Class

org.bdgenomics.adam.rdd.fragment

ParquetUnboundFragmentRDD

Related Doc: package fragment

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case class ParquetUnboundFragmentRDD extends FragmentRDD with Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, FragmentRDD, AvroRecordGroupGenomicDataset[Fragment, Fragment, FragmentRDD], GenomicDatasetWithLineage[Fragment, Fragment, FragmentRDD], AvroGenomicDataset[Fragment, Fragment, FragmentRDD], GenomicDataset[Fragment, Fragment, FragmentRDD], Logging, AnyRef, Any
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  1. ParquetUnboundFragmentRDD
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. FragmentRDD
  7. AvroRecordGroupGenomicDataset
  8. GenomicDatasetWithLineage
  9. AvroGenomicDataset
  10. GenomicDataset
  11. Logging
  12. AnyRef
  13. Any
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Value Members

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

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

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

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    Definition Classes
    AnyRef → Any
  4. def addProcessingStep(newProcessingStep: ProcessingStep): FragmentRDD

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    Merges a new processing record with the extant computational lineage.

    Merges a new processing record with the extant computational lineage.

    returns

    Returns a new GenomicDataset with new record groups merged in.

    Definition Classes
    GenomicDatasetWithLineage
  5. def addRecordGroup(recordGroupToAdd: RecordGroup): FragmentRDD

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    Adds a single record group to the extant record groups.

    Adds a single record group to the extant record groups.

    recordGroupToAdd

    The record group to append to the extant record groups.

    returns

    Returns a new GenomicDataset with the new record group added.

    Definition Classes
    AvroRecordGroupGenomicDataset
  6. def addRecordGroups(recordGroupsToAdd: RecordGroupDictionary): FragmentRDD

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    Merges a new set of record groups with the extant record groups.

    Merges a new set of record groups with the extant record groups.

    recordGroupsToAdd

    The record group dictionary to append to the extant record groups.

    returns

    Returns a new GenomicDataset with new record groups merged in.

    Definition Classes
    AvroRecordGroupGenomicDataset
  7. def addSequence(sequenceToAdd: SequenceRecord): FragmentRDD

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    Appends metadata for a single sequence to the current RDD.

    Appends metadata for a single sequence to the current RDD.

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicDataset with this sequence appended.

    Definition Classes
    GenomicDataset
  8. def addSequences(sequencesToAdd: SequenceDictionary): FragmentRDD

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    Appends sequence metadata to the current RDD.

    Appends sequence metadata to the current RDD.

    sequencesToAdd

    The new sequences to append.

    returns

    Returns a new GenomicDataset with the sequences appended.

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

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    Definition Classes
    Any
  10. def binQualityScores(bins: Seq[QualityScoreBin]): FragmentRDD

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    Rewrites the quality scores of fragments to place all quality scores in bins.

    Rewrites the quality scores of fragments to place all quality scores in bins.

    Quality score binning maps all quality scores to a limited number of discrete values, thus reducing the entropy of the quality score distribution, and reducing the amount of space that fragments consume on disk.

    bins

    The bins to use.

    returns

    Fragments whose quality scores are binned.

    Definition Classes
    FragmentRDD
  11. def broadcast()(implicit tTag: ClassTag[Fragment]): GenomicBroadcast[Fragment, Fragment, FragmentRDD]

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoin

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

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoinAndGroupByRight

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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    Attributes
    protected
    Definition Classes
    FragmentRDDGenomicDataset
  23. def cache(): FragmentRDD

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    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

    Cached GenomicDataset.

    Definition Classes
    GenomicDataset
  24. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  25. lazy val dataset: Dataset[Fragment]

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    These data as a Spark SQL Dataset.

    These data as a Spark SQL Dataset.

    Definition Classes
    ParquetUnboundFragmentRDDGenomicDataset
  26. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  27. def filterByOverlappingRegion(query: ReferenceRegion): FragmentRDD

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

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

    query

    The region to query for.

    returns

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

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

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

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

    querys

    The regions to query for.

    returns

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

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

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  30. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  31. def flattenRddByRegions(): RDD[(ReferenceRegion, Fragment)]

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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    Returns the regions that this fragment covers.

    Returns the regions that this fragment covers.

    Since a fragment may be chimeric or multi-mapped, we do not try to compute the hull of the underlying element.

    elem

    The Fragment to get the region from.

    returns

    Returns all regions covered by this fragment.

    Attributes
    protected
    Definition Classes
    FragmentRDDGenomicDataset
  38. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  39. def isSorted: Boolean

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    Definition Classes
    GenomicDataset
  40. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  41. lazy val jrdd: JavaRDD[Fragment]

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  50. def log: Logger

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

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

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

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

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  57. def logName: String

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

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

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  62. def markDuplicates(): FragmentRDD

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    Marks reads as possible fragment duplicates.

    Marks reads as possible fragment duplicates.

    returns

    A new RDD where reads have the duplicate read flag set. Duplicate reads are NOT filtered out.

    Definition Classes
    FragmentRDD
  63. final def ne(arg0: AnyRef): Boolean

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

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

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

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    Attributes
    protected
    Definition Classes
    ParquetUnboundFragmentRDDGenomicDataset
  67. def persist(sl: StorageLevel): FragmentRDD

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

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

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

    Java/PySpark friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

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

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

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

    SparkR friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

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

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

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    optTimeout

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

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  71. val processingSteps: Seq[ProcessingStep]

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    The processing steps that have been applied to this GenomicDataset.

    The processing steps that have been applied to this GenomicDataset.

    Definition Classes
    ParquetUnboundFragmentRDDGenomicDatasetWithLineage
  72. val productFn: (Fragment) ⇒ Fragment

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    Attributes
    protected
    Definition Classes
    FragmentRDDGenomicDataset
  73. lazy val rdd: RDD[Fragment]

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    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    ParquetUnboundFragmentRDDGenomicDataset
  74. val recordGroups: RecordGroupDictionary

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    A dictionary describing the record groups attached to this GenomicDataset.

    A dictionary describing the record groups attached to this GenomicDataset.

    Definition Classes
    ParquetUnboundFragmentRDDAvroRecordGroupGenomicDataset
  75. def replaceProcessingSteps(newProcessingSteps: Seq[ProcessingStep]): FragmentRDD

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    Replaces the processing steps attached to this RDD.

    Replaces the processing steps attached to this RDD.

    newProcessingSteps

    The new processing steps to attach to this RDD.

    returns

    Returns a new GenomicDataset with new processing lineage attached.

    Definition Classes
    ParquetUnboundFragmentRDDGenomicDatasetWithLineage
  76. def replaceRdd(newRdd: RDD[Fragment], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): FragmentRDD

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    Replaces the underlying RDD with a new RDD.

    Replaces the underlying RDD with a new RDD.

    newRdd

    The RDD to replace our underlying RDD with.

    returns

    Returns a new FragmentRDD where the underlying RDD has been swapped out.

    Attributes
    protected
    Definition Classes
    FragmentRDDGenomicDataset
  77. def replaceRecordGroups(newRecordGroups: RecordGroupDictionary): FragmentRDD

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    Replaces the record groups attached to this RDD.

    Replaces the record groups attached to this RDD.

    newRecordGroups

    The new record group dictionary to attach.

    returns

    Returns a new GenomicDataset with new record groups attached.

    Definition Classes
    ParquetUnboundFragmentRDDAvroRecordGroupGenomicDataset
  78. def replaceSequences(newSequences: SequenceDictionary): FragmentRDD

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  97. def save(filePath: String): Unit

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    Saves Fragments to Parquet.

    Saves Fragments to Parquet.

    filePath

    Path to save fragments at.

    Definition Classes
    FragmentRDD
  98. def saveAsParquet(filePath: String): Unit

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    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

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

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    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

    Whether or not to disable bit-packing.

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

    Permalink

    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

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

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

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    Saves an RDD to Parquet.

    Saves an RDD to Parquet.

    args

    The output format configuration to use when saving the data.

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

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

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

    filePath

    Path to save the file at.

    compressCodec

    Name of the compression codec to use.

    partitionSize

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

    Definition Classes
    AvroGenomicDataset
  103. 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
  104. def saveMetadata(filePath: String): Unit

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

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

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

    filePath

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

    Attributes
    protected
    Definition Classes
    AvroRecordGroupGenomicDatasetAvroGenomicDataset
  105. def savePartitionMap(filePath: String): Unit

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    Save the partition map to disk.

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

    filePath

    The filepath where we will save the partition map.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  106. def saveProcessingSteps(filePath: String): Unit

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    Save the processing steps to disk.

    Save the processing steps to disk.

    filePath

    The filepath to the directory within which we will save the processing step descriptions..

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

    Permalink

    Saves an RDD of Avro data to Parquet.

    Saves an RDD of Avro data to Parquet.

    pathName

    The path to save the file to.

    blockSize

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

    pageSize

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

    compressCodec

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

    disableDictionaryEncoding

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

    optSchema

    The optional schema to set. Defaults to None.

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

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    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  109. def saveRecordGroups(filePath: String): Unit

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    Save the record groups to disk.

    Save the record groups to disk.

    filePath

    The filepath to the file where we will save the record groups.

    Attributes
    protected
    Definition Classes
    AvroRecordGroupGenomicDataset
  110. def saveSequences(filePath: String): Unit

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    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    filePath

    The filepath where we will save the sequence dictionary.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  111. 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
    ParquetUnboundFragmentRDDGenomicDataset
  112. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Fragment], xTag: ClassTag[X], txTag: ClassTag[(Fragment, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Fragment, Y)]): GenericGenomicDataset[(Fragment, X), (Fragment, Y)]

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  120. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Fragment]): FragmentRDD

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

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

    partitions

    The number of partitions for the new RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sortLexicographically

  121. def sort(): FragmentRDD

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

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

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sortLexicographically

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

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

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

    partitions

    The number of partitions for the new RDD.

    storePartitionMap

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

    storageLevel

    The level at which to persist the resulting RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sort

  123. def sortLexicographically(): FragmentRDD

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

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

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sort

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

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    Definition Classes
    AnyRef
  125. def toDF(): DataFrame

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    returns

    This data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  126. def toReads(): AlignmentRecordRDD

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    Essentially, splits up the reads in a Fragment.

    Essentially, splits up the reads in a Fragment.

    returns

    Returns this RDD converted back to reads.

    Definition Classes
    FragmentRDD
  127. def toString(): String

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    Definition Classes
    AvroRecordGroupGenomicDatasetGenomicDataset → AnyRef → Any
  128. def transform(tFn: Function[JavaRDD[Fragment], JavaRDD[Fragment]]): FragmentRDD

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  129. def transform(tFn: (RDD[Fragment]) ⇒ RDD[Fragment]): FragmentRDD

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  130. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): FragmentRDD

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

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

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  131. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[Fragment]): FragmentRDD

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

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

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  132. def transformDataset(tFn: (Dataset[Fragment]) ⇒ Dataset[Fragment]): FragmentRDD

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

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

    tFn

    A function that transforms the underlying RDD as a Dataset.

    returns

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

    Definition Classes
    FragmentRDDGenomicDataset
  133. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Fragment], JavaRDD[X]], convFn: Function2[FragmentRDD, RDD[X], Z]): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

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

    Definition Classes
    GenomicDataset
  134. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[Fragment]) ⇒ RDD[X])(implicit convFn: (FragmentRDD, RDD[X]) ⇒ Z): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  135. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[Fragment, Fragment, FragmentRDD, X, Y, Z]): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

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

    Permalink

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  137. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[Fragment], Dataset[Y]], convFn: GenomicDatasetConversion[Fragment, Fragment, FragmentRDD, X, Y, Z]): Z

    Permalink

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

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

    Permalink

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  139. val uTag: scala.reflect.api.JavaUniverse.TypeTag[Fragment]

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    Definition Classes
    FragmentRDDGenomicDataset
  140. def union(rdds: FragmentRDD*): FragmentRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    FragmentRDDGenomicDataset
  141. def union(rdds: List[FragmentRDD]): FragmentRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    GenomicDataset
  142. def unpersist(): FragmentRDD

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    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  143. val unproductFn: (Fragment) ⇒ Fragment

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    Attributes
    protected
    Definition Classes
    FragmentRDDGenomicDataset
  144. final def wait(): Unit

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

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

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

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    Writes an RDD to disk as text and optionally merges.

    Writes an RDD to disk as text and optionally merges.

    rdd

    RDD to save.

    outputPath

    Output path to save text files to.

    asSingleFile

    If true, combines all partition shards.

    disableFastConcat

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

    optHeaderPath

    If provided, the header file to include.

    Attributes
    protected
    Definition Classes
    GenomicDataset

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from FragmentRDD

Inherited from GenomicDatasetWithLineage[Fragment, Fragment, FragmentRDD]

Inherited from AvroGenomicDataset[Fragment, Fragment, FragmentRDD]

Inherited from GenomicDataset[Fragment, Fragment, FragmentRDD]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped