c

org.bdgenomics.adam.ds.variant

RDDBoundVariantDataset

case class RDDBoundVariantDataset extends VariantDataset with Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, VariantDataset, VCFSupportingGenomicDataset[Variant, Variant, VariantDataset], AvroGenomicDataset[Variant, Variant, VariantDataset], GenomicDataset[Variant, Variant, VariantDataset], Logging, AnyRef, Any
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  1. RDDBoundVariantDataset
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. VariantDataset
  7. VCFSupportingGenomicDataset
  8. AvroGenomicDataset
  9. GenomicDataset
  10. Logging
  11. AnyRef
  12. Any
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Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. def addAllAlleleArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantDataset

    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): VariantDataset

    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): VariantDataset

    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): VariantDataset

    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): VariantDataset

    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): VariantDataset

    (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): VariantDataset

    (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): VariantDataset

    (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): VariantDataset

    (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): VariantDataset

    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): VariantDataset

    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]): VariantDataset

    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): VariantDataset

    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): VariantDataset

    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 addScalarFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantDataset

    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
  19. def addScalarInfoHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantDataset

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

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

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

    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

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

    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

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

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

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

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

  32. def buildTree(rdd: RDD[(ReferenceRegion, Variant)])(implicit tTag: ClassTag[Variant]): IntervalArray[ReferenceRegion, Variant]
    Attributes
    protected
    Definition Classes
    VariantDatasetGenomicDataset
  33. def cache(): VariantDataset

    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

    Cached GenomicDataset.

    Definition Classes
    GenomicDataset
  34. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  35. lazy val dataset: Dataset[Variant]

    A SQL Dataset of reads.

    A SQL Dataset of reads.

    Definition Classes
    RDDBoundVariantDatasetGenomicDataset
  36. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  37. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  38. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  39. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  40. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  41. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  42. def error(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  43. def filterByOverlappingRegion(query: ReferenceRegion): VariantDataset

    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
  44. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): VariantDataset

    (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
  45. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): VariantDataset

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  46. def filterByQuality(minimumQuality: Double): VariantDataset

    Filter this VariantDataset by quality (VCF column 6 "QUAL").

    Filter this VariantDataset by quality (VCF column 6 "QUAL"). Variants split for multi-allelic sites will also be filtered out.

    minimumQuality

    Minimum quality to filter by, inclusive.

    returns

    VariantDataset filtered by quality.

    Definition Classes
    VariantDataset
  47. def filterByReadDepth(minimumReadDepth: Int): VariantDataset

    Filter this VariantDataset by total read depth (VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (filterByReferenceReadDepth) and the alternate allele (this method)).

    Filter this VariantDataset by total read depth (VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (filterByReferenceReadDepth) and the alternate allele (this method)).

    minimumReadDepth

    Minimum total read depth to filter by, inclusive.

    returns

    VariantDataset filtered by total read depth.

    Definition Classes
    VariantDataset
  48. def filterByReferenceReadDepth(minimumReferenceReadDepth: Int): VariantDataset

    Filter this VariantDataset by reference total read depth (VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the alternate allele (filterByReadDepth) and the reference allele (this method)).

    Filter this VariantDataset by reference total read depth (VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the alternate allele (filterByReadDepth) and the reference allele (this method)).

    minimumReferenceReadDepth

    Minimum reference total read depth to filter by, inclusive.

    returns

    VariantDataset filtered by reference total read depth.

    Definition Classes
    VariantDataset
  49. def filterIndels(): VariantDataset

    Filter insertions and deletions (indels) from this VariantDataset.

    Filter insertions and deletions (indels) from this VariantDataset.

    returns

    VariantDataset filtered to remove insertions and deletions (indels).

    Definition Classes
    VariantDataset
  50. def filterMultipleNucleotideVariants(): VariantDataset

    Filter multiple nucleotide variants (MNPs) from this VariantDataset.

    Filter multiple nucleotide variants (MNPs) from this VariantDataset.

    returns

    VariantDataset filtered to remove multiple nucleotide variants (MNPs).

    Definition Classes
    VariantDataset
  51. def filterSingleNucleotideVariants(): VariantDataset

    Filter single nucleotide variants (SNPs) from this VariantDataset.

    Filter single nucleotide variants (SNPs) from this VariantDataset.

    returns

    VariantDataset filtered to remove single nucleotide variants (SNPs).

    Definition Classes
    VariantDataset
  52. def filterToFiltersPassed(): VariantDataset

    Filter this VariantDataset to filters passed (VCF column 7 "FILTER" value PASS).

    Filter this VariantDataset to filters passed (VCF column 7 "FILTER" value PASS).

    returns

    VariantDataset filtered to filters passed.

    Definition Classes
    VariantDataset
  53. def filterToIndels(): VariantDataset

    Filter this VariantDataset to include only insertions and deletions (indels).

    Filter this VariantDataset to include only insertions and deletions (indels).

    returns

    VariantDataset filtered to include only insertions and deletions (indels).

    Definition Classes
    VariantDataset
  54. def filterToMultipleNucleotideVariants(): VariantDataset

    Filter this VariantDataset to include only multiple nucleotide variants (MNPs).

    Filter this VariantDataset to include only multiple nucleotide variants (MNPs).

    returns

    VariantDataset filtered to include only multiple nucleotide variants (MNPs).

    Definition Classes
    VariantDataset
  55. def filterToReferenceName(referenceName: String): VariantDataset

    Filter this VariantDataset by reference name to those that match the specified reference name.

    Filter this VariantDataset by reference name to those that match the specified reference name.

    referenceName

    Reference name to filter by.

    returns

    VariantDataset filtered by the specified reference name.

    Definition Classes
    VariantDataset
  56. def filterToSingleNucleotideVariants(): VariantDataset

    Filter this VariantDataset to include only single nucleotide variants (SNPs).

    Filter this VariantDataset to include only single nucleotide variants (SNPs).

    returns

    VariantDataset filtered to include only single nucleotide variants (SNPs).

    Definition Classes
    VariantDataset
  57. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  58. def flattenRddByRegions(): RDD[(ReferenceRegion, Variant)]
    Attributes
    protected
    Definition Classes
    GenomicDataset
  59. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Variant], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Variant], Option[Y])]): GenericGenomicDataset[(Option[Variant], Option[X]), (Option[Variant], 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
  60. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Variant], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Variant], Option[Y])]): GenericGenomicDataset[(Option[Variant], Option[X]), (Option[Variant], 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
  61. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Variant], Option[X]), (Option[Variant], 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
  62. def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Variant], Option[X]), (Option[Variant], 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
  63. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  64. def getReferenceRegions(elem: Variant): Seq[ReferenceRegion]

    elem

    The variant to get a reference region for.

    returns

    Returns the singular region this variant covers.

    Attributes
    protected
    Definition Classes
    VariantDatasetGenomicDataset
  65. val headerLines: Seq[VCFHeaderLine]
    Definition Classes
    RDDBoundVariantDataset → VCFSupportingGenomicDataset
  66. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  67. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  68. def info(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  69. def isDebugEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  70. def isErrorEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  71. def isInfoEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  72. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  73. def isSorted: Boolean
    Definition Classes
    GenomicDataset
  74. def isTraceEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  75. def isWarnEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  76. lazy val jrdd: JavaRDD[Variant]

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicDataset
  77. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], toxTag: ClassTag[(Variant, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Option[Y])]): GenericGenomicDataset[(Variant, Option[X]), (Variant, 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
  78. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], toxTag: ClassTag[(Variant, Option[X])], uoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Option[Y])]): GenericGenomicDataset[(Variant, Option[X]), (Variant, 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
  79. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Variant, Option[X]), (Variant, 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
  80. def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Variant, Option[X]), (Variant, 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
  81. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], toxTag: ClassTag[(Variant, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Seq[Y])]): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  82. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], toxTag: ClassTag[(Variant, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Seq[Y])]): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  83. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  84. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  85. def logger: Logger
    Attributes
    protected
    Definition Classes
    Logging
  86. def loggerName: String
    Attributes
    protected
    Definition Classes
    Logging
  87. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  88. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  89. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  90. val optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]
    Definition Classes
    RDDBoundVariantDatasetGenomicDataset
  91. def persist(sl: StorageLevel): VariantDataset

    Persists underlying RDD in memory or disk.

    Persists underlying RDD in memory or disk.

    sl

    new StorageLevel

    returns

    Persisted GenomicDataset.

    Definition Classes
    GenomicDataset
  92. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Variant, Variant, VariantDataset, W]](cmd: List[String], files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[VariantDataset, 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
  93. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Variant, Variant, VariantDataset, W]](cmd: Seq[Any], files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[W], xFormatter: OutFormatter[X], convFn: Function2[VariantDataset, 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
  94. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[Variant, Variant, VariantDataset, 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[Variant, Variant, VariantDataset, W], xFormatter: OutFormatter[X], convFn: (VariantDataset, RDD[X]) ⇒ Z, tManifest: ClassTag[Variant], 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
  95. val productFn: (Variant) ⇒ Variant
    Attributes
    protected
    Definition Classes
    VariantDatasetGenomicDataset
  96. val rdd: RDD[Variant]

    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    RDDBoundVariantDatasetGenomicDataset
  97. 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
    RDDBoundVariantDatasetGenomicDataset
  98. def replaceHeaderLines(newHeaderLines: Seq[VCFHeaderLine]): VariantDataset

    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
    RDDBoundVariantDataset → VCFSupportingGenomicDataset
  99. def replaceRdd(newRdd: RDD[Variant], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): VariantDataset

    newRdd

    An RDD to replace the underlying RDD with.

    returns

    Returns a new VariantDataset with the underlying RDD replaced.

    Attributes
    protected
    Definition Classes
    VariantDatasetGenomicDataset
  100. def replaceReferences(newReferences: SequenceDictionary): VariantDataset

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

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

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

    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

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

    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

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

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

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

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

  111. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], otxTag: ClassTag[(Option[Variant], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Variant], Y)]): GenericGenomicDataset[(Option[Variant], X), (Option[Variant], 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
  112. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], otxTag: ClassTag[(Option[Variant], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Variant], Y)]): GenericGenomicDataset[(Option[Variant], X), (Option[Variant], 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
  113. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Variant], X), (Option[Variant], 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
  114. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Variant], X), (Option[Variant], 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
  115. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], otixTag: ClassTag[(Option[Variant], Iterable[X])], otsyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Variant], Seq[Y])]): GenericGenomicDataset[(Option[Variant], Iterable[X]), (Option[Variant], 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
  116. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], otixTag: ClassTag[(Option[Variant], Iterable[X])], ousyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[Variant], Seq[Y])]): GenericGenomicDataset[(Option[Variant], Iterable[X]), (Option[Variant], 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
  117. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[Variant], Iterable[X]), (Option[Variant], 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
  118. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Variant], Iterable[X]), (Option[Variant], 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
  119. def saveAsParquet(pathName: String): Unit

    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

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

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

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

    pathName

    Path to save the file at.

    blockSize

    The size in bytes of blocks to write.

    pageSize

    The size in bytes of pages to write.

    compressionCodec

    The compression codec to apply to pages.

    disableDictionaryEncoding

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

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

    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressionCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

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

    Definition Classes
    AvroGenomicDatasetGenomicDataset
  122. 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
  123. 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
  124. 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
  125. def saveMetadata(filePath: String): Unit

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

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

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

    Attributes
    protected
    Definition Classes
    VariantDatasetAvroGenomicDatasetGenomicDataset
  126. def savePartitionMap(pathName: String): Unit

    Save the partition map to disk.

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

    pathName

    The filepath where we will save the partition map.

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

    Saves a genomic dataset of Avro data to Parquet.

    Saves a genomic dataset of Avro data to Parquet.

    pathName

    The path to save the file to.

    blockSize

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

    pageSize

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

    compressionCodec

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

    disableDictionaryEncoding

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

    optSchema

    The optional schema to set. Defaults to None.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  128. def saveRddAsParquet(args: SaveArgs): Unit
    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  129. 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
  130. def saveVcfHeaders(filePath: String): Unit

    Save the VCF headers to disk.

    Save the VCF headers to disk.

    filePath

    The filepath to the file where we will save the VCF headers.

    Definition Classes
    VariantDataset
  131. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], txTag: ClassTag[(Variant, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Y)]): GenericGenomicDataset[(Variant, X), (Variant, 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
  132. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], txTag: ClassTag[(Variant, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Y)]): GenericGenomicDataset[(Variant, X), (Variant, 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
  133. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Variant, X), (Variant, 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
  134. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Variant, X), (Variant, 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
  135. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], tixTag: ClassTag[(Variant, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Seq[Y])]): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  136. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Long)(implicit tTag: ClassTag[Variant], xTag: ClassTag[X], tixTag: ClassTag[(Variant, Iterable[X])], uiyTag: scala.reflect.api.JavaUniverse.TypeTag[(Variant, Seq[Y])]): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  137. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  138. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Variant, Iterable[X]), (Variant, 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
  139. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Variant]): VariantDataset

    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

  140. def sort(): VariantDataset

    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

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

    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

  142. def sortLexicographically(): VariantDataset

    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

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

    returns

    These data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  146. def toString(): String
    Definition Classes
    GenomicDataset → AnyRef → Any
  147. def toVariantContexts(): VariantContextDataset

    returns

    Returns this VariantDataset as a VariantContextDataset.

    Definition Classes
    VariantDataset
  148. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  149. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  150. def trace(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  151. def transform(tFn: Function[JavaRDD[Variant], JavaRDD[Variant]]): VariantDataset

    (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
  152. def transform(tFn: (RDD[Variant]) ⇒ RDD[Variant]): VariantDataset

    (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
  153. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): VariantDataset

    (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
  154. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[Variant]): VariantDataset

    (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
  155. def transformDataset(tFn: Function[Dataset[Variant], Dataset[Variant]]): VariantDataset

    (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
    VariantDatasetGenomicDataset
  156. def transformDataset(tFn: (Dataset[Variant]) ⇒ Dataset[Variant]): VariantDataset

    (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
    VariantDatasetGenomicDataset
  157. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Variant], JavaRDD[X]], convFn: Function2[VariantDataset, 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
  158. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[Variant]) ⇒ RDD[X])(implicit convFn: (VariantDataset, 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
  159. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[Variant, Variant, VariantDataset, 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
  160. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (DataFrame) ⇒ DataFrame)(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (VariantDataset, 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
  161. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[Variant], Dataset[Y]], convFn: GenomicDatasetConversion[Variant, Variant, VariantDataset, 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
  162. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (Dataset[Variant]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (VariantDataset, 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
  163. val uTag: scala.reflect.api.JavaUniverse.TypeTag[Variant]
    Definition Classes
    VariantDatasetGenomicDataset
  164. def union(rdds: VariantDataset*): VariantDataset

    (Scala-specific) Unions together multiple genomic datasets.

    (Scala-specific) Unions together multiple genomic datasets.

    Definition Classes
    VariantDatasetGenomicDataset
  165. def union(datasets: List[VariantDataset]): VariantDataset

    (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
  166. def unpersist(): VariantDataset

    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  167. val unproductFn: (Variant) ⇒ Variant
    Attributes
    protected
    Definition Classes
    VariantDatasetGenomicDataset
  168. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  169. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  170. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  171. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  172. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  173. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  174. def writePartitionedParquetFlag(pathName: String, partitionSize: Int): Unit

    Save partition size into the partitioned Parquet flag file.

    Save partition size into the partitioned Parquet flag file.

    pathName

    Path to save the file at.

    partitionSize

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

    Definition Classes
    AvroGenomicDatasetGenomicDataset
  175. 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 VariantDataset

Inherited from VCFSupportingGenomicDataset[Variant, Variant, VariantDataset]

Inherited from AvroGenomicDataset[Variant, Variant, VariantDataset]

Inherited from GenomicDataset[Variant, Variant, VariantDataset]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped