Class

org.bdgenomics.adam.rdd.feature

ParquetUnboundCoverageRDD

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case class ParquetUnboundCoverageRDD extends CoverageRDD with Product with Serializable

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Serializable, Serializable, Product, Equals, CoverageRDD, GenomicDataset[Coverage, Coverage, CoverageRDD], GenomicRDD[Coverage, CoverageRDD], Logging, AnyRef, Any
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  1. ParquetUnboundCoverageRDD
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  3. Serializable
  4. Product
  5. Equals
  6. CoverageRDD
  7. GenomicDataset
  8. GenomicRDD
  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): CoverageRDD

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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 GenomicRDD with this sequence appended.

    Definition Classes
    GenomicRDD
  5. def addSequences(sequencesToAdd: SequenceDictionary): CoverageRDD

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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 GenomicRDD with the sequences appended.

    Definition Classes
    GenomicRDD
  6. def aggregatedCoverage(bpPerBin: Int = 1): CoverageRDD

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    Gets coverage overlapping specified ReferenceRegion.

    Gets coverage overlapping specified ReferenceRegion.

    For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is the mean coverage over all base pairs in that bin.

    bpPerBin

    base pairs per bin, number of bases to combine to one bin.

    returns

    RDD of Coverage Records.

    Definition Classes
    CoverageRDD
  7. def aggregatedCoverage(bpPerBin: Integer): CoverageRDD

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    Gets coverage overlapping specified ReferenceRegion.

    Gets coverage overlapping specified ReferenceRegion.

    For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is the mean coverage over all base pairs in that bin. Java friendly variant.

    bpPerBin

    base pairs per bin, number of bases to combine to one bin.

    returns

    RDD of Coverage Records.

    Definition Classes
    CoverageRDD
  8. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  9. def broadcast()(implicit tTag: ClassTag[Coverage]): Broadcast[IntervalArray[ReferenceRegion, Coverage]]

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    Definition Classes
    GenomicRDD
  10. def broadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)]): GenericGenomicRDD[(Coverage, X)]

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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
    GenomicRDD
    See also

    broadcastRegionJoinAgainst

  11. def broadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)]): GenericGenomicRDD[(Coverage, X)]

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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
    GenomicRDD
    See also

    broadcastRegionJoinAgainst

  12. def broadcastRegionJoinAgainst[X](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X]): GenericGenomicRDD[(X, Coverage)]

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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.

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    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 <: GenomicRDD[X, Y]](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X]): GenericGenomicRDD[(Iterable[X], Coverage)]

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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.

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    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 <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)]): GenericGenomicRDD[(Iterable[Coverage], X)]

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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
    GenomicRDD
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  15. def broadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)]): GenericGenomicRDD[(Iterable[Coverage], X)]

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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
    GenomicRDD
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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    Attributes
    protected
    Definition Classes
    CoverageRDDGenomicRDD
  17. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  18. def collapse(): CoverageRDD

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    Merges adjacent ReferenceRegions with the same coverage value.

    Merges adjacent ReferenceRegions with the same coverage value. This reduces the loss of coverage information while reducing the number of records in the RDD. For example, adjacent records Coverage("chr1", 1, 10, 3.0) and Coverage("chr1", 10, 20, 3.0) would be merged into one record Coverage("chr1", 1, 20, 3.0).

    returns

    merged tuples of adjacent ReferenceRegions and coverage.

    Definition Classes
    CoverageRDD
    Note

    Data must be sorted before collapse is called.

  19. def coverage(bpPerBin: Int = 1): CoverageRDD

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    Gets coverage overlapping specified ReferenceRegion.

    Gets coverage overlapping specified ReferenceRegion. For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is coverage of the first base pair in that bin.

    bpPerBin

    base pairs per bin, number of bases to combine to one bin.

    returns

    RDD of Coverage Records.

    Definition Classes
    CoverageRDD
  20. def coverage(bpPerBin: Integer): CoverageRDD

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    Gets coverage overlapping specified ReferenceRegion.

    Gets coverage overlapping specified ReferenceRegion.

    For large ReferenceRegions, base pairs per bin (bpPerBin) can be specified to bin together ReferenceRegions of equal size. The coverage of each bin is coverage of the first base pair in that bin. Java friendly variant.

    bpPerBin

    base pairs per bin, number of bases to combine to one bin.

    returns

    RDD of Coverage Records.

    Definition Classes
    CoverageRDD
  21. lazy val dataset: Dataset[Coverage]

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    This data as a Spark SQL Dataset.

    This data as a Spark SQL Dataset.

    Definition Classes
    ParquetUnboundCoverageRDDGenomicDataset
  22. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  23. def filterByOverlappingRegion(query: ReferenceRegion): CoverageRDD

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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 GenomicRDD containing only data that overlaps the query region.

    Definition Classes
    GenomicRDD
  24. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): CoverageRDD

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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 GenomicRDD containing only data that overlaps the querys region.

    Definition Classes
    GenomicRDD
  25. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  26. def flatten(): CoverageRDD

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    Gets flattened RDD of coverage, with coverage mapped to a ReferenceRegion at each base pair.

    Gets flattened RDD of coverage, with coverage mapped to a ReferenceRegion at each base pair.

    returns

    CoverageRDD of flattened Coverage records.

    Definition Classes
    CoverageRDD
  27. def flattenRddByRegions(): RDD[(ReferenceRegion, Coverage)]

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    Attributes
    protected
    Definition Classes
    GenomicRDD
  28. def fullOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Coverage], Option[X])]): GenericGenomicRDD[(Option[Coverage], Option[X])]

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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
    GenomicRDD
  29. def fullOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Coverage], Option[X])]): GenericGenomicRDD[(Option[Coverage], Option[X])]

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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
    GenomicRDD
  30. final def getClass(): Class[_]

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

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    Gets sequence of ReferenceRegions from Coverage element.

    Gets sequence of ReferenceRegions from Coverage element. Since coverage maps directly to a single genomic region, this method will always return a Seq of exactly one ReferenceRegion.

    elem

    The Coverage to get an underlying region for.

    returns

    Sequence of ReferenceRegions extracted from Coverage.

    Attributes
    protected
    Definition Classes
    CoverageRDDGenomicRDD
  32. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  33. def isSorted: Boolean

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    Definition Classes
    GenomicRDD
  34. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  35. lazy val jrdd: JavaRDD[Coverage]

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    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicRDD
  36. def leftOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Option[X])]): GenericGenomicRDD[(Coverage, Option[X])]

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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
    GenomicRDD
  37. def leftOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Option[X])]): GenericGenomicRDD[(Coverage, Option[X])]

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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
    GenomicRDD
  38. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Iterable[X])]): GenericGenomicRDD[(Coverage, Iterable[X])]

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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
    GenomicRDD
  39. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], toxTag: ClassTag[(Coverage, Iterable[X])]): GenericGenomicRDD[(Coverage, Iterable[X])]

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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
    GenomicRDD
  40. def log: Logger

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

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

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

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

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  47. def logName: String

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

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

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  52. final def ne(arg0: AnyRef): Boolean

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

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

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

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    Attributes
    protected
    Definition Classes
    ParquetUnboundCoverageRDDGenomicRDD
  56. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[Coverage, CoverageRDD, V]](cmd: String, files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[V], xFormatter: OutFormatter[X], convFn: Function2[CoverageRDD, RDD[X], Y]): Y

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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 GenomicRDD containing X's.

    V

    The InFormatter to use for formatting the data being piped to the command.

    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 GenomicRDD of type Y.

    Definition Classes
    GenomicRDD
  57. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[Coverage, CoverageRDD, V]](cmd: String, files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[V], xFormatter: OutFormatter[X], convFn: Function2[CoverageRDD, RDD[X], Y]): Y

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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 GenomicRDD containing X's.

    V

    The InFormatter to use for formatting the data being piped to the command.

    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 GenomicRDD of type Y.

    Definition Classes
    GenomicRDD
  58. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[Coverage, CoverageRDD, V]](cmd: String, files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0)(implicit tFormatterCompanion: InFormatterCompanion[Coverage, CoverageRDD, V], xFormatter: OutFormatter[X], convFn: (CoverageRDD, RDD[X]) ⇒ Y, tManifest: ClassTag[Coverage], xManifest: ClassTag[X]): Y

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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 GenomicRDD. 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 GenomicRDD containing X's.

    V

    The InFormatter to use for formatting the data being piped to the command.

    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.

    returns

    Returns a new GenomicRDD of type Y.

    Definition Classes
    GenomicRDD
  59. lazy val rdd: RDD[Coverage]

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    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    ParquetUnboundCoverageRDDGenomicRDD
  60. def replaceRdd(newRdd: RDD[Coverage], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): CoverageRDD

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    newRdd

    The RDD to replace the underlying RDD with.

    returns

    Returns a new CoverageRDD with the underlying RDD replaced.

    Attributes
    protected
    Definition Classes
    CoverageRDDGenomicRDD
  61. def replaceSequences(newSequences: SequenceDictionary): CoverageRDD

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    Replaces the sequence dictionary attached to a GenomicRDD.

    Replaces the sequence dictionary attached to a GenomicRDD.

    newSequences

    The new sequence dictionary to attach.

    returns

    Returns a new GenomicRDD with the sequences replaced.

    Definition Classes
    ParquetUnboundCoverageRDDGenomicRDD
  62. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)]): GenericGenomicRDD[(Option[Coverage], X)]

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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
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoin

  63. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)]): GenericGenomicRDD[(Option[Coverage], X)]

    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 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
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoin

  64. def rightOuterBroadcastRegionJoinAgainst[X](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X]): GenericGenomicRDD[(Option[X], Coverage)]

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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.

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    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

  65. def rightOuterBroadcastRegionJoinAgainstAndGroupByRight[X, Y <: GenomicRDD[X, Y]](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X]): GenericGenomicRDD[(Iterable[X], Coverage)]

    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 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.

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    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

  66. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)]): GenericGenomicRDD[(Iterable[Coverage], X)]

    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.

    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
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  67. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Coverage], X)]): GenericGenomicRDD[(Iterable[Coverage], X)]

    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.

    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
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  68. def rightOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)]): GenericGenomicRDD[(Option[Coverage], X)]

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    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
    GenomicRDD
  69. def rightOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otxTag: ClassTag[(Option[Coverage], X)]): GenericGenomicRDD[(Option[Coverage], X)]

    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
    GenomicRDD
  70. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otixTag: ClassTag[(Option[Coverage], Iterable[X])]): GenericGenomicRDD[(Option[Coverage], Iterable[X])]

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    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
    GenomicRDD
  71. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], otixTag: ClassTag[(Option[Coverage], Iterable[X])]): GenericGenomicRDD[(Option[Coverage], Iterable[X])]

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    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
    GenomicRDD
  72. def save(filePath: String, asSingleFile: Boolean, disableFastConcat: Boolean): Unit

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    Saves coverage as feature file.

    Saves coverage as feature file.

    filePath

    The location to write the output.

    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.

    disableFastConcat

    If asSingleFile is true, disables the use of the fast file concatenation engine.

    Definition Classes
    CoverageRDD
    See also

    FeatureRDD.save Supported file formats include bed, narrowPeak and parquet. Coverage is saved as a feature where coverage is stored in score attribute. val chrom = feature.getContigName val start = feature.getStart val end = feature.getEnd val name = Features.nameOf(feature) val coverage = feature.getScore

  73. val sequences: SequenceDictionary

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    The sequence dictionary describing the reference assembly this dataset is aligned to.

    The sequence dictionary describing the reference assembly this dataset is aligned to.

    Definition Classes
    ParquetUnboundCoverageRDDGenomicRDD
  74. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)]): GenericGenomicRDD[(Coverage, X)]

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    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
    GenomicRDD
  75. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], txTag: ClassTag[(Coverage, X)]): GenericGenomicRDD[(Coverage, X)]

    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
    GenomicRDD
  76. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], tixTag: ClassTag[(Coverage, Iterable[X])]): GenericGenomicRDD[(Coverage, Iterable[X])]

    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
    GenomicRDD
  77. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Coverage], xTag: ClassTag[X], tixTag: ClassTag[(Coverage, Iterable[X])]): GenericGenomicRDD[(Coverage, Iterable[X])]

    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
    GenomicRDD
  78. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Coverage]): CoverageRDD

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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
    GenomicRDD
    Note

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

    See also

    sortLexicographically

  79. def sort(): CoverageRDD

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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
    GenomicRDD
    See also

    sortLexicographically

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

    Permalink

    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
    GenomicRDD
    Note

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

    See also

    sort

  81. def sortLexicographically(): CoverageRDD

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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
    GenomicRDD
    See also

    sort

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

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    Definition Classes
    AnyRef
  83. def toDF(): DataFrame

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    returns

    This data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  84. def toFeatures(): FeatureRDD

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    Converts CoverageRDD to FeatureRDD.

    Converts CoverageRDD to FeatureRDD.

    returns

    Returns a FeatureRDD from CoverageRDD.

    Definition Classes
    ParquetUnboundCoverageRDDCoverageRDD
  85. def toString(): String

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    Definition Classes
    GenomicRDD → AnyRef → Any
  86. def transform(tFn: Function[JavaRDD[Coverage], JavaRDD[Coverage]]): CoverageRDD

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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) is copied without modification.

    Definition Classes
    GenomicRDD
  87. def transform(tFn: (RDD[Coverage]) ⇒ RDD[Coverage]): CoverageRDD

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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) is copied without modification.

    Definition Classes
    GenomicRDD
  88. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): CoverageRDD

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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) is copied without modification.

    Definition Classes
    GenomicDataset
  89. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[Coverage]): CoverageRDD

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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) is copied without modification.

    Definition Classes
    GenomicDataset
  90. def transformDataset(tFn: (Dataset[Coverage]) ⇒ Dataset[Coverage]): CoverageRDD

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

    Applies a function that transforms the underlying Dataset into a new Dataset 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
    CoverageRDDGenomicDataset
  91. def transmute[X, Y <: GenomicRDD[X, Y]](tFn: Function[JavaRDD[Coverage], JavaRDD[X]], convFn: Function2[CoverageRDD, RDD[X], Y]): Y

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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) is copied without modification.

    Definition Classes
    GenomicRDD
  92. def transmute[X, Y <: GenomicRDD[X, Y]](tFn: (RDD[Coverage]) ⇒ RDD[X])(implicit convFn: (CoverageRDD, RDD[X]) ⇒ Y): Y

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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) is copied without modification.

    Definition Classes
    GenomicRDD
  93. def transmuteDataFrame[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[Coverage, CoverageRDD, X, Y]): Y

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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) is copied without modification.

    Definition Classes
    GenomicDataset
  94. def transmuteDataFrame[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: (DataFrame) ⇒ DataFrame)(implicit xTag: scala.reflect.api.JavaUniverse.TypeTag[X], convFn: (CoverageRDD, Dataset[X]) ⇒ Y): Y

    Permalink

    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) is copied without modification.

    Definition Classes
    GenomicDataset
  95. def transmuteDataset[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: Function[Dataset[Coverage], Dataset[X]], convFn: GenomicDatasetConversion[Coverage, CoverageRDD, X, Y]): Y

    Permalink

    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) is copied without modification.

    Definition Classes
    GenomicDataset
  96. def transmuteDataset[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: (Dataset[Coverage]) ⇒ Dataset[X])(implicit xTag: scala.reflect.api.JavaUniverse.TypeTag[X], convFn: (CoverageRDD, Dataset[X]) ⇒ Y): Y

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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) is copied without modification.

    Definition Classes
    GenomicDataset
  97. val uTag: scala.reflect.api.JavaUniverse.TypeTag[Coverage]

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    Definition Classes
    CoverageRDDGenomicDataset
  98. def union(rdds: CoverageRDD*): CoverageRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    CoverageRDDGenomicRDD
  99. def union(rdds: List[CoverageRDD]): CoverageRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    GenomicRDD
  100. final def wait(): Unit

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  103. 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
    GenomicRDD

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from CoverageRDD

Inherited from GenomicRDD[Coverage, CoverageRDD]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped