Class/Object

org.bdgenomics.adam.rdd.variant

VariantContextRDD

Related Docs: object VariantContextRDD | package variant

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sealed abstract class VariantContextRDD extends MultisampleGenomicDataset[VariantContext, VariantContext, VariantContextRDD] with GenomicDataset[VariantContext, VariantContext, VariantContextRDD] with Logging with VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextRDD]

An RDD containing VariantContexts attached to a reference and samples.

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  1. VariantContextRDD
  2. VCFSupportingGenomicDataset
  3. MultisampleGenomicDataset
  4. GenomicDataset
  5. Logging
  6. AnyRef
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Abstract Value Members

  1. abstract val dataset: Dataset[VariantContext]

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    These data as a Spark SQL Dataset.

    These data as a Spark SQL Dataset.

    Definition Classes
    GenomicDataset
  2. abstract val headerLines: Seq[VCFHeaderLine]

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    Definition Classes
    VariantContextRDD → VCFSupportingGenomicDataset
  3. abstract val optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]

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    Attributes
    protected
    Definition Classes
    GenomicDataset
  4. abstract val rdd: RDD[VariantContext]

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    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    GenomicDataset
  5. abstract def replaceHeaderLines(newHeaderLines: Seq[VCFHeaderLine]): VariantContextRDD

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    Replaces the header lines attached to this RDD.

    Replaces the header lines attached to this RDD.

    newHeaderLines

    The new header lines to attach to this RDD.

    returns

    A new RDD with the header lines replaced.

    Definition Classes
    VariantContextRDD → VCFSupportingGenomicDataset
  6. abstract def replaceSamples(newSamples: Iterable[Sample]): VariantContextRDD

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    Replaces the sample metadata attached to the RDD.

    Replaces the sample metadata attached to the RDD.

    newSamples

    The new sample metadata to attach.

    returns

    A GenomicDataset with new sample metadata.

    Definition Classes
    MultisampleGenomicDataset
  7. abstract def replaceSequences(newSequences: SequenceDictionary): VariantContextRDD

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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
    GenomicDataset
  8. abstract 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
    MultisampleGenomicDataset
  9. abstract 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
    GenomicDataset

Concrete 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): VariantContextRDD

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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 RDD with the new header line added.

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

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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 RDD with the new header line added.

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

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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 RDD with the new header line added.

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

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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 RDD with the new header line added.

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

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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 RDD with the new header line added.

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

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    Adds a VCF header line describing an array format field, with fixed count.

    Adds a VCF header line describing an array format field, with fixed count.

    Java friendly variant.

    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 RDD with the new header line added.

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

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    Adds a VCF header line describing an array format field, with fixed count.

    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 RDD with the new header line added.

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

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    Adds a VCF header line describing an array info field, with fixed count.

    Adds a VCF header line describing an array info field, with fixed count.

    Java friendly variant.

    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 RDD with the new header line added.

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

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    Adds a VCF header line describing an array info field, with fixed count.

    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 RDD with the new header line added.

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

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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 RDD with the new header line added.

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

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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 RDD with the new header line added.

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

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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 RDD with the new header lines added.

    Definition Classes
    VCFSupportingGenomicDataset
  16. def addSample(sampleToAdd: Sample): VariantContextRDD

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    Adds a single sample to the current RDD.

    Adds a single sample to the current RDD.

    sampleToAdd

    A single sample to add.

    returns

    Returns a new RDD with this sample added.

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

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    Adds samples to the current RDD.

    Adds samples to the current RDD.

    samplesToAdd

    Zero or more samples to add.

    returns

    Returns a new RDD with samples added.

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

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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 RDD with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  19. def addScalarInfoHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextRDD

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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 RDD with the new header line added.

    Definition Classes
    VCFSupportingGenomicDataset
  20. def addSequence(sequenceToAdd: SequenceRecord): VariantContextRDD

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    Appends metadata for a single sequence to the current RDD.

    Appends metadata for a single sequence to the current RDD.

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicDataset with this sequence appended.

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

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    Appends sequence metadata to the current RDD.

    Appends sequence metadata to the current RDD.

    sequencesToAdd

    The new sequences to append.

    returns

    Returns a new GenomicDataset with the sequences appended.

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

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainst

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoin

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

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    broadcastRegionJoinAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

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    Attributes
    protected
    Definition Classes
    VariantContextRDDGenomicDataset
  35. def cache(): VariantContextRDD

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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. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  38. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  39. def filterByOverlappingRegion(query: ReferenceRegion): VariantContextRDD

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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
  40. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): VariantContextRDD

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  41. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): VariantContextRDD

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicDataset
  42. def finalize(): Unit

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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    elem

    The variant context to get a reference region for.

    returns

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

    Attributes
    protected
    Definition Classes
    VariantContextRDDGenomicDataset
  50. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  51. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  52. def isSorted: Boolean

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    Definition Classes
    GenomicDataset
  53. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  54. lazy val jrdd: JavaRDD[VariantContext]

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
  63. def log: Logger

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

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

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

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

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  70. def logName: String

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

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

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

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

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

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

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

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    Definition Classes
    AnyRef
  78. def persist(sl: StorageLevel): VariantContextRDD

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

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

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

    Java/PySpark friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

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

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

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

    SparkR friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  81. def pipe[X, Y <: Product, Z <: GenomicDataset[X, Y, Z], W <: InFormatter[VariantContext, VariantContext, VariantContextRDD, W]](cmd: Seq[String], files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0, optTimeout: Option[Int] = None)(implicit tFormatterCompanion: InFormatterCompanion[VariantContext, VariantContext, VariantContextRDD, W], xFormatter: OutFormatter[X], convFn: (VariantContextRDD, RDD[X]) ⇒ Z, tManifest: ClassTag[VariantContext], xManifest: ClassTag[X]): Z

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

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

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

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

    X

    The type of the record created by the piped command.

    Y

    A GenomicDataset containing X's.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    optTimeout

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

    returns

    Returns a new GenomicDataset of type Y.

    Definition Classes
    GenomicDataset
  82. val productFn: (VariantContext) ⇒ VariantContext

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    Attributes
    protected
    Definition Classes
    VariantContextRDDGenomicDataset
  83. def replaceRdd(newRdd: RDD[VariantContext], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): VariantContextRDD

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    newRdd

    The RDD of VariantContexts to replace the underlying RDD.

    returns

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

    Attributes
    protected
    Definition Classes
    VariantContextRDDGenomicDataset
  84. def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otxTag: ClassTag[(Option[VariantContext], X)], ouyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Y)]): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], Y)]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoin

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoin

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

    Permalink

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

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

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

    returns

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

    Definition Classes
    GenomicDataset
    Note

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

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicDataset
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

    Saves an RDD of Avro data to Parquet.

    Saves an RDD of Avro data to Parquet.

    blockSize

    The size in bytes of blocks to write.

    pageSize

    The size in bytes of pages to write.

    compressCodec

    The compression codec to apply to pages.

    disableDictionaryEncoding

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

    Definition Classes
    VariantContextRDDGenomicDataset
  103. def saveAsParquet(args: SaveArgs): Unit

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    Saves an RDD to Parquet.

    Saves an RDD to Parquet.

    args

    The output format configuration to use when saving the data.

    Definition Classes
    GenomicDataset
  104. def saveAsVcf(filePath: String, asSingleFile: Boolean, deferMerging: Boolean, disableFastConcat: Boolean, stringency: ValidationStringency): Unit

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    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

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

    filePath

    The file path to save to.

    asSingleFile

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

    deferMerging

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

    disableFastConcat

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

    stringency

    The validation stringency to use when writing the VCF.

  105. def saveAsVcf(filePath: String): Unit

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    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves as a single file to disk as VCF.

    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves as a single file to disk as VCF. Uses lenient validation stringency.

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

    filePath

    The file path to save to.

  106. def saveAsVcf(args: ADAMSaveAnyArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): Unit

    Permalink

    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

    Converts an RDD of ADAM VariantContexts to HTSJDK VariantContexts and saves to disk as VCF.

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

    args

    Arguments defining where to save the file.

    stringency

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

  107. 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
  108. def saveMetadata(filePath: String): Unit

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    Attributes
    protected
  109. def saveSamples(filePath: String): Unit

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    Save the samples to disk.

    Save the samples to disk.

    filePath

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

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

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    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    filePath

    The filepath where we will save the sequence dictionary.

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

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  112. def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicRdd: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], txTag: ClassTag[(VariantContext, X)], uyTag: scala.reflect.api.JavaUniverse.TypeTag[(VariantContext, Y)]): GenericGenomicDataset[(VariantContext, X), (VariantContext, Y)]

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

    Permalink

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

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

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

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

    partitions

    The number of partitions for the new RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sortLexicographically

  121. def sort(): VariantContextRDD

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

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

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sortLexicographically

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

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

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

    partitions

    The number of partitions for the new RDD.

    storePartitionMap

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

    storageLevel

    The level at which to persist the resulting RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    Note

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

    See also

    sort

  123. def sortLexicographically(): VariantContextRDD

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

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

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicDataset
    See also

    sort

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

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    Definition Classes
    AnyRef
  125. def toDF(): DataFrame

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    returns

    This data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  126. def toGenotypes(): GenotypeRDD

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    returns

    Returns a GenotypeRDD containing the Genotypes in this RDD.

  127. def toString(): String

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    Definition Classes
    MultisampleGenomicDatasetGenomicDataset → AnyRef → Any
  128. def toVariants(): VariantRDD

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    returns

    Returns the Variants in this RDD.

  129. def transform(tFn: Function[JavaRDD[VariantContext], JavaRDD[VariantContext]]): VariantContextRDD

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  130. def transform(tFn: (RDD[VariantContext]) ⇒ RDD[VariantContext]): VariantContextRDD

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  133. def transformDataset(tFn: (Dataset[VariantContext]) ⇒ Dataset[VariantContext]): VariantContextRDD

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

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

    tFn

    A function that transforms the underlying RDD as a Dataset.

    returns

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

    Definition Classes
    VariantContextRDDGenomicDataset
  134. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[VariantContext], JavaRDD[X]], convFn: Function2[VariantContextRDD, RDD[X], Z]): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

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

    Definition Classes
    GenomicDataset
  135. def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[VariantContext]) ⇒ RDD[X])(implicit convFn: (VariantContextRDD, RDD[X]) ⇒ Z): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  136. def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[VariantContext, VariantContext, VariantContextRDD, X, Y, Z]): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  138. def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[VariantContext], Dataset[Y]], convFn: GenomicDatasetConversion[VariantContext, VariantContext, VariantContextRDD, X, Y, Z]): Z

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  140. val uTag: scala.reflect.api.JavaUniverse.TypeTag[VariantContext]

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    Definition Classes
    VariantContextRDDGenomicDataset
  141. def union(rdds: VariantContextRDD*): VariantContextRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    VariantContextRDDGenomicDataset
  142. def union(rdds: List[VariantContextRDD]): VariantContextRDD

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    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    GenomicDataset
  143. def unpersist(): VariantContextRDD

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    Unpersists underlying RDD from memory or disk.

    Unpersists underlying RDD from memory or disk.

    returns

    Uncached GenomicDataset.

    Definition Classes
    GenomicDataset
  144. val unproductFn: (VariantContext) ⇒ VariantContext

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    Attributes
    protected
    Definition Classes
    VariantContextRDDGenomicDataset
  145. final def wait(): Unit

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  148. 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 VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextRDD]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped