Class/Object

org.bdgenomics.adam.rdd.sequence

SliceDataset

Related Docs: object SliceDataset | package sequence

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sealed abstract class SliceDataset extends AvroGenomicDataset[Slice, Slice, SliceDataset]

Linear Supertypes
AvroGenomicDataset[Slice, Slice, SliceDataset], GenomicDataset[Slice, Slice, SliceDataset], Logging, AnyRef, Any
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  1. SliceDataset
  2. AvroGenomicDataset
  3. GenomicDataset
  4. Logging
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Abstract Value Members

  1. abstract val dataset: Dataset[Slice]

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    These data as a Spark SQL Dataset.

    These data as a Spark SQL Dataset.

    Definition Classes
    GenomicDataset
  2. abstract val optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]

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    Attributes
    protected
    Definition Classes
    GenomicDataset
  3. abstract val rdd: RDD[Slice]

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    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    GenomicDataset
  4. abstract def replaceSequences(newSequences: SequenceDictionary): SliceDataset

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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
    GenomicDataset
  5. abstract 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
    GenomicDataset

Concrete 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): SliceDataset

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    Appends metadata for a single sequence to the current genomic dataset.

    Appends metadata for a single sequence to the current genomic dataset.

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicDataset with this sequence appended.

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

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    Appends sequence metadata to the current genomic dataset.

    Appends sequence metadata to the current genomic dataset.

    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[Slice]): GenomicBroadcast[Slice, Slice, SliceDataset]

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

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    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset in the join.

    returns

    Returns a new genomic dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], txTag: ClassTag[(Slice, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Y)]): GenericGenomicDataset[(Slice, X), (Slice, Y)]

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    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Slice, X), (Slice, Y)]

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    (Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    (Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Slice, X), (Slice, Y)]

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    (R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset 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[Slice], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, Slice)]): GenericGenomicDataset[(X, Slice), (Y, Slice)]

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

    Performs a broadcast inner join between this genomic dataset 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 genomic dataset are dropped. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.

    broadcast

    The data on the left side of the join.

    returns

    Returns a new genomic dataset 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 genomic dataset 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[Slice], xTag: ClassTag[X], syuTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Y], Slice)]): GenericGenomicDataset[(Iterable[X], Slice), (Seq[Y], Slice)]

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    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    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 genomic dataset are dropped. As compared to broadcastRegionJoin, this function allows the broadcast object to be reused across multiple joins.

    broadcast

    The data on the left side of the join.

    returns

    Returns a new genomic dataset 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 genomic dataset 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]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Slice], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Slice], Y)]): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], Y)]

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    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset in the join.

    returns

    Returns a new genomic dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Slice], X)], iuyTag: scala.reflect.api.JavaUniverse.TypeTag[(Seq[Slice], Y)]): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], Y)]

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    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], Y)]

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    (Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    (Java-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], Y)]

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    (R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a broadcast inner join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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    Attributes
    protected
    Definition Classes
    SliceDatasetGenomicDataset
  19. def cache(): SliceDataset

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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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    (Java-friendly) Counts the k-mers contained in this genomic dataset of slices.

    (Java-friendly) Counts the k-mers contained in this genomic dataset of slices.

    kmerLength

    The length of k-mers to count.

    returns

    Returns an RDD containing k-mer/count pairs.

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

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    (Scala-friendly) Counts the k-mers contained in this genomic dataset of slices.

    (Scala-friendly) Counts the k-mers contained in this genomic dataset of slices.

    kmerLength

    The length of k-mers to count.

    returns

    Returns an RDD containing k-mer/count pairs.

  23. def createSequenceDictionary(): SliceDataset

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    Replace the sequence dictionary for this SliceDataset with one created from the slices in this SliceDataset.

    Replace the sequence dictionary for this SliceDataset with one created from the slices in this SliceDataset.

    returns

    Returns a new SliceDataset with the sequence dictionary replaced.

  24. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
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    Definition Classes
    Logging
  25. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Logging
  26. def debug(msg: ⇒ Any): Unit

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    Logging
  27. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  28. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  29. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
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    Logging
  30. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Logging
  31. def error(msg: ⇒ Any): Unit

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    Logging
  32. def extract(region: ReferenceRegion): String

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    Extract the specified region from this genomic dataset of slices as a string, merging slices if necessary.

    Extract the specified region from this genomic dataset of slices as a string, merging slices if necessary.

    region

    Region to extract.

    returns

    Return the specified region from this genomic dataset of slices as a string, merging slices if necessary.

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

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    Extract the specified regions from this genomic dataset of slices as an RDD of (ReferenceRegion, String) tuples, merging slices if necessary.

    Extract the specified regions from this genomic dataset of slices as an RDD of (ReferenceRegion, String) tuples, merging slices if necessary.

    regions

    Zero or more regions to extract.

    returns

    Return the specified regions from this genomic dataset of slices as an RDD of (ReferenceRegion, String) tuples, merging slices if necessary.

  34. def filterByOverlappingRegion(query: ReferenceRegion): SliceDataset

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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
  35. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): SliceDataset

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    (Java-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.

    (Java-specific) 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
  36. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): SliceDataset

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    (Scala-specific) Runs a filter that selects data in the underlying RDD that overlaps several genomic regions.

    (Scala-specific) 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
  37. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  38. def flankAdjacent(flankLength: Int): SliceDataset

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    (Scala-friendly) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.

    (Scala-friendly) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.

    flankLength

    The length to extend adjacent slices by.

    returns

    Returns this genomic dataset, with all adjacent slices extended with flanking sequence.

  39. def flankAdjacent(flankLength: Integer): SliceDataset

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    (Java-friendly) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.

    (Java-friendly) For all adjacent slices in this genomic dataset, we extend the slices so that the adjacent slices now overlap by _n_ bases, where _n_ is the flank length.

    flankLength

    The length to extend adjacent slices by.

    returns

    Returns this genomic dataset, with all adjacent slices extended with flanking sequence.

  40. def flattenRddByRegions(): RDD[(ReferenceRegion, Slice)]

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset in the join.

    returns

    Returns a new genomic dataset 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
  42. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Slice], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Option[Y])]): GenericGenomicDataset[(Option[Slice], Option[X]), (Option[Slice], Option[Y])]

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset 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 dataset 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
  43. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Slice], Option[X]), (Option[Slice], Option[Y])]

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    (Python-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.

    (Python-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset 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 dataset 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
  44. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Slice], Option[X]), (Option[Slice], Option[Y])]

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    (R-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a sort-merge full outer join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset does not overlap any values in the other genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset 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 dataset 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
  45. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  46. def getReferenceRegions(slice: Slice): Seq[ReferenceRegion]

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    slice

    Slice to extract a region from.

    returns

    Returns a reference region that covers the entirety of the slice.

    Attributes
    protected
    Definition Classes
    SliceDatasetGenomicDataset
  47. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  48. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Logging
  49. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  50. def info(msg: ⇒ Any): Unit

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  51. def isDebugEnabled: Boolean

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  52. def isErrorEnabled: Boolean

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  53. def isInfoEnabled: Boolean

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    Logging
  54. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  55. def isSorted: Boolean

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    Definition Classes
    GenomicDataset
  56. def isTraceEnabled: Boolean

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    Logging
  57. def isWarnEnabled: Boolean

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    Logging
  58. lazy val jrdd: JavaRDD[Slice]

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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
  59. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], toxTag: ClassTag[(Slice, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Option[Y])]): GenericGenomicDataset[(Slice, Option[X]), (Slice, Option[Y])]

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  61. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Slice, Option[X]), (Slice, Option[Y])]

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    (Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.

    (Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  62. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Slice, Option[X]), (Slice, Option[Y])]

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    (R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  65. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, Seq[Y])]

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    (Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    (Java-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  66. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, Seq[Y])]

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    (R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    (R-specific) Performs a sort-merge left outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the left genomic dataset are dropped. If a value from the left genomic dataset does not overlap any values in the right genomic dataset, it will be paired with an empty Iterable in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  67. def logger: Logger

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    Attributes
    protected
    Definition Classes
    Logging
  68. def loggerName: String

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    Attributes
    protected
    Definition Classes
    Logging
  69. def merge(): SequenceDataset

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    Merge slices into sequences.

    Merge slices into sequences.

    returns

    Returns a SequenceDataset containing merged slices.

  70. final def ne(arg0: AnyRef): Boolean

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

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

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    Definition Classes
    AnyRef
  73. def persist(sl: StorageLevel): SliceDataset

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

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    (Java/Python-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.

    (Java/Python-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.

    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 genomic dataset.

    returns

    Returns a new GenomicDataset of type Y.

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

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    (R-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.

    (R-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.

    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 genomic dataset.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  76. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Slice, Slice, SliceDataset, 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[Slice, Slice, SliceDataset, W], xFormatter: OutFormatter[X], convFn: (SliceDataset, RDD[X]) ⇒ Z, tManifest: ClassTag[Slice], xManifest: ClassTag[X]): Z

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    (Scala-specific) Pipes genomic data to a subprocess that runs in parallel using Spark.

    (Scala-specific) 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
  77. val productFn: (Slice) ⇒ Slice

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    Attributes
    protected
    Definition Classes
    SliceDatasetGenomicDataset
  78. def replaceRdd(newRdd: RDD[Slice], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): SliceDataset

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    newRdd

    The RDD to replace the underlying RDD with.

    newPartitionMap

    New partition map, if any.

    returns

    Returns a new SliceDataset with the underlying RDD replaced.

    Attributes
    protected
    Definition Classes
    SliceDatasetGenomicDataset
  79. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], otxTag: ClassTag[(Option[Slice], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Slice], Y)]): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], Y)]

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    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

  81. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], Y)]

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    (Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    (Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  82. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], Y)]

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    (R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    In a broadcast join, the left genomic dataset (this genomic dataset) 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

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

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

    Performs a broadcast right outer join between this genomic dataset 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 genomic dataset are dropped. If a value from the right genomic dataset 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.

    broadcast

    The data on the left side of the join.

    returns

    Returns a new genomic dataset 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 genomic dataset as the right side of the join, and not the left.

    See also

    rightOuterBroadcastRegionJoin

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

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    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    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 genomic dataset are dropped. If a value from the right genomic dataset 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.

    broadcast

    The data on the left side of the join.

    returns

    Returns a new genomic dataset 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 genomic dataset as the right side of the join, and not the left.

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

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

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    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  87. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], Y)]

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    (Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    (Java-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  88. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Iterable[Slice], X), (Seq[Slice], Y)]

    Permalink

    (R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a broadcast right outer join between this genomic dataset and another genomic dataset.

    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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  91. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], Y)]

    Permalink

    (Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.

    (Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  92. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Slice], X), (Option[Slice], Y)]

    Permalink

    (R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset that do not overlap a value from the right genomic dataset are dropped. If a value from the right genomic dataset does not overlap any values in the left genomic dataset, it will be paired with a None in the product of the join.

    genomicDataset

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

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a None key.

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a None key.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  95. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Slice], Iterable[X]), (Option[Slice], Seq[Y])]

    Permalink

    (Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.

    (Java-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.

    In a sort-merge join, both genomic datasets 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 genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a None key.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  96. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Slice], Iterable[X]), (Option[Slice], Seq[Y])]

    Permalink

    (R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.

    (R-specific) Performs a sort-merge right outer join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value, if not null.

    In a sort-merge join, both genomic datasets 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 genomic dataset. Since this is a right outer join, all values from the right genomic dataset who did not overlap a value from the left genomic dataset are placed into a length-1 Iterable with a None key.

    genomicDataset

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

    Definition Classes
    GenomicDataset
  97. def save(filePath: String, asSingleFile: Boolean, disableFastConcat: Boolean): Unit

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    Save slices as Parquet or FASTA.

    Save slices as Parquet or FASTA.

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

    filePath

    Path to save files to.

    asSingleFile

    If true, saves output as a single file.

    disableFastConcat

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

  98. def saveAsFasta(filePath: String, asSingleFile: Boolean = false, disableFastConcat: Boolean = false, lineWidth: Int = 60): Unit

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    Save slices in FASTA format.

    Save slices in FASTA format.

    The coordinate fields for this slice are appended to the description field for the FASTA description line:

    >description start-slice:strand
    

    filePath

    Path to save files to.

    asSingleFile

    If true, saves output as a single file.

    disableFastConcat

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

    lineWidth

    Hard wrap FASTA formatted slice at line width, default 60.

  99. def saveAsParquet(pathName: String): Unit

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    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

    Definition Classes
    AvroGenomicDataset
  100. def saveAsParquet(pathName: String, blockSize: Integer, pageSize: Integer, compressionCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit

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    (Java-specific) Saves this genomic dataset to disk as a Parquet file.

    (Java-specific) Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

    blockSize

    The size in bytes of blocks to write.

    pageSize

    The size in bytes of pages to write.

    compressionCodec

    The compression codec to apply to pages.

    disableDictionaryEncoding

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

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

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    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressionCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

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

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

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    Saves a genomic dataset to Parquet.

    Saves a genomic dataset to Parquet.

    args

    The output format configuration to use when saving the data.

    Definition Classes
    GenomicDataset
  103. def saveAsPartitionedParquet(pathName: String, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, partitionSize: Int = 1000000): Unit

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    Saves this RDD to disk in range binned partitioned Parquet format.

    Saves this RDD to disk in range binned partitioned Parquet format.

    pathName

    The path to save the partitioned Parquet file to.

    compressionCodec

    Name of the compression codec to use.

    partitionSize

    Size of partitions used when writing Parquet, in base pairs (bp). Defaults to 1,000,000 bp.

    Definition Classes
    GenomicDataset
  104. 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
  105. def saveMetadata(pathName: String): Unit

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    Called in saveAsParquet after saving genomic dataset to Parquet to save metadata.

    Called in saveAsParquet after saving genomic dataset to Parquet to save metadata.

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

    pathName

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

    Attributes
    protected
    Definition Classes
    AvroGenomicDatasetGenomicDataset
  106. def savePartitionMap(pathName: 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.

    pathName

    The filepath where we will save the partition map.

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

    Permalink

    Saves a genomic dataset of Avro data to Parquet.

    Saves a genomic dataset 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.

    compressionCodec

    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
  108. def saveRddAsParquet(args: SaveArgs): Unit

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    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  109. def saveSequences(pathName: String): Unit

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    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    pathName

    The path to save the sequence dictionary to.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  110. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], txTag: ClassTag[(Slice, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Y)]): GenericGenomicDataset[(Slice, X), (Slice, Y)]

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset in the join.

    returns

    Returns a new genomic dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Slice], xTag: ClassTag[X], txTag: ClassTag[(Slice, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Slice, Y)]): GenericGenomicDataset[(Slice, X), (Slice, Y)]

    Permalink

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset 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]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Slice, X), (Slice, Y)]

    Permalink

    (Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.

    (Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset containing all pairs of keys that overlapped in the genomic coordinate space.

    Definition Classes
    GenomicDataset
  113. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Slice, X), (Slice, Y)]

    Permalink

    (R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.

    (R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset.

    In a sort-merge join, both genomic datasets 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 genomic dataset are dropped.

    genomicDataset

    The right genomic dataset 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 dataset containing all pairs of keys that overlapped in the genomic coordinate space.

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

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset are dropped. In the same operation, we group all values by the left item in the genomic dataset.

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

    Permalink

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

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

    In a sort-merge join, both genomic datasets 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 genomic dataset are dropped. In the same operation, we group all values by the left item in the genomic dataset.

    genomicDataset

    The right genomic dataset 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 dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset.

    Definition Classes
    GenomicDataset
  116. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, Seq[Y])]

    Permalink

    (Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    (Java-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    In a sort-merge join, both genomic datasets 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 genomic dataset.

    genomicDataset

    The right genomic dataset 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 dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset.

    Definition Classes
    GenomicDataset
  117. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Slice, Iterable[X]), (Slice, Seq[Y])]

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    (R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    (R-specific) Performs a sort-merge inner join between this genomic dataset and another genomic dataset, followed by a groupBy on the left value.

    In a sort-merge join, both genomic datasets 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 genomic dataset.

    genomicDataset

    The right genomic dataset 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 dataset containing all pairs of keys that overlapped in the genomic coordinate space, grouped together by the value they overlapped in the left genomic dataset.

    Definition Classes
    GenomicDataset
  118. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Slice]): SliceDataset

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

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

    partitions

    The number of partitions for the new genomic dataset.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sortLexicographically

  119. def sort(): SliceDataset

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

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

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sortLexicographically

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

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

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

    partitions

    The number of partitions for the new genomic dataset.

    storePartitionMap

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

    storageLevel

    The level at which to persist the resulting genomic dataset.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new genomic dataset 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

  121. def sortLexicographically(): SliceDataset

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

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

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sort

  122. lazy val spark: SparkSession

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    Definition Classes
    GenomicDataset
  123. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  124. def toDF(): DataFrame

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    returns

    These data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  125. def toReads: ReadDataset

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    Convert this genomic dataset of slices into reads.

    Convert this genomic dataset of slices into reads.

    returns

    Returns a new ReadDataset converted from this genomic dataset of slices.

  126. def toSequences: SequenceDataset

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    Convert this genomic dataset of slices into sequences.

    Convert this genomic dataset of slices into sequences.

    returns

    Returns a new SequenceDataset converted from this genomic dataset of slices.

  127. def toString(): String

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    Definition Classes
    GenomicDataset → AnyRef → Any
  128. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  129. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  130. def trace(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  131. def transform(tFn: Function[JavaRDD[Slice], JavaRDD[Slice]]): SliceDataset

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    (Java-specific) Applies a function that transforms the underlying RDD into a new RDD.

    (Java-specific) Applies a function that transforms the underlying RDD into a new RDD.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new genomic dataset 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 transform(tFn: (RDD[Slice]) ⇒ RDD[Slice]): SliceDataset

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    (Scala-specific) Applies a function that transforms the underlying RDD into a new RDD.

    (Scala-specific) Applies a function that transforms the underlying RDD into a new RDD.

    tFn

    A function that transforms the underlying RDD.

    returns

    A new genomic dataset 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 transformDataFrame(tFn: Function[DataFrame, DataFrame]): SliceDataset

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    (Java-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.

    (Java-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.

    tFn

    A function that transforms the underlying DataFrame as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  134. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[Slice]): SliceDataset

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    (Scala-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.

    (Scala-specific) Applies a function that transforms the underlying DataFrame into a new DataFrame using the Spark SQL API.

    tFn

    A function that transforms the underlying data as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  135. def transformDataset(tFn: Function[Dataset[Slice], Dataset[Slice]]): SliceDataset

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    (Java-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.

    (Java-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.

    tFn

    A function that transforms the underlying Dataset as a Dataset.

    returns

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

    Definition Classes
    SliceDatasetGenomicDataset
  136. def transformDataset(tFn: (Dataset[Slice]) ⇒ Dataset[Slice]): SliceDataset

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    (Scala-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.

    (Scala-specific) Applies a function that transforms the underlying Dataset into a new Dataset using the Spark SQL API.

    tFn

    A function that transforms the underlying Dataset as a Dataset.

    returns

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

    Definition Classes
    SliceDatasetGenomicDataset
  137. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Slice], JavaRDD[X]], convFn: Function2[SliceDataset, RDD[X], Z]): Z

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    (Java-specific) Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    (Java-specific) Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

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

    Definition Classes
    GenomicDataset
  138. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[Slice]) ⇒ RDD[X])(implicit convFn: (SliceDataset, RDD[X]) ⇒ Z): Z

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    (Scala-specific) Applies a function that transmutes the underlying RDD into a new RDD of a different type.

    (Scala-specific) 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 genomic dataset where the RDD of genomic data has been replaced, but the metadata (sequence dictionary, and etc) are copied without modification.

    Definition Classes
    GenomicDataset
  139. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[Slice, Slice, SliceDataset, X, Y, Z]): Z

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    (Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.

    (Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.

    tFn

    A function that transforms the underlying DataFrame.

    returns

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

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

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    (Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.

    (Java-specific) Applies a function that transmutes the underlying DataFrame into a new DataFrame of a different type.

    tFn

    A function that transforms the underlying DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  141. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[Slice], Dataset[Y]], convFn: GenomicDatasetConversion[Slice, Slice, SliceDataset, X, Y, Z]): Z

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    (Java-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.

    (Java-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.

    tFn

    A function that transforms the underlying Dataset.

    returns

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

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

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    (Scala-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.

    (Scala-specific) Applies a function that transmutes the underlying Dataset into a new Dataset of a different type.

    tFn

    A function that transforms the underlying Dataset.

    returns

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

    Definition Classes
    GenomicDataset
  143. val uTag: scala.reflect.api.JavaUniverse.TypeTag[Slice]

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    Definition Classes
    SliceDatasetGenomicDataset
  144. def union(datasets: SliceDataset*): SliceDataset

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    (Scala-specific) Unions together multiple genomic datasets.

    (Scala-specific) Unions together multiple genomic datasets.

    datasets

    Genomic datasets to union with this genomic dataset.

    Definition Classes
    SliceDatasetGenomicDataset
  145. def union(datasets: List[SliceDataset]): SliceDataset

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    (Java-specific) Unions together multiple genomic datasets.

    (Java-specific) Unions together multiple genomic datasets.

    datasets

    Genomic datasets to union with this genomic dataset.

    Definition Classes
    GenomicDataset
  146. def unpersist(): SliceDataset

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    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  147. val unproductFn: (Slice) ⇒ Slice

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    Attributes
    protected
    Definition Classes
    SliceDatasetGenomicDataset
  148. final def wait(): Unit

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  151. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  152. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  153. def warn(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  154. def writePartitionedParquetFlag(pathName: String, partitionSize: Int): Unit

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    Save partition size into the partitioned Parquet flag file.

    Save partition size into the partitioned Parquet flag file.

    pathName

    Path to save the file at.

    partitionSize

    Partition bin size, in base pairs, used in Hive-style partitioning.

    Definition Classes
    AvroGenomicDatasetGenomicDataset
  155. 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 AvroGenomicDataset[Slice, Slice, SliceDataset]

Inherited from GenomicDataset[Slice, Slice, SliceDataset]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped