentRDD

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    Replaces the sequence dictionary attached to a GenomicDataset.

    Replaces the sequence dictionary attached to a GenomicDataset.

    newSequences

    The new sequence dictionary to attach.

    returns

    Returns a new GenomicDataset with the sequences replaced.

    Definition Classes
    RDDBoundNucleotideContigFragmentRDDGenomicDataset
  77. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[NucleotideContigFragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

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    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

  78. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[NucleotideContigFragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

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    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

  79. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

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    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join. PySpark/Java friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
  80. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

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    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left RDD (this RDD) is collected to the driver, and broadcast to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join. SparkR friendly version.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
  81. def rightOuterBroadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], oyuTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Y], NucleotideContigFragment)]): GenericGenomicDataset[(Option[X], NucleotideContigFragment), (Option[Y], NucleotideContigFragment)]

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    Performs a broadcast right outer join between this RDD and data that has been broadcast.

    Performs a broadcast right outer join between this RDD and data that has been broadcast.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left table that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left table, it will be paired with a None in the product of the join. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    rightOuterBroadcastRegionJoin

  82. def rightOuterBroadcastRegionJoinAgainstAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], NucleotideContigFragment)]): GenericGenomicDataset[(Iterable[X], NucleotideContigFragment), (Seq[Y], NucleotideContigFragment)]

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    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left table that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left table, it will be paired with a None in the product of the join. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    Note

    This function differs from other region joins as it treats the calling RDD as the right side of the join, and not the left.

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

  83. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[NucleotideContigFragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

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    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  84. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[NucleotideContigFragment], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

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    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  85. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

    Permalink

    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  86. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[NucleotideContigFragment], X), (Seq[NucleotideContigFragment], Y)]

    Permalink

    Performs a broadcast right outer join between this RDD and another RDD.

    Performs a broadcast right outer join between this RDD and another RDD.

    In a broadcast join, the left side of the join (broadcastTree) is broadcast to to all the nodes in the cluster. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  87. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[NucleotideContigFragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD.

    Performs a sort-merge right outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
  88. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otxTag: ClassTag[(Option[NucleotideContigFragment], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Y)]): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD.

    Performs a sort-merge right outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
  89. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD.

    Performs a sort-merge right outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
  90. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[NucleotideContigFragment], X), (Option[NucleotideContigFragment], Y)]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD.

    Performs a sort-merge right outer join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is a right outer join, all values in the left RDD that do not overlap a value from the right RDD are dropped. If a value from the right RDD does not overlap any values in the left RDD, it will be paired with a None in the product of the join. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, and all keys from the right RDD that did not overlap a key in the left RDD.

    Definition Classes
    GenomicDataset
  91. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otixTag: ClassTag[(Option[NucleotideContigFragment], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Seq[Y])]): GenericGenomicDataset[(Option[NucleotideContigFragment], Iterable[X]), (Option[NucleotideContigFragment], Seq[Y])]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the RDD. Since this is a right outer join, all values from the right RDD who did not overlap a value from the left RDD are placed into a length-1 Iterable with a None key.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD, and all values from the right RDD that did not overlap an item in the left RDD.

    Definition Classes
    GenomicDataset
  92. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], otixTag: ClassTag[(Option[NucleotideContigFragment], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[NucleotideContigFragment], Seq[Y])]): GenericGenomicDataset[(Option[NucleotideContigFragment], Iterable[X]), (Option[NucleotideContigFragment], Seq[Y])]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the RDD. Since this is a right outer join, all values from the right RDD who did not overlap a value from the left RDD are placed into a length-1 Iterable with a None key.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD, and all values from the right RDD that did not overlap an item in the left RDD.

    Definition Classes
    GenomicDataset
  93. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[NucleotideContigFragment], Iterable[X]), (Option[NucleotideContigFragment], Seq[Y])]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the RDD. Since this is a right outer join, all values from the right RDD who did not overlap a value from the left RDD are placed into a length-1 Iterable with a None key. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD, and all values from the right RDD that did not overlap an item in the left RDD.

    Definition Classes
    GenomicDataset
  94. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[NucleotideContigFragment], Iterable[X]), (Option[NucleotideContigFragment], Seq[Y])]

    Permalink

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    Performs a sort-merge right outer join between this RDD and another RDD, followed by a groupBy on the left value, if not null.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the RDD. Since this is a right outer join, all values from the right RDD who did not overlap a value from the left RDD are placed into a length-1 Iterable with a None key. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD, and all values from the right RDD that did not overlap an item in the left RDD.

    Definition Classes
    GenomicDataset
  95. def save(fileName: String, asSingleFile: Boolean): Unit

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    Save nucleotide contig fragments as Parquet or FASTA.

    Save nucleotide contig fragments as Parquet or FASTA.

    If filename ends in .fa or .fasta, saves as Fasta. If not, saves fragments to Parquet. Defaults to 60 character line length, if saving to FASTA.

    fileName

    file name

    asSingleFile

    If false, writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.

    Definition Classes
    NucleotideContigFragmentRDD
  96. def saveAsFasta(fileName: String, lineWidth: Int = 60, asSingleFile: Boolean = false, disableFastConcat: Boolean = false): Unit

    Permalink

    Save nucleotide contig fragments in FASTA format.

    Save nucleotide contig fragments in FASTA format.

    fileName

    file name

    lineWidth

    hard wrap FASTA formatted sequence at line width, default 60

    asSingleFile

    By default (false), writes file to disk as shards with one shard per partition. If true, we save the file to disk as a single file by merging the shards.

    disableFastConcat

    If asSingleFile is true, disables the use of the parallel file merging engine.

    Definition Classes
    NucleotideContigFragmentRDD
  97. def saveAsParquet(filePath: String): Unit

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    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    Definition Classes
    AvroGenomicDataset
  98. def saveAsParquet(filePath: String, blockSize: Integer, pageSize: Integer, compressCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit

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    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

    Whether or not to disable bit-packing.

    Definition Classes
    AvroGenomicDataset
  99. def saveAsParquet(filePath: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false): Unit

    Permalink

    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

    Whether or not to disable bit-packing. Default is false.

    Definition Classes
    AvroGenomicDatasetGenomicDataset
  100. def saveAsParquet(args: SaveArgs): Unit

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    Saves an RDD to Parquet.

    Saves an RDD to Parquet.

    args

    The output format configuration to use when saving the data.

    Definition Classes
    GenomicDataset
  101. def saveAsPartitionedParquet(filePath: String, compressCodec: CompressionCodecName = CompressionCodecName.GZIP, partitionSize: Int = 1000000): Unit

    Permalink

    Saves this RDD to disk in range binned partitioned Parquet + Avro format

    Saves this RDD to disk in range binned partitioned Parquet + Avro format

    filePath

    Path to save the file at.

    compressCodec

    Name of the compression codec to use.

    partitionSize

    size of partitions used when writing parquet, in base pairs. Defaults to 1000000.

    Definition Classes
    AvroGenomicDataset
  102. def saveAvro[U <: SpecificRecordBase](pathName: String, sc: SparkContext, schema: Schema, avro: Seq[U])(implicit tUag: ClassTag[U]): Unit

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    Saves Avro data to a Hadoop file system.

    Saves Avro data to a Hadoop file system.

    This method uses a SparkContext to identify our underlying file system, which we then save to.

    Frustratingly enough, although all records generated by the Avro IDL compiler have a static SCHEMA$ field, this field does not belong to the SpecificRecordBase abstract class, or the SpecificRecord interface. As such, we must force the user to pass in the schema.

    U

    The type of the specific record we are saving.

    pathName

    Path to save records to.

    sc

    SparkContext used for identifying underlying file system.

    schema

    Schema of records we are saving.

    avro

    Seq of records we are saving.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  103. def saveMetadata(filePath: String): Unit

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    Called in saveAsParquet after saving RDD to Parquet to save metadata.

    Called in saveAsParquet after saving RDD to Parquet to save metadata.

    Writes any necessary metadata to disk. If not overridden, writes the sequence dictionary to disk as Avro.

    filePath

    The filepath to the file where we will save the Metadata.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  104. def savePartitionMap(filePath: String): Unit

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    Save the partition map to disk.

    Save the partition map to disk. This is done by adding the partition map to the schema.

    filePath

    The filepath where we will save the partition map.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  105. def saveRddAsParquet(pathName: String, blockSize: Int = 128 * 1024 * 1024, pageSize: Int = 1 * 1024 * 1024, compressCodec: CompressionCodecName = CompressionCodecName.GZIP, disableDictionaryEncoding: Boolean = false, optSchema: Option[Schema] = None): Unit

    Permalink

    Saves an RDD of Avro data to Parquet.

    Saves an RDD of Avro data to Parquet.

    pathName

    The path to save the file to.

    blockSize

    The size in bytes of blocks to write. Defaults to 128 * 1024 * 1024.

    pageSize

    The size in bytes of pages to write. Defaults to 1 * 1024 * 1024.

    compressCodec

    The compression codec to apply to pages. Defaults to CompressionCodecName.GZIP.

    disableDictionaryEncoding

    If false, dictionary encoding is used. If true, delta encoding is used. Defaults to false.

    optSchema

    The optional schema to set. Defaults to None.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  106. def saveRddAsParquet(args: SaveArgs): Unit

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    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  107. def saveSequences(filePath: String): Unit

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    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    filePath

    The filepath where we will save the sequence dictionary.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  108. val sequences: SequenceDictionary

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    Sequence dictionary computed from rdd

    Sequence dictionary computed from rdd

    Definition Classes
    RDDBoundNucleotideContigFragmentRDDGenomicDataset
  109. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], txTag: ClassTag[(NucleotideContigFragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Y)]): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

    Permalink

    Performs a sort-merge inner join between this RDD and another RDD.

    Performs a sort-merge inner join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  110. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], txTag: ClassTag[(NucleotideContigFragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Y)]): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

    Permalink

    Performs a sort-merge inner join between this RDD and another RDD.

    Performs a sort-merge inner join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  111. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

    Permalink

    Performs a sort-merge inner join between this RDD and another RDD.

    Performs a sort-merge inner join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  112. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(NucleotideContigFragment, X), (NucleotideContigFragment, Y)]

    Permalink

    Performs a sort-merge inner join between this RDD and another RDD.

    Performs a sort-merge inner join between this RDD and another RDD.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  113. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], tixTag: ClassTag[(NucleotideContigFragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Seq[Y])]): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

    Permalink

    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. In the same operation, we group all values by the left item in the RDD.

    genomicRdd

    The right RDD in the join.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD..

    Definition Classes
    GenomicDataset
  114. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[NucleotideContigFragment], xTag: ClassTag[X], tixTag: ClassTag[(NucleotideContigFragment, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(NucleotideContigFragment, Seq[Y])]): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

    Permalink

    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. Since this is an inner join, all values who do not overlap a value from the other RDD are dropped. In the same operation, we group all values by the left item in the RDD.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD..

    Definition Classes
    GenomicDataset
  115. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

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    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the RDD. PySpark/Java friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD.

    Definition Classes
    GenomicDataset
  116. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(NucleotideContigFragment, Iterable[X]), (NucleotideContigFragment, Seq[Y])]

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    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    Performs a sort-merge inner join between this RDD and another RDD, followed by a groupBy on the left value.

    In a sort-merge join, both RDDs are co-partitioned and sorted. The partitions are then zipped, and we do a merge join on each partition. The key equality function used for this join is the reference region overlap function. In the same operation, we group all values by the left item in the RDD. SparkR friendly variant.

    genomicRdd

    The right RDD in the join.

    flankSize

    Sets a flankSize for the distance between elements to be joined. If set to 0, an overlap is required to join two elements.

    returns

    Returns a new genomic RDD containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left RDD.

    Definition Classes
    GenomicDataset
  117. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[NucleotideContigFragment]): NucleotideContigFragmentRDD

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    Sorts our genome aligned data by reference positions, with contigs ordered by index.

    Sorts our genome aligned data by reference positions, with contigs ordered by index.

    partitions

    The number of partitions for the new RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

    Uses ValidationStringency to handle unaligned or where objects align to multiple positions.

    See also

    sortLexicographically

  118. def sort(): NucleotideContigFragmentRDD

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    Sorts our genome aligned data by reference positions, with contigs ordered by index.

    Sorts our genome aligned data by reference positions, with contigs ordered by index.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sortLexicographically

  119. def sortLexicographically(partitions: Int = rdd.partitions.length, storePartitionMap: Boolean = false, storageLevel: StorageLevel = StorageLevel.MEMORY_ONLY, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[NucleotideContigFragment]): NucleotideContigFragmentRDD

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    Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.

    Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.

    partitions

    The number of partitions for the new RDD.

    storePartitionMap

    A Boolean flag to determine whether to store the partition bounds from the resulting RDD.

    storageLevel

    The level at which to persist the resulting RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

    Uses ValidationStringency to handle data that is unaligned or where objects align to multiple positions.

    See also

    sort

  120. def sortLexicographically(): NucleotideContigFragmentRDD

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    Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.

    Sorts our genome aligned data by reference positions, with contigs ordered lexicographically.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sort

  121. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  122. def toDF(): DataFrame

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    returns

    This data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  123. def toReads: RDD[AlignmentRecord]

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    Converts an RDD of nucleotide contig fragments into reads.

    Converts an RDD of nucleotide contig fragments into reads. Adjacent contig fragments are combined.

    returns

    Returns an RDD of reads.

    Definition Classes
    NucleotideContigFragmentRDD
  124. def toString(): String

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    Definition Classes
    GenomicDataset → AnyRef → Any
  125. def transform(tFn: Function[JavaRDD[NucleotideContigFragment], JavaRDD[NucleotideContigFragment]]): NucleotideContigFragmentRDD

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    Applies a function that transforms the underlying RDD into a new RDD.

    Applies a function that transforms the underlying RDD into a new RDD.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  126. def transform(tFn: (RDD[NucleotideContigFragment]) ⇒ RDD[NucleotideContigFragment]): NucleotideContigFragmentRDD

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    Applies a function that transforms the underlying RDD into a new RDD.

    Applies a function that transforms the underlying RDD into a new RDD.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  127. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): NucleotideContigFragmentRDD

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    Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.

    Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API. Java-friendly variant.

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  128. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[NucleotideContigFragment]): NucleotideContigFragmentRDD

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    Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.

    Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  129. def transformDataset(tFn: (Dataset[NucleotideContigFragment]) ⇒ Dataset[NucleotideContigFragment]): NucleotideContigFragmentRDD

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    Applies a function that transforms the underlying RDD into a new RDD using the Spark SQL API.

    Applies a function that transforms the underlying RDD into a new RDD using the Spark SQL API.

    tFn

    A function that transforms the underlying RDD as a Dataset.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) is copied without modification.

    Definition Classes
    NucleotideContigFragmentRDDGenomicDataset
  130. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[NucleotideContigFragment], JavaRDD[X]], convFn: Function2[NucleotideContigFragmentRDD, RDD[X], Z]): Z

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    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    Applies a function that transmutes the underlying RDD into a new RDD of a different type. Java friendly version.

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  131. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[NucleotideContigFragment]) ⇒ RDD[X])(implicit convFn: (NucleotideContigFragmentRDD, RDD[X]) ⇒ Z): Z

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    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  132. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD, X, Y, Z]): Z

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    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    Applies a function that transmutes the underlying RDD into a new RDD of a different type. Java friendly variant.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  133. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (DataFrame) ⇒ DataFrame)(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (NucleotideContigFragmentRDD, Dataset[Y]) ⇒ Z): Z

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    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    Applies a function that transmutes the underlying RDD into a new RDD of a different type. Java friendly variant.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  134. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[NucleotideContigFragment], Dataset[Y]], convFn: GenomicDatasetConversion[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD, X, Y, Z]): Z

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    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    Applies a function that transmutes the underlying RDD into a new RDD of a different type. Java friendly variant.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  135. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (Dataset[NucleotideContigFragment]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (NucleotideContigFragmentRDD, Dataset[Y]) ⇒ Z): Z

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    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new RDD where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  136. val uTag: scala.reflect.api.JavaUniverse.TypeTag[NucleotideContigFragment]

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  137. def union(rdds: NucleotideContigFragmentRDD*): NucleotideContigFragmentRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    NucleotideContigFragmentRDDGenomicDataset
  138. def union(rdds: List[NucleotideContigFragmentRDD]): NucleotideContigFragmentRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    GenomicDataset
  139. def unpersist(): NucleotideContigFragmentRDD

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    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  140. val unproductFn: (NucleotideContigFragment) ⇒ NucleotideContigFragment

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    Attributes
    protected
    Definition Classes
    NucleotideContigFragmentRDDGenomicDataset
  141. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  142. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  143. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  144. def writeTextRdd[T](rdd: RDD[T], outputPath: String, asSingleFile: Boolean, disableFastConcat: Boolean, optHeaderPath: Option[String] = None): Unit

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    Writes an RDD to disk as text and optionally merges.

    Writes an RDD to disk as text and optionally merges.

    rdd

    RDD to save.

    outputPath

    Output path to save text files to.

    asSingleFile

    If true, combines all partition shards.

    disableFastConcat

    If asSingleFile is true, disables the use of the parallel file merging engine.

    optHeaderPath

    If provided, the header file to include.

    Attributes
    protected
    Definition Classes
    GenomicDataset

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AvroGenomicDataset[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

Inherited from GenomicDataset[NucleotideContigFragment, NucleotideContigFragment, NucleotideContigFragmentRDD]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped