c

org.bdgenomics.adam.ds.variant

DatasetBoundVariantContextDataset

case class DatasetBoundVariantContextDataset extends VariantContextDataset with DatasetBoundGenomicDataset[VariantContext, VariantContext, VariantContextDataset] with Product with Serializable

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  1. DatasetBoundVariantContextDataset
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. DatasetBoundGenomicDataset
  7. VariantContextDataset
  8. VCFSupportingGenomicDataset
  9. MultisampleGenomicDataset
  10. GenomicDataset
  11. Logging
  12. AnyRef
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  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 addAllAlleleArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing an 'R' array format field.

    Adds a VCF header line describing an 'R' array format field.

    This adds a format field that is an array whose length is equal to the total number of alleles (including the reference allele) for the genotype we are annotating.

    id

    The identifier for the field.

    description

    A description of the data stored in this format field.

    lineType

    The type of the data stored in this format field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  5. def addAllAlleleArrayInfoHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing an 'R' array info field.

    Adds a VCF header line describing an 'R' array info field.

    This adds a info field that is an array whose length is equal to the total number of alleles (including the reference allele) for the genotype we are annotating.

    id

    The identifier for the field.

    description

    A description of the data stored in this info field.

    lineType

    The type of the data stored in this info field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  6. def addAlternateAlleleArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing an 'A' array format field.

    Adds a VCF header line describing an 'A' array format field.

    This adds a format field that is an array whose length is equal to the number of alternate alleles for the genotype we are annotating.

    id

    The identifier for the field.

    description

    A description of the data stored in this format field.

    lineType

    The type of the data stored in this format field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  7. def addAlternateAlleleArrayInfoHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing an 'A' array info field.

    Adds a VCF header line describing an 'A' array info field.

    This adds a info field that is an array whose length is equal to the number of alternate alleles for the genotype we are annotating.

    id

    The identifier for the field.

    description

    A description of the data stored in this info field.

    lineType

    The type of the data stored in this info field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  8. def addFilterHeaderLine(id: String, description: String): VariantContextDataset

    Adds a VCF header line describing a variant/genotype filter.

    Adds a VCF header line describing a variant/genotype filter.

    id

    The identifier for the filter.

    description

    A description of the filter.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  9. def addFixedArrayFormatHeaderLine(id: String, count: Integer, lineType: VCFHeaderLineType, description: String): VariantContextDataset

    (Java-specific) Adds a VCF header line describing an array format field, with fixed count.

    (Java-specific) Adds a VCF header line describing an array format field, with fixed count.

    id

    The identifier for the field.

    count

    The number of elements in the array.

    lineType

    The type of the data stored in this format field.

    description

    A description of the data stored in this format field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  10. def addFixedArrayFormatHeaderLine(id: String, count: Int, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    (Scala-specific) Adds a VCF header line describing an array format field, with fixed count.

    (Scala-specific) Adds a VCF header line describing an array format field, with fixed count.

    id

    The identifier for the field.

    count

    The number of elements in the array.

    description

    A description of the data stored in this format field.

    lineType

    The type of the data stored in this format field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  11. def addFixedArrayInfoHeaderLine(id: String, count: Integer, lineType: VCFHeaderLineType, description: String): VariantContextDataset

    (Java-specific) Adds a VCF header line describing an array info field, with fixed count.

    (Java-specific) Adds a VCF header line describing an array info field, with fixed count.

    id

    The identifier for the field.

    count

    The number of elements in the array.

    lineType

    The type of the data stored in this info field.

    description

    A description of the data stored in this info field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  12. def addFixedArrayInfoHeaderLine(id: String, count: Int, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    (Scala-specific) Adds a VCF header line describing an array info field, with fixed count.

    (Scala-specific) Adds a VCF header line describing an array info field, with fixed count.

    id

    The identifier for the field.

    count

    The number of elements in the array.

    description

    A description of the data stored in this info field.

    lineType

    The type of the data stored in this info field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  13. def addGenotypeArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing an 'G' array format field.

    Adds a VCF header line describing an 'G' array format field.

    This adds a format field that is an array whose length is equal to the number of genotypes for the genotype we are annotating.

    id

    The identifier for the field.

    description

    A description of the data stored in this format field.

    lineType

    The type of the data stored in this format field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  14. def addHeaderLine(headerLineToAdd: VCFHeaderLine): VariantContextDataset

    Appends a new header line to the existing lines.

    Appends a new header line to the existing lines.

    headerLineToAdd

    A header line to add.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  15. def addHeaderLines(headerLinesToAdd: Seq[VCFHeaderLine]): VariantContextDataset

    Appends new header lines to the existing lines.

    Appends new header lines to the existing lines.

    headerLinesToAdd

    Zero or more header lines to add.

    returns

    A new genomic dataset with the new header lines added.

    Definition Classes
    VCFSupportingGenomicDataset
  16. def addReference(referenceToAdd: SequenceRecord): VariantContextDataset

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

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

    referenceToAdd

    The reference sequence to add.

    returns

    Returns a new GenomicDataset with this reference sequence appended.

    Definition Classes
    GenomicDataset
  17. def addReferences(referencesToAdd: SequenceDictionary): VariantContextDataset

    Appends reference sequence metadata to the current genomic dataset.

    Appends reference sequence metadata to the current genomic dataset.

    referencesToAdd

    The new reference sequences to append.

    returns

    Returns a new GenomicDataset with the reference sequences appended.

    Definition Classes
    GenomicDataset
  18. def addSample(sampleToAdd: Sample): VariantContextDataset

    Adds a single sample to the current genomic dataset.

    Adds a single sample to the current genomic dataset.

    sampleToAdd

    A single sample to add.

    returns

    Returns a new genomic dataset with this sample added.

    Definition Classes
    MultisampleGenomicDataset
  19. def addSamples(samplesToAdd: Iterable[Sample]): VariantContextDataset

    Adds samples to the current genomic dataset.

    Adds samples to the current genomic dataset.

    samplesToAdd

    Zero or more samples to add.

    returns

    Returns a new genomic dataset with samples added.

    Definition Classes
    MultisampleGenomicDataset
  20. def addScalarFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing a scalar format field.

    Adds a VCF header line describing a scalar format field.

    id

    The identifier for the field.

    description

    A description of the data stored in this format field.

    lineType

    The type of the data stored in this format field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  21. def addScalarInfoHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing a scalar info field.

    Adds a VCF header line describing a scalar info field.

    id

    The identifier for the field.

    description

    A description of the data stored in this info field.

    lineType

    The type of the data stored in this info field.

    returns

    A new genomic dataset with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  22. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  23. def broadcast()(implicit tTag: ClassTag[VariantContext]): GenomicBroadcast[VariantContext, VariantContext, VariantContextDataset]
    Definition Classes
    GenomicDataset
  24. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], txTag: ClassTag[(VariantContext, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Y)]): GenericGenomicDataset[(VariantContext, X), (VariantContext, 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

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

  26. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(VariantContext, X), (VariantContext, 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
  27. def broadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(VariantContext, X), (VariantContext, 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
  28. def broadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Y, VariantContext)]): GenericGenomicDataset[(X, VariantContext), (Y, VariantContext)]

    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

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

    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

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

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

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

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

  34. def buildTree(rdd: RDD[(ReferenceRegion, VariantContext)])(implicit tTag: ClassTag[VariantContext]): IntervalArray[ReferenceRegion, VariantContext]
    Attributes
    protected
    Definition Classes
    VariantContextDatasetGenomicDataset
  35. def cache(): VariantContextDataset

    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

    Cached GenomicDataset.

    Definition Classes
    DatasetBoundGenomicDatasetGenomicDataset
  36. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  37. def convertToVcf(stringency: ValidationStringency): (VCFHeader, RDD[VariantContext])

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts.

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts.

    stringency

    Validation stringency to use.

    returns

    Return a tuple of VCFHeader and an RDD of HTSJDK VariantContexts.

    Definition Classes
    VariantContextDataset
  38. val dataset: Dataset[VariantContext]

    These data as a Spark SQL Dataset.

    These data as a Spark SQL Dataset.

    Definition Classes
    DatasetBoundVariantContextDatasetGenomicDataset
  39. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  40. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  41. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  42. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  43. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  44. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  45. def error(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  46. def filterByOverlappingRegion(query: ReferenceRegion): VariantContextDataset

    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
  47. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): VariantContextDataset

    (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
    DatasetBoundGenomicDatasetGenomicDataset
  48. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): VariantContextDataset

    (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
  49. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  50. def flattenRddByRegions(): RDD[(ReferenceRegion, VariantContext)]
    Attributes
    protected
    Definition Classes
    GenomicDataset
  51. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otoxTag: ClassTag[(Option[VariantContext], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Option[Y])]): GenericGenomicDataset[(Option[VariantContext], Option[X]), (Option[VariantContext], 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
  52. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otoxTag: ClassTag[(Option[VariantContext], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Option[Y])]): GenericGenomicDataset[(Option[VariantContext], Option[X]), (Option[VariantContext], 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
  53. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[VariantContext], Option[X]), (Option[VariantContext], 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
  54. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[VariantContext], Option[X]), (Option[VariantContext], 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
  55. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  56. def getReferenceRegions(elem: VariantContext): Seq[ReferenceRegion]

    elem

    The variant context to get a reference region for.

    returns

    Returns a seq containing the position key from the variant context.

    Attributes
    protected
    Definition Classes
    VariantContextDatasetGenomicDataset
  57. val headerLines: Seq[VCFHeaderLine]
    Definition Classes
    DatasetBoundVariantContextDatasetVariantContextDataset → VCFSupportingGenomicDataset
  58. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  59. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  60. def info(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  61. def isDebugEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  62. def isErrorEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  63. def isInfoEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  64. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  65. val isPartitioned: Boolean
  66. def isSorted: Boolean
    Definition Classes
    GenomicDataset
  67. def isTraceEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  68. def isWarnEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  69. lazy val jrdd: JavaRDD[VariantContext]

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicDataset
  70. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], toxTag: ClassTag[(VariantContext, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Option[Y])]): GenericGenomicDataset[(VariantContext, Option[X]), (VariantContext, 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
  71. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], toxTag: ClassTag[(VariantContext, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Option[Y])]): GenericGenomicDataset[(VariantContext, Option[X]), (VariantContext, 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
  72. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(VariantContext, Option[X]), (VariantContext, 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
  73. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(VariantContext, Option[X]), (VariantContext, 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
  74. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], toxTag: ClassTag[(VariantContext, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Seq[Y])]): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  75. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], toxTag: ClassTag[(VariantContext, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Seq[Y])]): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  76. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  77. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  78. def logger: Logger
    Attributes
    protected
    Definition Classes
    Logging
  79. def loggerName: String
    Attributes
    protected
    Definition Classes
    Logging
  80. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  81. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  82. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  83. val optLookbackPartitions: Option[Int]
  84. val optPartitionBinSize: Option[Int]
  85. lazy val optPartitionMap: None.type
    Attributes
    protected
    Definition Classes
    DatasetBoundVariantContextDatasetGenomicDataset
  86. def persist(sl: StorageLevel): VariantContextDataset

    Persists underlying RDD in memory or disk.

    Persists underlying RDD in memory or disk.

    sl

    new StorageLevel

    returns

    Persisted GenomicDataset.

    Definition Classes
    DatasetBoundGenomicDatasetGenomicDataset
  87. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[VariantContext, VariantContext, VariantContextDataset, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[VariantContextDataset, 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
  88. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[VariantContext, VariantContext, VariantContextDataset, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[VariantContextDataset, 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
  89. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[VariantContext, VariantContext, VariantContextDataset, 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[VariantContext, VariantContext, VariantContextDataset, W], xFormatter: OutFormatter[X], convFn: (VariantContextDataset, RDD[X]) ⇒ Z, tManifest: ClassTag[VariantContext], 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
  90. val productFn: (VariantContext) ⇒ VariantContext
    Attributes
    protected
    Definition Classes
    VariantContextDatasetGenomicDataset
  91. lazy val rdd: RDD[VariantContext]

    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    DatasetBoundVariantContextDatasetGenomicDataset
  92. val references: 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
    DatasetBoundVariantContextDatasetGenomicDataset
  93. def replaceHeaderLines(newHeaderLines: Seq[VCFHeaderLine]): VariantContextDataset

    Replaces the header lines attached to this genomic dataset.

    Replaces the header lines attached to this genomic dataset.

    newHeaderLines

    The new header lines to attach to this genomic dataset.

    returns

    A new genomic dataset with the header lines replaced.

    Definition Classes
    DatasetBoundVariantContextDatasetVariantContextDataset → VCFSupportingGenomicDataset
  94. def replaceRdd(newRdd: RDD[VariantContext], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): VariantContextDataset

    newRdd

    The RDD of VariantContexts to replace the underlying RDD.

    returns

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

    Attributes
    protected
    Definition Classes
    VariantContextDatasetGenomicDataset
  95. def replaceReferences(newReferences: SequenceDictionary): VariantContextDataset

    Replaces the reference sequence dictionary attached to a GenomicDataset.

    Replaces the reference sequence dictionary attached to a GenomicDataset.

    newReferences

    The new reference sequence dictionary to attach.

    returns

    Returns a new GenomicDataset with the reference sequences replaced.

    Definition Classes
    DatasetBoundVariantContextDatasetGenomicDataset
  96. def replaceSamples(newSamples: Iterable[Sample]): VariantContextDataset

    Replaces the sample metadata attached to the genomic dataset.

    Replaces the sample metadata attached to the genomic dataset.

    newSamples

    The new sample metadata to attach.

    returns

    A GenomicDataset with new sample metadata.

    Definition Classes
    DatasetBoundVariantContextDatasetMultisampleGenomicDataset
  97. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otxTag: ClassTag[(Option[VariantContext], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Y)]): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], 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

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

  99. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], 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
  100. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], 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
  101. def rightOuterBroadcastRegionJoinAgainst[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](broadcast: GenomicBroadcast[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], oyuTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Y], VariantContext)]): GenericGenomicDataset[(Option[X], VariantContext), (Option[Y], VariantContext)]

    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

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

    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

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

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

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

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

  107. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otxTag: ClassTag[(Option[VariantContext], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Y)]): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], 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
  108. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otxTag: ClassTag[(Option[VariantContext], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Y)]): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], 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
  109. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], 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
  110. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], 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
  111. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otixTag: ClassTag[(Option[VariantContext], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Seq[Y])]): GenericGenomicDataset[(Option[VariantContext], Iterable[X]), (Option[VariantContext], 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
  112. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otixTag: ClassTag[(Option[VariantContext], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Seq[Y])]): GenericGenomicDataset[(Option[VariantContext], Iterable[X]), (Option[VariantContext], 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
  113. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[VariantContext], Iterable[X]), (Option[VariantContext], 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
  114. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[VariantContext], Iterable[X]), (Option[VariantContext], 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
  115. val samples: Seq[Sample]

    The samples who have data contained in this GenomicDataset.

    The samples who have data contained in this GenomicDataset.

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

    Saves a genomic dataset to Parquet.

    Saves a genomic dataset to Parquet.

    pathName

    The path to save the file to.

    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
    VariantContextDatasetGenomicDataset
  117. 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
  118. 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
  119. def saveAsVcf(filePath: String, asSingleFile: Boolean, deferMerging: Boolean, disableFastConcat: Boolean, stringency: ValidationStringency): Unit

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    File paths that end in .gz or .bgz will be saved as block GZIP compressed VCFs.

    filePath

    The file path to save to.

    asSingleFile

    If true, saves the output as a single file by merging the sharded output after completing the write to HDFS. If false, the output of this call will be written as shards, where each shard has a valid VCF header.

    deferMerging

    If true and asSingleFile is true, we will save the output shards as a headerless file, but we will not merge the shards.

    disableFastConcat

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

    stringency

    The validation stringency to use when writing the VCF.

    Definition Classes
    VariantContextDataset
  120. def saveAsVcf(filePath: String): Unit

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts and saves as a single file to disk as VCF.

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts and saves as a single file to disk as VCF. Uses lenient validation stringency.

    File paths that end in .gz or .bgz will be saved as block GZIP compressed VCFs.

    filePath

    The file path to save to.

    Definition Classes
    VariantContextDataset
  121. def saveAsVcf(args: ADAMSaveAnyArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): Unit

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    File paths that end in .gz or .bgz will be saved as block GZIP compressed VCFs.

    args

    Arguments defining where to save the file.

    stringency

    The validation stringency to use when writing the VCF. Defaults to LENIENT.

    Definition Classes
    VariantContextDataset
  122. 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
  123. def saveMetadata(filePath: String): Unit

    Writes any necessary metadata to disk.

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

    Attributes
    protected
    Definition Classes
    VariantContextDatasetGenomicDataset
  124. def saveReferences(pathName: String): Unit

    Save the reference sequence dictionary to disk.

    Save the reference sequence dictionary to disk.

    pathName

    The path to save the reference sequence dictionary to.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  125. def saveSamples(pathName: String): Unit

    Save the samples to disk.

    Save the samples to disk.

    pathName

    The path to save samples to.

    Attributes
    protected
    Definition Classes
    MultisampleGenomicDataset
  126. def saveVcfHeaders(filePath: String): Unit
    Definition Classes
    VariantContextDataset
  127. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], txTag: ClassTag[(VariantContext, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Y)]): GenericGenomicDataset[(VariantContext, X), (VariantContext, 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
  128. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], txTag: ClassTag[(VariantContext, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Y)]): GenericGenomicDataset[(VariantContext, X), (VariantContext, 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
  129. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(VariantContext, X), (VariantContext, 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
  130. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(VariantContext, X), (VariantContext, 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
  131. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], tixTag: ClassTag[(VariantContext, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Seq[Y])]): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  132. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], tixTag: ClassTag[(VariantContext, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Seq[Y])]): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  133. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  134. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(VariantContext, Iterable[X]), (VariantContext, 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
  135. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[VariantContext]): VariantContextDataset

    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

  136. def sort(): VariantContextDataset

    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

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

    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

  138. def sortLexicographically(): VariantContextDataset

    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

  139. lazy val spark: SparkSession
    Definition Classes
    GenomicDataset
    Annotations
    @transient()
  140. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  141. def toDF(): DataFrame

    returns

    These data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  142. def toGenotypes(): GenotypeDataset

    returns

    Returns a GenotypeDataset containing the Genotypes in this genomic dataset.

    Definition Classes
    VariantContextDataset
  143. def toString(): String
    Definition Classes
    MultisampleGenomicDatasetGenomicDataset → AnyRef → Any
  144. def toVariants(): VariantDataset

    returns

    Returns the Variants in this genomic dataset.

    Definition Classes
    VariantContextDataset
  145. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  146. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  147. def trace(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  148. def transform(tFn: Function[JavaRDD[VariantContext], JavaRDD[VariantContext]]): VariantContextDataset

    (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
  149. def transform(tFn: (RDD[VariantContext]) ⇒ RDD[VariantContext]): VariantContextDataset

    (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
  150. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): VariantContextDataset

    (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
  151. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[VariantContext]): VariantContextDataset

    (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
  152. def transformDataset(tFn: Function[Dataset[VariantContext], Dataset[VariantContext]]): VariantContextDataset

    (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
    DatasetBoundVariantContextDatasetVariantContextDatasetGenomicDataset
  153. def transformDataset(tFn: (Dataset[VariantContext]) ⇒ Dataset[VariantContext]): VariantContextDataset

    (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
    DatasetBoundVariantContextDatasetVariantContextDatasetGenomicDataset
  154. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[VariantContext], JavaRDD[X]], convFn: Function2[VariantContextDataset, 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
  155. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[VariantContext]) ⇒ RDD[X])(implicit convFn: (VariantContextDataset, 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
  156. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[VariantContext, VariantContext, VariantContextDataset, 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
  157. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (DataFrame) ⇒ DataFrame)(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (VariantContextDataset, 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
  158. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[VariantContext], Dataset[Y]], convFn: GenomicDatasetConversion[VariantContext, VariantContext, VariantContextDataset, 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
  159. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (Dataset[VariantContext]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (VariantContextDataset, 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
  160. val uTag: scala.reflect.api.JavaUniverse.TypeTag[VariantContext]
    Definition Classes
    VariantContextDatasetGenomicDataset
  161. def union(datasets: VariantContextDataset*): VariantContextDataset

    (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
    VariantContextDatasetGenomicDataset
  162. def union(datasets: List[VariantContextDataset]): VariantContextDataset

    (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
  163. def unpersist(): VariantContextDataset

    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    DatasetBoundGenomicDatasetGenomicDataset
  164. val unproductFn: (VariantContext) ⇒ VariantContext
    Attributes
    protected
    Definition Classes
    VariantContextDatasetGenomicDataset
  165. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  166. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  167. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  168. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  169. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  170. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  171. 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 Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from VariantContextDataset

Inherited from VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextDataset]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped