Class

org.bdgenomics.adam.rdd.variant

RDDBoundGenotypeDataset

Related Doc: package variant

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case class RDDBoundGenotypeDataset extends GenotypeDataset with Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, GenotypeDataset, VCFSupportingGenomicDataset[Genotype, Genotype, GenotypeDataset], MultisampleAvroGenomicDataset[Genotype, Genotype, GenotypeDataset], MultisampleGenomicDataset[Genotype, Genotype, GenotypeDataset], AvroGenomicDataset[Genotype, Genotype, GenotypeDataset], GenomicDataset[Genotype, Genotype, GenotypeDataset], Logging, AnyRef, Any
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  1. RDDBoundGenotypeDataset
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. GenotypeDataset
  7. VCFSupportingGenomicDataset
  8. MultisampleAvroGenomicDataset
  9. MultisampleGenomicDataset
  10. AvroGenomicDataset
  11. GenomicDataset
  12. Logging
  13. AnyRef
  14. Any
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Value Members

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

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

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

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    Definition Classes
    AnyRef → Any
  4. def addAllAlleleArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): GenotypeDataset

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    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): GenotypeDataset

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    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): GenotypeDataset

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    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): GenotypeDataset

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    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): GenotypeDataset

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    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): GenotypeDataset

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    (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): GenotypeDataset

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    (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): GenotypeDataset

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    (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): GenotypeDataset

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    (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): GenotypeDataset

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    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): GenotypeDataset

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    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]): GenotypeDataset

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    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 addSample(sampleToAdd: Sample): GenotypeDataset

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    Adds a single sample to the current genomic dataset.

    Adds a single sample to the current genomic dataset.

    sampleToAdd

    A single sample to add.

    returns

    Returns a new genomic dataset with this sample added.

    Definition Classes
    MultisampleGenomicDataset
  17. def addSamples(samplesToAdd: Iterable[Sample]): GenotypeDataset

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    Adds samples to the current genomic dataset.

    Adds samples to the current genomic dataset.

    samplesToAdd

    Zero or more samples to add.

    returns

    Returns a new genomic dataset with samples added.

    Definition Classes
    MultisampleGenomicDataset
  18. def addScalarFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): GenotypeDataset

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    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): GenotypeDataset

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    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. def addSequence(sequenceToAdd: SequenceRecord): GenotypeDataset

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

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

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicDataset with this sequence appended.

    Definition Classes
    GenomicDataset
  21. def addSequences(sequencesToAdd: SequenceDictionary): GenotypeDataset

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    Appends sequence metadata to the current genomic dataset.

    Appends sequence metadata to the current genomic dataset.

    sequencesToAdd

    The new sequences to append.

    returns

    Returns a new GenomicDataset with the sequences appended.

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

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    Definition Classes
    Any
  23. def broadcast()(implicit tTag: ClassTag[Genotype]): GenomicBroadcast[Genotype, Genotype, GenotypeDataset]

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoin

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

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoinAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

    Permalink

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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    Attributes
    protected
    Definition Classes
    GenotypeDatasetGenomicDataset
  35. def cache(): GenotypeDataset

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    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

    Cached GenomicDataset.

    Definition Classes
    GenomicDataset
  36. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. def copyVariantEndToAttribute(): GenotypeDataset

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    Copy variant end to a variant attribute (VCF INFO field "END").

    Copy variant end to a variant attribute (VCF INFO field "END").

    returns

    GenotypeDataset with variant end copied to a variant attribute.

    Definition Classes
    GenotypeDataset
  38. lazy val dataset: Dataset[Genotype]

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    A SQL Dataset of genotypes.

    A SQL Dataset of genotypes.

    Definition Classes
    RDDBoundGenotypeDatasetGenomicDataset
  39. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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

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    Attributes
    protected
    Definition Classes
    Logging
  41. def debug(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  42. final def eq(arg0: AnyRef): Boolean

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  45. def error(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  46. def filterByAlternateReadDepth(minimumAlternateReadDepth: Int): GenotypeDataset

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    Filter this GenotypeDataset by alternate read depth (VCF FORMAT field "AD").

    Filter this GenotypeDataset by alternate read depth (VCF FORMAT field "AD").

    minimumAlternateReadDepth

    Minimum alternate read depth to filter by, inclusive.

    returns

    GenotypeDataset filtered by alternate read depth.

    Definition Classes
    GenotypeDataset
  47. def filterByOverlappingRegion(query: ReferenceRegion): GenotypeDataset

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

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

    query

    The region to query for.

    returns

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

    Definition Classes
    GenomicDataset
  48. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): GenotypeDataset

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  49. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): GenotypeDataset

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  50. def filterByQuality(minimumQuality: Double): GenotypeDataset

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    Filter this GenotypeDataset by quality (VCF FORMAT field "GQ").

    Filter this GenotypeDataset by quality (VCF FORMAT field "GQ").

    minimumQuality

    Minimum quality to filter by, inclusive.

    returns

    GenotypeDataset filtered by quality.

    Definition Classes
    GenotypeDataset
  51. def filterByReadDepth(minimumReadDepth: Int): GenotypeDataset

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    Filter this GenotypeDataset by read depth (VCF FORMAT field "DP").

    Filter this GenotypeDataset by read depth (VCF FORMAT field "DP").

    minimumReadDepth

    Minimum read depth to filter by, inclusive.

    returns

    GenotypeDataset filtered by read depth.

    Definition Classes
    GenotypeDataset
  52. def filterByReferenceReadDepth(minimumReferenceReadDepth: Int): GenotypeDataset

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    Filter this GenotypeDataset by reference read depth (VCF FORMAT field "AD").

    Filter this GenotypeDataset by reference read depth (VCF FORMAT field "AD").

    minimumReferenceReadDepth

    Minimum reference read depth to filter by, inclusive.

    returns

    GenotypeDataset filtered by reference read depth.

    Definition Classes
    GenotypeDataset
  53. def filterNoCalls(): GenotypeDataset

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    Filter genotypes containing NO_CALL alleles from this GenotypeDataset.

    Filter genotypes containing NO_CALL alleles from this GenotypeDataset.

    returns

    GenotypeDataset filtered to remove genotypes containing NO_CALL alleles.

    Definition Classes
    GenotypeDataset
  54. def filterToFiltersPassed(): GenotypeDataset

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    Filter this GenotypeDataset to genotype filters passed (VCF FORMAT field "FT" value PASS).

    Filter this GenotypeDataset to genotype filters passed (VCF FORMAT field "FT" value PASS).

    returns

    GenotypeDataset filtered to genotype filters passed.

    Definition Classes
    GenotypeDataset
  55. def filterToSample(sampleId: String): GenotypeDataset

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    Filter this GenotypeDataset by sample to those that match the specified sample.

    Filter this GenotypeDataset by sample to those that match the specified sample.

    sampleId

    Sample to filter by. return GenotypeDataset filtered by sample.

    Definition Classes
    GenotypeDataset
  56. def filterToSamples(sampleIds: Seq[String]): GenotypeDataset

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    (Scala-specific) Filter this GenotypeDataset by sample to those that match the specified samples.

    (Scala-specific) Filter this GenotypeDataset by sample to those that match the specified samples.

    sampleIds

    Sequence of samples to filter by. return GenotypeDataset filtered by one or more samples.

    Definition Classes
    GenotypeDataset
  57. def filterToSamples(sampleIds: List[String]): GenotypeDataset

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    (Java-specific) Filter this GenotypeDataset by sample to those that match the specified samples.

    (Java-specific) Filter this GenotypeDataset by sample to those that match the specified samples.

    sampleIds

    List of samples to filter by. return GenotypeDataset filtered by one or more samples.

    Definition Classes
    GenotypeDataset
  58. def finalize(): Unit

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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    elem

    The genotype to get a reference region for.

    returns

    Returns the singular region this genotype covers.

    Attributes
    protected
    Definition Classes
    GenotypeDatasetGenomicDataset
  66. val headerLines: Seq[VCFHeaderLine]

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    Definition Classes
    RDDBoundGenotypeDataset → VCFSupportingGenomicDataset
  67. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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

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    Attributes
    protected
    Definition Classes
    Logging
  69. def info(msg: ⇒ Any): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  70. def isDebugEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  71. def isErrorEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  72. def isInfoEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  73. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  74. def isSorted: Boolean

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    Definition Classes
    GenomicDataset
  75. def isTraceEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  76. def isWarnEnabled: Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  77. lazy val jrdd: JavaRDD[Genotype]

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    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  86. def logger: Logger

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    Attributes
    protected
    Definition Classes
    Logging
  87. def loggerName: String

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    Attributes
    protected
    Definition Classes
    Logging
  88. final def ne(arg0: AnyRef): Boolean

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

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

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

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  92. def persist(sl: StorageLevel): GenotypeDataset

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    Persists underlying RDD in memory or disk.

    Persists underlying RDD in memory or disk.

    sl

    new StorageLevel

    returns

    Persisted GenomicDataset.

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final genomic dataset.

    returns

    Returns a new GenomicDataset of type Y.

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final genomic dataset.

    returns

    Returns a new GenomicDataset of type Y.

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

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

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    optTimeout

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

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  96. val productFn: (Genotype) ⇒ Genotype

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    Attributes
    protected
    Definition Classes
    GenotypeDatasetGenomicDataset
  97. val rdd: RDD[Genotype]

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    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    RDDBoundGenotypeDatasetGenomicDataset
  98. def replaceHeaderLines(newHeaderLines: Seq[VCFHeaderLine]): GenotypeDataset

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    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
    RDDBoundGenotypeDataset → VCFSupportingGenomicDataset
  99. def replaceRdd(newRdd: RDD[Genotype], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): GenotypeDataset

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    newRdd

    An RDD to replace the underlying RDD with.

    returns

    Returns a new GenotypeDataset with the underlying RDD replaced.

    Attributes
    protected
    Definition Classes
    GenotypeDatasetGenomicDataset
  100. def replaceSamples(newSamples: Iterable[Sample]): GenotypeDataset

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    Replaces the sample metadata attached to the genomic dataset.

    Replaces the sample metadata attached to the genomic dataset.

    newSamples

    The new sample metadata to attach.

    returns

    A GenomicDataset with new sample metadata.

    Definition Classes
    RDDBoundGenotypeDatasetMultisampleGenomicDataset
  101. def replaceSequences(newSequences: SequenceDictionary): GenotypeDataset

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    Replaces the sequence dictionary attached to a GenomicDataset.

    Replaces the sequence dictionary attached to a GenomicDataset.

    newSequences

    The new sequence dictionary to attach.

    returns

    Returns a new GenomicDataset with the sequences replaced.

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    broadcast

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

    In a broadcast join, the left 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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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    (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
  115. def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Genotype], X), (Option[Genotype], Y)]

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

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    (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
  119. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[Genotype], Iterable[X]), (Option[Genotype], Seq[Y])]

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    (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
  120. val samples: Seq[Sample]

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    The samples who have data contained in this GenomicDataset.

    The samples who have data contained in this GenomicDataset.

    Definition Classes
    RDDBoundGenotypeDatasetMultisampleGenomicDataset
  121. def saveAsParquet(pathName: String): Unit

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    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

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

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

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

    pathName

    Path to save the file at.

    blockSize

    The size in bytes of blocks to write.

    pageSize

    The size in bytes of pages to write.

    compressionCodec

    The compression codec to apply to pages.

    disableDictionaryEncoding

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

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

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    Saves this genomic dataset to disk as a Parquet file.

    Saves this genomic dataset to disk as a Parquet file.

    pathName

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressionCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

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

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

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    Saves a genomic dataset to Parquet.

    Saves a genomic dataset to Parquet.

    args

    The output format configuration to use when saving the data.

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

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

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

    pathName

    The path to save the partitioned Parquet file to.

    compressionCodec

    Name of the compression codec to use.

    partitionSize

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

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

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    Saves Avro data to a Hadoop file system.

    Saves Avro data to a Hadoop file system.

    This method uses a SparkContext to identify our underlying file system, which we then save to.

    Frustratingly enough, although all records generated by the Avro IDL compiler have a static SCHEMA$ field, this field does not belong to the SpecificRecordBase abstract class, or the SpecificRecord interface. As such, we must force the user to pass in the schema.

    U

    The type of the specific record we are saving.

    pathName

    Path to save records to.

    sc

    SparkContext used for identifying underlying file system.

    schema

    Schema of records we are saving.

    avro

    Seq of records we are saving.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  127. def saveMetadata(filePath: String): Unit

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

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

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

    Attributes
    protected
    Definition Classes
    GenotypeDatasetMultisampleAvroGenomicDatasetAvroGenomicDatasetGenomicDataset
  128. def savePartitionMap(pathName: String): Unit

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    Save the partition map to disk.

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

    pathName

    The filepath where we will save the partition map.

    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  129. 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

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    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
  130. def saveRddAsParquet(args: SaveArgs): Unit

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    Attributes
    protected
    Definition Classes
    AvroGenomicDataset
  131. def saveSamples(pathName: String): Unit

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    Save the samples to disk.

    Save the samples to disk.

    pathName

    The path to save samples to.

    Attributes
    protected
    Definition Classes
    MultisampleGenomicDataset
  132. def saveSequences(pathName: String): Unit

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    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    pathName

    The path to save the sequence dictionary to.

    Attributes
    protected
    Definition Classes
    GenomicDataset
  133. def saveVcfHeaders(filePath: String): Unit

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    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
    GenotypeDataset
  134. val sequences: SequenceDictionary

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

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    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
  137. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Genotype, X), (Genotype, Y)]

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    (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
  138. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Genotype, X), (Genotype, Y)]

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    returns

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

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

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    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
  141. def shuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Genotype, Iterable[X]), (Genotype, Seq[Y])]

    Permalink

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

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

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

    genomicDataset

    The right genomic dataset in the join.

    flankSize

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

    returns

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

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

    Permalink

    (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
  143. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Genotype]): GenotypeDataset

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

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

    partitions

    The number of partitions for the new genomic dataset.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sortLexicographically

  144. def sort(): GenotypeDataset

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

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

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sortLexicographically

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

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

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

    partitions

    The number of partitions for the new genomic dataset.

    storePartitionMap

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

    storageLevel

    The level at which to persist the resulting genomic dataset.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sort

  146. def sortLexicographically(): GenotypeDataset

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

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

    returns

    Returns a new genomic dataset containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sort

  147. lazy val spark: SparkSession

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

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    Definition Classes
    AnyRef
  149. def toDF(): DataFrame

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    returns

    These data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  150. def toString(): String

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    Definition Classes
    MultisampleGenomicDatasetGenomicDataset → AnyRef → Any
  151. def toVariantContexts(): VariantContextDataset

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    returns

    Returns this GenotypeDataset squared off as a VariantContextDataset.

    Definition Classes
    GenotypeDataset
  152. def toVariants(dedupe: Boolean): VariantDataset

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    Extracts the variants contained in this genomic dataset of genotypes.

    Extracts the variants contained in this genomic dataset of genotypes.

    Does not perform any filtering looking at whether the variant was called or not.

    dedupe

    If true, drops variants described in more than one genotype record.

    returns

    Returns the variants described by this GenotypeDataset.

    Definition Classes
    GenotypeDataset
  153. def toVariants(): VariantDataset

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    Extracts the variants contained in this genomic dataset of genotypes.

    Extracts the variants contained in this genomic dataset of genotypes.

    Does not perform any filtering looking at whether the variant was called or not. Does not dedupe the variants.

    returns

    Returns the variants described by this GenotypeDataset.

    Definition Classes
    GenotypeDataset
  154. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  157. def transform(tFn: Function[JavaRDD[Genotype], JavaRDD[Genotype]]): GenotypeDataset

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  158. def transform(tFn: (RDD[Genotype]) ⇒ RDD[Genotype]): GenotypeDataset

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  159. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): GenotypeDataset

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

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

    tFn

    A function that transforms the underlying DataFrame as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  160. def transformDataFrame(tFn: (DataFrame) ⇒ DataFrame)(implicit uTag: scala.reflect.api.JavaUniverse.TypeTag[Genotype]): GenotypeDataset

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

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

    tFn

    A function that transforms the underlying data as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  161. def transformDataset(tFn: Function[Dataset[Genotype], Dataset[Genotype]]): GenotypeDataset

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

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

    tFn

    A function that transforms the underlying Dataset as a Dataset.

    returns

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

    Definition Classes
    GenotypeDatasetGenomicDataset
  162. def transformDataset(tFn: (Dataset[Genotype]) ⇒ Dataset[Genotype]): GenotypeDataset

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

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

    tFn

    A function that transforms the underlying Dataset as a Dataset.

    returns

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

    Definition Classes
    GenotypeDatasetGenomicDataset
  163. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[Genotype], JavaRDD[X]], convFn: Function2[GenotypeDataset, RDD[X], Z]): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

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

    Definition Classes
    GenomicDataset
  164. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[Genotype]) ⇒ RDD[X])(implicit convFn: (GenotypeDataset, RDD[X]) ⇒ Z): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  165. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[Genotype, Genotype, GenotypeDataset, X, Y, Z]): Z

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

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

    tFn

    A function that transforms the underlying DataFrame.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  167. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[Genotype], Dataset[Y]], convFn: GenomicDatasetConversion[Genotype, Genotype, GenotypeDataset, X, Y, Z]): Z

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

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

    tFn

    A function that transforms the underlying Dataset.

    returns

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

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

    Permalink

    (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
  169. val uTag: scala.reflect.api.JavaUniverse.TypeTag[Genotype]

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    Definition Classes
    GenotypeDatasetGenomicDataset
  170. def union(datasets: GenotypeDataset*): GenotypeDataset

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    (Scala-specific) Unions together multiple genomic datasets.

    (Scala-specific) Unions together multiple genomic datasets.

    datasets

    Genomic datasets to union with this genomic dataset.

    Definition Classes
    GenotypeDatasetGenomicDataset
  171. def union(datasets: List[GenotypeDataset]): GenotypeDataset

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    (Java-specific) Unions together multiple genomic datasets.

    (Java-specific) Unions together multiple genomic datasets.

    datasets

    Genomic datasets to union with this genomic dataset.

    Definition Classes
    GenomicDataset
  172. def unpersist(): GenotypeDataset

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    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  173. val unproductFn: (Genotype) ⇒ Genotype

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    Attributes
    protected
    Definition Classes
    GenotypeDatasetGenomicDataset
  174. final def wait(): Unit

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

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

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

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

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

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

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    Save partition size into the partitioned Parquet flag file.

    Save partition size into the partitioned Parquet flag file.

    pathName

    Path to save the file at.

    partitionSize

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

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

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    Writes an RDD to disk as text and optionally merges.

    Writes an RDD to disk as text and optionally merges.

    rdd

    RDD to save.

    outputPath

    Output path to save text files to.

    asSingleFile

    If true, combines all partition shards.

    disableFastConcat

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

    optHeaderPath

    If provided, the header file to include.

    Attributes
    protected
    Definition Classes
    GenomicDataset

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from GenotypeDataset

Inherited from VCFSupportingGenomicDataset[Genotype, Genotype, GenotypeDataset]

Inherited from AvroGenomicDataset[Genotype, Genotype, GenotypeDataset]

Inherited from GenomicDataset[Genotype, Genotype, GenotypeDataset]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped