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sealed abstract class FragmentDataset extends AvroReadGroupGenomicDataset[Fragment, Fragment, FragmentDataset]

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  1. FragmentDataset
  2. AvroReadGroupGenomicDataset
  3. GenomicDatasetWithLineage
  4. AvroGenomicDataset
  5. GenomicDataset
  6. Logging
  7. AnyRef
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Abstract Value Members

  1. abstract val dataset: Dataset[Fragment]

    These data as a Spark SQL Dataset.

    These data as a Spark SQL Dataset.

    Definition Classes
    GenomicDataset
  2. abstract val optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]
    Attributes
    protected
    Definition Classes
    GenomicDataset
  3. abstract val processingSteps: Seq[ProcessingStep]

    The processing steps that have been applied to this GenomicDataset.

    The processing steps that have been applied to this GenomicDataset.

    Definition Classes
    GenomicDatasetWithLineage
  4. abstract val rdd: RDD[Fragment]

    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    GenomicDataset
  5. abstract val readGroups: ReadGroupDictionary

    A dictionary describing the read groups attached to this GenomicDataset.

    A dictionary describing the read groups attached to this GenomicDataset.

    Definition Classes
    AvroReadGroupGenomicDataset
  6. abstract def replaceProcessingSteps(newProcessingSteps: Seq[ProcessingStep]): FragmentDataset

    Replaces the processing steps attached to this genomic dataset.

    Replaces the processing steps attached to this genomic dataset.

    newProcessingSteps

    The new processing steps to attach to this genomic dataset.

    returns

    Returns a new GenomicDataset with new processing lineage attached.

    Definition Classes
    GenomicDatasetWithLineage
  7. abstract def replaceReadGroups(newReadGroups: ReadGroupDictionary): FragmentDataset

    Replaces the read groups attached to this genomic dataset.

    Replaces the read groups attached to this genomic dataset.

    newReadGroups

    The new read group dictionary to attach.

    returns

    Returns a new GenomicDataset with new read groups attached.

    Definition Classes
    AvroReadGroupGenomicDataset
  8. abstract def replaceSequences(newSequences: SequenceDictionary): FragmentDataset

    Replaces the sequence dictionary attached to a GenomicDataset.

    Replaces the sequence dictionary attached to a GenomicDataset.

    newSequences

    The new sequence dictionary to attach.

    returns

    Returns a new GenomicDataset with the sequences replaced.

    Definition Classes
    GenomicDataset
  9. abstract val sequences: SequenceDictionary

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

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

    Definition Classes
    GenomicDataset

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. def addProcessingStep(newProcessingStep: ProcessingStep): FragmentDataset

    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 read groups merged in.

    Definition Classes
    GenomicDatasetWithLineage
  5. def addReadGroup(readGroupToAdd: ReadGroup): FragmentDataset

    Adds a single read group to the extant read groups.

    Adds a single read group to the extant read groups.

    readGroupToAdd

    The read group to append to the extant read groups.

    returns

    Returns a new GenomicDataset with the new read group added.

    Definition Classes
    AvroReadGroupGenomicDataset
  6. def addReadGroups(readGroupsToAdd: ReadGroupDictionary): FragmentDataset

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

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

    readGroupsToAdd

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

    returns

    Returns a new GenomicDataset with new read groups merged in.

    Definition Classes
    AvroReadGroupGenomicDataset
  7. def addSequence(sequenceToAdd: SequenceRecord): FragmentDataset

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

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

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicDataset with this sequence appended.

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

    Appends sequence metadata to the current genomic dataset.

    Appends sequence metadata to the current genomic dataset.

    sequencesToAdd

    The new sequences to append.

    returns

    Returns a new GenomicDataset with the sequences appended.

    Definition Classes
    GenomicDataset
  9. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  10. def binQualityScores(bins: Seq[QualityScoreBin]): FragmentDataset

    (Scala-specific) Rewrites the quality scores of fragments to place all quality scores in bins.

    (Scala-specific) 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.

  11. def binQualityScores(bins: List[QualityScoreBin]): FragmentDataset

    (Java-specific) Rewrites the quality scores of fragments to place all quality scores in bins.

    (Java-specific) 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.

  12. def broadcast()(implicit tTag: ClassTag[Fragment]): GenomicBroadcast[Fragment, Fragment, FragmentDataset]
    Definition Classes
    GenomicDataset
  13. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

  14. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  17. 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)]

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoin

  18. 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)]

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoinAndGroupByRight

  19. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  20. def broadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  23. def buildTree(rdd: RDD[(ReferenceRegion, Fragment)])(implicit tTag: ClassTag[Fragment]): IntervalArray[ReferenceRegion, Fragment]
    Attributes
    protected
    Definition Classes
    FragmentDatasetGenomicDataset
  24. def cache(): FragmentDataset

    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

    Cached GenomicDataset.

    Definition Classes
    GenomicDataset
  25. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  26. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  27. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  28. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  29. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  30. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  31. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  32. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  33. def error(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  34. def filterByOverlappingRegion(query: ReferenceRegion): FragmentDataset

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

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

    query

    The region to query for.

    returns

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

    Definition Classes
    GenomicDataset
  35. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): FragmentDataset

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  36. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): FragmentDataset

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  37. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  38. def flattenRddByRegions(): RDD[(ReferenceRegion, Fragment)]
    Attributes
    protected
    Definition Classes
    GenomicDataset
  39. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
  40. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  43. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  44. def getReferenceRegions(elem: Fragment): Seq[ReferenceRegion]

    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
    FragmentDatasetGenomicDataset
  45. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  46. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  47. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  48. def info(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  49. def isDebugEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  50. def isErrorEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  51. def isInfoEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  52. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  53. def isSorted: Boolean
    Definition Classes
    GenomicDataset
  54. def isTraceEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  55. def isWarnEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  56. lazy val jrdd: JavaRDD[Fragment]

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicDataset
  57. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
  58. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  61. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
  62. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  65. def logger: Logger
    Attributes
    protected
    Definition Classes
    Logging
  66. def loggerName: String
    Attributes
    protected
    Definition Classes
    Logging
  67. def markDuplicates(): FragmentDataset

    Marks reads as possible fragment duplicates.

    Marks reads as possible fragment duplicates.

    returns

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

  68. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  69. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  70. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  71. def persist(sl: StorageLevel): FragmentDataset

    Persists underlying RDD in memory or disk.

    Persists underlying RDD in memory or disk.

    sl

    new StorageLevel

    returns

    Persisted GenomicDataset.

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final genomic dataset.

    returns

    Returns a new GenomicDataset of type Y.

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final genomic dataset.

    returns

    Returns a new GenomicDataset of type Y.

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

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

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    optTimeout

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

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  75. val productFn: (Fragment) ⇒ Fragment
    Attributes
    protected
    Definition Classes
    FragmentDatasetGenomicDataset
  76. def replaceRdd(newRdd: RDD[Fragment], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): FragmentDataset

    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 FragmentDataset where the underlying RDD has been swapped out.

    Attributes
    protected
    Definition Classes
    FragmentDatasetGenomicDataset
  77. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

  78. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  81. 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)]

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoin

  82. 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)]

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

  83. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  84. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  87. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
  88. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  91. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
  92. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

    Saves Fragments to Parquet.

    Saves Fragments to Parquet.

    filePath

    Path to save fragments at.

  96. def saveAsParquet(pathName: String): Unit

    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

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

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

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

    pathName

    Path to save the file at.

    blockSize

    The size in bytes of blocks to write.

    pageSize

    The size in bytes of pages to write.

    compressionCodec

    The compression codec to apply to pages.

    disableDictionaryEncoding

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

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

    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressionCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

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

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

    Saves a genomic dataset to Parquet.

    Saves a genomic dataset to Parquet.

    args

    The output format configuration to use when saving the data.

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

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

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

    pathName

    The path to save the partitioned Parquet file to.

    compressionCodec

    Name of the compression codec to use.

    partitionSize

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

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

    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
  102. def saveMetadata(pathName: String): Unit

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

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

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

    pathName

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

    Attributes
    protected
    Definition Classes
    AvroReadGroupGenomicDatasetAvroGenomicDatasetGenomicDataset
  103. def savePartitionMap(pathName: String): Unit

    Save the partition map to disk.

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

    pathName

    The filepath where we will save the partition map.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  104. def saveProcessingSteps(pathName: String): Unit

    Save the processing steps to disk.

    Save the processing steps to disk.

    pathName

    The path to save processing steps to.

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

    Saves a genomic dataset of Avro data to Parquet.

    Saves a genomic dataset of Avro data to Parquet.

    pathName

    The path to save the file to.

    blockSize

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

    pageSize

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

    compressionCodec

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

    disableDictionaryEncoding

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

    optSchema

    The optional schema to set. Defaults to None.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  106. def saveRddAsParquet(args: SaveArgs): Unit
    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  107. def saveReadGroups(pathName: String): Unit

    Save the read groups to disk.

    Save the read groups to disk.

    pathName

    The path to save read groups to.

    Attributes
    protected
    Definition Classes
    AvroReadGroupGenomicDataset
  108. def saveSequences(pathName: String): Unit

    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    pathName

    The path to save the sequence dictionary to.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  109. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
  110. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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)]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  113. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
  114. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: 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])]

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

    partitions

    The number of partitions for the new genomic dataset.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sortLexicographically

  118. def sort(): FragmentDataset

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

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

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sortLexicographically

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

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

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

    partitions

    The number of partitions for the new genomic dataset.

    storePartitionMap

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

    storageLevel

    The level at which to persist the resulting genomic dataset.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sort

  120. def sortLexicographically(): FragmentDataset

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

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

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sort

  121. lazy val spark: SparkSession
    Definition Classes
    GenomicDataset
    Annotations
    @transient()
  122. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  123. def toAlignments(): AlignmentDataset

    Splits up the reads in a Fragment back into alignments.

    Splits up the reads in a Fragment back into alignments.

    returns

    Returns this genomic dataset converted to alignments.

  124. def toDF(): DataFrame

    returns

    These data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  125. def toString(): String
    Definition Classes
    AvroReadGroupGenomicDatasetGenomicDataset → AnyRef → Any
  126. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  127. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  128. def trace(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  129. def transform(tFn: Function[JavaRDD[Fragment], JavaRDD[Fragment]]): FragmentDataset

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  130. def transform(tFn: (RDD[Fragment]) ⇒ RDD[Fragment]): FragmentDataset

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  131. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): FragmentDataset

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

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

    tFn

    A function that transforms the underlying DataFrame as a DataFrame.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying data as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  133. def transformDataset(tFn: Function[Dataset[Fragment], Dataset[Fragment]]): FragmentDataset

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

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

    tFn

    A function that transforms the underlying Dataset as a Dataset.

    returns

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

    Definition Classes
    FragmentDatasetGenomicDataset
  134. def transformDataset(tFn: (Dataset[Fragment]) ⇒ Dataset[Fragment]): FragmentDataset

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

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

    tFn

    A function that transforms the underlying Dataset as a Dataset.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying DataFrame.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying DataFrame.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying Dataset.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying Dataset.

    returns

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

    Definition Classes
    GenomicDataset
  141. val uTag: scala.reflect.api.JavaUniverse.TypeTag[Fragment]
    Definition Classes
    FragmentDatasetGenomicDataset
  142. def union(datasets: FragmentDataset*): FragmentDataset

    (Scala-specific) Unions together multiple genomic datasets.

    (Scala-specific) Unions together multiple genomic datasets.

    datasets

    Genomic datasets to union with this genomic dataset.

    Definition Classes
    FragmentDatasetGenomicDataset
  143. def union(datasets: List[FragmentDataset]): FragmentDataset

    (Java-specific) Unions together multiple genomic datasets.

    (Java-specific) Unions together multiple genomic datasets.

    datasets

    Genomic datasets to union with this genomic dataset.

    Definition Classes
    GenomicDataset
  144. def unpersist(): FragmentDataset

    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  145. val unproductFn: (Fragment) ⇒ Fragment
    Attributes
    protected
    Definition Classes
    FragmentDatasetGenomicDataset
  146. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  147. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  148. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  149. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  150. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  151. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  152. def writePartitionedParquetFlag(pathName: String, partitionSize: Int): Unit

    Save partition size into the partitioned Parquet flag file.

    Save partition size into the partitioned Parquet flag file.

    pathName

    Path to save the file at.

    partitionSize

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

    Definition Classes
    AvroGenomicDatasetGenomicDataset
  153. def writeTextRdd[T](rdd: RDD[T], outputPath: String, asSingleFile: Boolean, disableFastConcat: Boolean, optHeaderPath: Option[String] = None): Unit

    Writes an RDD to disk as text and optionally merges.

    Writes an RDD to disk as text and optionally merges.

    rdd

    RDD to save.

    outputPath

    Output path to save text files to.

    asSingleFile

    If true, combines all partition shards.

    disableFastConcat

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

    optHeaderPath

    If provided, the header file to include.

    Attributes
    protected
    Definition Classes
    GenomicDataset

Inherited from AvroGenomicDataset[Fragment, Fragment, FragmentDataset]

Inherited from GenomicDataset[Fragment, Fragment, FragmentDataset]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped