org.bdgenomics.adam.rdd.variant

# VariantContextDataset

###
Related Docs: object VariantContextDataset | package variant

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

An genomic dataset containing VariantContexts attached to a reference and samples.

Linear Supertypes
VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextDataset], MultisampleGenomicDataset[VariantContext, VariantContext, VariantContextDataset], GenomicDataset[VariantContext, VariantContext, VariantContextDataset], Logging, AnyRef, Any
Known Subclasses
DatasetBoundVariantContextDataset, RDDBoundVariantContextDataset
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Inherited

1. VariantContextDataset
2. VCFSupportingGenomicDataset
3. MultisampleGenomicDataset
4. GenomicDataset
5. Logging
6. AnyRef
7. Any

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Visibility

1. Public
2. All

### Abstract Value Members

1. #### abstract val dataset: Dataset[VariantContext]

   These data as a Spark SQL Dataset.

   These data as a Spark SQL Dataset.

   Definition Classes
     GenomicDataset

2. #### abstract val headerLines: Seq[VCFHeaderLine]

   Definition Classes
     VariantContextDataset → VCFSupportingGenomicDataset

3. #### abstract val optPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]]

   Attributes
     protected
   Definition Classes
     GenomicDataset

4. #### abstract val rdd: RDD[VariantContext]

   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]): VariantContextDataset

   Replaces the header lines attached to this genomic dataset.

   Replaces the header lines attached to this genomic dataset.

   newHeaderLines

     The new header lines to attach to this genomic dataset.

   returns

     A new genomic dataset with the header lines replaced.

   Definition Classes
     VariantContextDataset → VCFSupportingGenomicDataset

6. #### abstract def replaceSamples(newSamples: Iterable[Sample]): VariantContextDataset

   Replaces the sample metadata attached to the genomic dataset.

   Replaces the sample metadata attached to the genomic dataset.

   newSamples

     The new sample metadata to attach.

   returns

     A GenomicDataset with new sample metadata.

   Definition Classes
     MultisampleGenomicDataset

7. #### abstract def replaceSequences(newSequences: SequenceDictionary): VariantContextDataset

   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]

   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

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

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

   Definition Classes
     GenomicDataset

### Concrete Value Members

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

   Definition Classes
     AnyRef → Any

2. #### final def ##(): Int

   Definition Classes
     AnyRef → Any

3. #### final def ==(arg0: Any): Boolean

   Definition Classes
     AnyRef → Any

4. #### def addAllAlleleArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

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

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

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

   id

     The identifier for the field.

   description

     A description of the data stored in this format field.

   lineType

     The type of the data stored in this format field.

   returns

     A new genomic dataset with the new header line added.

   Definition Classes
     VCFSupportingGenomicDataset

5. #### def addAllAlleleArrayInfoHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

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

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

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

   id

     The identifier for the field.

   description

     A description of the data stored in this info field.

   lineType

     The type of the data stored in this info field.

   returns

     A new genomic dataset with the new header line added.

   Definition Classes
     VCFSupportingGenomicDataset

6. #### def addAlternateAlleleArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

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

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

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

   id

     The identifier for the field.

   description

     A description of the data stored in this format field.

   lineType

     The type of the data stored in this format field.

   returns

     A new genomic dataset with the new header line added.

   Definition Classes
     VCFSupportingGenomicDataset

7. #### def addAlternateAlleleArrayInfoHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

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

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

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

   id

     The identifier for the field.

   description

     A description of the data stored in this info field.

   lineType

     The type of the data stored in this info field.

   returns

     A new genomic dataset with the new header line added.

   Definition Classes
     VCFSupportingGenomicDataset

8. #### def addFilterHeaderLine(id: String, description: String): VariantContextDataset

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

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

   id

     The identifier for the filter.

   description

     A description of the filter.

   returns

     A new genomic dataset with the new header line added.

   Definition Classes
     VCFSupportingGenomicDataset

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

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

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

   id

     The identifier for the field.

   count

     The number of elements in the array.

   lineType

     The type of the data stored in this format field.

   description

     A description of the data stored in this format field.

   returns

     A new genomic dataset with the new header line added.

   Definition Classes
     VCFSupportingGenomicDataset

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

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

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

    id

      The identifier for the field.

    count

      The number of elements in the array.

    description

      A description of the data stored in this format field.

    lineType

      The type of the data stored in this format field.

    returns

      A new genomic dataset with the new header line added.

    Definition Classes
      VCFSupportingGenomicDataset

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

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

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

    id

      The identifier for the field.

    count

      The number of elements in the array.

    lineType

      The type of the data stored in this info field.

    description

      A description of the data stored in this info field.

    returns

      A new genomic dataset with the new header line added.

    Definition Classes
      VCFSupportingGenomicDataset

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

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

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

    id

      The identifier for the field.

    count

      The number of elements in the array.

    description

      A description of the data stored in this info field.

    lineType

      The type of the data stored in this info field.

    returns

      A new genomic dataset with the new header line added.

    Definition Classes
      VCFSupportingGenomicDataset

13. #### def addGenotypeArrayFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

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

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

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

    id

      The identifier for the field.

    description

      A description of the data stored in this format field.

    lineType

      The type of the data stored in this format field.

    returns

      A new genomic dataset with the new header line added.

    Definition Classes
      VCFSupportingGenomicDataset

14. #### def addHeaderLine(headerLineToAdd: VCFHeaderLine): VariantContextDataset

    Appends a new header line to the existing lines.

    Appends a new header line to the existing lines.

    headerLineToAdd

      A header line to add.

    returns

      A new genomic dataset with the new header line added.

    Definition Classes
      VCFSupportingGenomicDataset

15. #### def addHeaderLines(headerLinesToAdd: Seq[VCFHeaderLine]): VariantContextDataset

    Appends new header lines to the existing lines.

    Appends new header lines to the existing lines.

    headerLinesToAdd

      Zero or more header lines to add.

    returns

      A new genomic dataset with the new header lines added.

    Definition Classes
      VCFSupportingGenomicDataset

16. #### def addSample(sampleToAdd: Sample): VariantContextDataset

    Adds a single sample to the current genomic dataset.

    Adds a single sample to the current genomic dataset.

    sampleToAdd

      A single sample to add.

    returns

      Returns a new genomic dataset with this sample added.

    Definition Classes
      MultisampleGenomicDataset

17. #### def addSamples(samplesToAdd: Iterable[Sample]): VariantContextDataset

    Adds samples to the current genomic dataset.

    Adds samples to the current genomic dataset.

    samplesToAdd

      Zero or more samples to add.

    returns

      Returns a new genomic dataset with samples added.

    Definition Classes
      MultisampleGenomicDataset

18. #### def addScalarFormatHeaderLine(id: String, description: String, lineType: VCFHeaderLineType): VariantContextDataset

    Adds a VCF header line describing a scalar format field.

    Adds a VCF header line describing a scalar format field.

    id

      The identifier for the field.

    description

      A description of the data stored in this format field.

    lineType

      The type of the data stored in this format field.

    returns

      A new genomic dataset with the new header line added.

    Definition Classes
      VCFSupportingGenomicDataset

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

    Adds a VCF header line describing a scalar info field.

    Adds a VCF header line describing a scalar info field.

    id

      The identifier for the field.

    description

      A description of the data stored in this info field.

    lineType

      The type of the data stored in this info field.

    returns

      A new genomic dataset with the new header line added.

    Definition Classes
      VCFSupportingGenomicDataset

20. #### def addSequence(sequenceToAdd: SequenceRecord): VariantContextDataset

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

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

    sequenceToAdd

      The sequence to add.

    returns

      Returns a new GenomicDataset with this sequence appended.

    Definition Classes
      GenomicDataset

21. #### def addSequences(sequencesToAdd: SequenceDictionary): VariantContextDataset

    Appends sequence metadata to the current genomic dataset.

    Appends sequence metadata to the current genomic dataset.

    sequencesToAdd

      The new sequences to append.

    returns

      Returns a new GenomicDataset with the sequences appended.

    Definition Classes
      GenomicDataset

22. #### final def asInstanceOf[T0]: T0

    Definition Classes
      Any

23. #### def broadcast()(implicit tTag: ClassTag[VariantContext]): GenomicBroadcast[VariantContext, VariantContext, VariantContextDataset]

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset
    See also

      broadcastRegionJoinAgainst

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      broadcastRegionJoinAgainst

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    broadcast

      The data on the left side of the join.

    returns

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

    Definition Classes
      GenomicDataset
    Note

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

    See also

      broadcastRegionJoin

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

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

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

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

    broadcast

      The data on the left side of the join.

    returns

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

    Definition Classes
      GenomicDataset
    Note

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

    See also

      broadcastRegionJoinAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset
    See also

      broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      broadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      broadcastRegionJoinAgainstAndGroupByRight

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

    Attributes
      protected
    Definition Classes
      VariantContextDataset → GenomicDataset

35. #### def cache(): VariantContextDataset

    Caches underlying RDD in memory.

    Caches underlying RDD in memory.

    returns

      Cached GenomicDataset.

    Definition Classes
      GenomicDataset

36. #### def clone(): AnyRef

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

37. #### def convertToVcf(stringency: ValidationStringency): (VCFHeader, RDD[VariantContext])

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts.

    Converts this genomic dataset of ADAM VariantContexts to HTSJDK VariantContexts.

    stringency

      Validation stringency to use.

    returns

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

38. #### def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

39. #### def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

40. #### def debug(msg: ⇒ Any): Unit

    Attributes
      protected
    Definition Classes
      Logging

41. #### final def eq(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

42. #### def equals(arg0: Any): Boolean

    Definition Classes
      AnyRef → Any

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

    Attributes
      protected
    Definition Classes
      Logging

44. #### def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

45. #### def error(msg: ⇒ Any): Unit

    Attributes
      protected
    Definition Classes
      Logging

46. #### def filterByOverlappingRegion(query: ReferenceRegion): VariantContextDataset

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

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

    query

      The region to query for.

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

    querys

      The regions to query for.

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

    querys

      The regions to query for.

    returns

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

    Definition Classes
      GenomicDataset

49. #### def finalize(): Unit

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )

50. #### def flattenRddByRegions(): RDD[(ReferenceRegion, VariantContext)]

    Attributes
      protected
    Definition Classes
      GenomicDataset

51. #### def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X], otoxTag: ClassTag[(Option[VariantContext], Option[X])], ouoyTag: scala.reflect.api.JavaUniverse.TypeTag[(Option[VariantContext], Option[Y])]): GenericGenomicDataset[(Option[VariantContext], Option[X]), (Option[VariantContext], Option[Y])]

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

53. #### def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[VariantContext], Option[X]), (Option[VariantContext], Option[Y])]

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

54. #### def fullOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[VariantContext], Option[X]), (Option[VariantContext], Option[Y])]

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

55. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

56. #### def getReferenceRegions(elem: VariantContext): Seq[ReferenceRegion]

    elem

      The variant context to get a reference region for.

    returns

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

    Attributes
      protected
    Definition Classes
      VariantContextDataset → GenomicDataset

57. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

58. #### def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

59. #### def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

60. #### def info(msg: ⇒ Any): Unit

    Attributes
      protected
    Definition Classes
      Logging

61. #### def isDebugEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

62. #### def isErrorEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

63. #### def isInfoEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

64. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

65. #### def isSorted: Boolean

    Definition Classes
      GenomicDataset

66. #### def isTraceEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

67. #### def isWarnEnabled: Boolean

    Attributes
      protected
    Definition Classes
      Logging

68. #### lazy val jrdd: JavaRDD[VariantContext]

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

71. #### def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(VariantContext, Option[X]), (VariantContext, Option[Y])]

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

72. #### def leftOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(VariantContext, Option[X]), (VariantContext, Option[Y])]

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

77. #### def logger: Logger

    Attributes
      protected
    Definition Classes
      Logging

78. #### def loggerName: String

    Attributes
      protected
    Definition Classes
      Logging

79. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

80. #### final def notify(): Unit

    Definition Classes
      AnyRef

81. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

82. #### def persist(sl: StorageLevel): VariantContextDataset

    Persists underlying RDD in memory or disk.

    Persists underlying RDD in memory or disk.

    sl

      new StorageLevel

    returns

      Persisted GenomicDataset.

    Definition Classes
      GenomicDataset

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

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

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

    X

      The type of the record created by the piped command.

    Y

      A GenomicDataset containing X's.

    cmd

      Command to run.

    files

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

    environment

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

    flankSize

      Number of bases to flank each command invocation by.

    tFormatter

      Class of formatter for data going into pipe command.

    xFormatter

      Formatter for data coming out of the pipe command.

    convFn

      The conversion function used to build the final genomic dataset.

    returns

      Returns a new GenomicDataset of type Y.

    Definition Classes
      GenomicDataset

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

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

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

    X

      The type of the record created by the piped command.

    Y

      A GenomicDataset containing X's.

    cmd

      Command to run.

    files

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

    environment

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

    flankSize

      Number of bases to flank each command invocation by.

    tFormatter

      Class of formatter for data going into pipe command.

    xFormatter

      Formatter for data coming out of the pipe command.

    convFn

      The conversion function used to build the final genomic dataset.

    returns

      Returns a new GenomicDataset of type Y.

    Definition Classes
      GenomicDataset

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

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

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

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

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

    X

      The type of the record created by the piped command.

    Y

      A GenomicDataset containing X's.

    cmd

      Command to run.

    files

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

    environment

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

    flankSize

      Number of bases to flank each command invocation by.

    optTimeout

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

    returns

      Returns a new GenomicDataset of type Y.

    Definition Classes
      GenomicDataset

86. #### val productFn: (VariantContext) ⇒ VariantContext

    Attributes
      protected
    Definition Classes
      VariantContextDataset → GenomicDataset

87. #### def replaceRdd(newRdd: RDD[VariantContext], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): VariantContextDataset

    newRdd

      The RDD of VariantContexts to replace the underlying RDD.

    returns

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

    Attributes
      protected
    Definition Classes
      VariantContextDataset → GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset
    See also

      rightOuterBroadcastRegionJoin

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      rightOuterBroadcastRegionJoin

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

91. #### def rightOuterBroadcastRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], Y)]

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    broadcast

      The data on the left side of the join.

    returns

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

    Definition Classes
      GenomicDataset
    Note

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

    See also

      rightOuterBroadcastRegionJoin

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

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

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

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

    broadcast

      The data on the left side of the join.

    returns

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

    Definition Classes
      GenomicDataset
    Note

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

    See also

      rightOuterBroadcastRegionJoinAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset
    See also

      rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset
    See also

      rightOuterBroadcastRegionJoinAgainstAndGroupByRight

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    returns

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

    Definition Classes
      GenomicDataset

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

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

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

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

    genomicDataset

      The right genomic dataset in the join.

    flankSize

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

    returns

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

    Definition Classes
      GenomicDataset

100. #### def rightOuterShuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[VariantContext], X), (Option[VariantContext], Y)]

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

104. #### def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(Option[VariantContext], Iterable[X]), (Option[VariantContext], Seq[Y])]

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

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

     Saves a genomic dataset to Parquet.

     Saves a genomic dataset to Parquet.

     pathName

       The path to save the file to.

     blockSize

       The size in bytes of blocks to write.

     pageSize

       The size in bytes of pages to write.

     compressionCodec

       The compression codec to apply to pages.

     disableDictionaryEncoding

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

     Definition Classes
       VariantContextDataset → GenomicDataset

107. #### def saveAsParquet(args: SaveArgs): Unit

     Saves a genomic dataset to Parquet.

     Saves a genomic dataset to Parquet.

     args

       The output format configuration to use when saving the data.

     Definition Classes
       GenomicDataset

108. #### def saveAsPartitionedParquet(pathName: String, compressionCodec: CompressionCodecName = CompressionCodecName.GZIP, partitionSize: Int = 1000000): Unit

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

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

     pathName

       The path to save the partitioned Parquet file to.

     compressionCodec

       Name of the compression codec to use.

     partitionSize

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

     Definition Classes
       GenomicDataset

109. #### def saveAsVcf(filePath: String, asSingleFile: Boolean, deferMerging: Boolean, disableFastConcat: Boolean, stringency: ValidationStringency): Unit

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

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

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

     filePath

       The file path to save to.

     asSingleFile

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

     deferMerging

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

     disableFastConcat

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

     stringency

       The validation stringency to use when writing the VCF.

110. #### def saveAsVcf(filePath: String): Unit

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

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

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

     filePath

       The file path to save to.

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

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

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

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

     args

       Arguments defining where to save the file.

     stringency

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

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

     Saves Avro data to a Hadoop file system.

     Saves Avro data to a Hadoop file system.

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

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

     U

       The type of the specific record we are saving.

     pathName

       Path to save records to.

     sc

       SparkContext used for identifying underlying file system.

     schema

       Schema of records we are saving.

     avro

       Seq of records we are saving.

     Attributes
       protected
     Definition Classes
       GenomicDataset

113. #### def saveMetadata(filePath: String): Unit

     Writes any necessary metadata to disk.

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

     Attributes
       protected
     Definition Classes
       VariantContextDataset → GenomicDataset

114. #### def saveSamples(pathName: String): Unit

     Save the samples to disk.

     Save the samples to disk.

     pathName

       The path to save samples to.

     Attributes
       protected
     Definition Classes
       MultisampleGenomicDataset

115. #### def saveSequences(pathName: String): Unit

     Save the sequence dictionary to disk.

     Save the sequence dictionary to disk.

     pathName

       The path to save the sequence dictionary to.

     Attributes
       protected
     Definition Classes
       GenomicDataset

116. #### def saveVcfHeaders(filePath: String): Unit

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

119. #### def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Integer): GenericGenomicDataset[(VariantContext, X), (VariantContext, Y)]

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

120. #### def shuffleRegionJoin[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](genomicDataset: GenomicDataset[X, Y, Z], flankSize: Double): GenericGenomicDataset[(VariantContext, X), (VariantContext, Y)]

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

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

     genomicDataset

       The right genomic dataset in the join.

     flankSize

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

     returns

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

     Definition Classes
       GenomicDataset

125. #### def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[VariantContext]): VariantContextDataset

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

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

     partitions

       The number of partitions for the new genomic dataset.

     stringency

       The level of ValidationStringency to enforce.

     returns

       Returns a new genomic dataset containing sorted data.

     Definition Classes
       GenomicDataset
     Note

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

     See also

       sortLexicographically

126. #### def sort(): VariantContextDataset

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

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

     returns

       Returns a new genomic dataset containing sorted data.

     Definition Classes
       GenomicDataset
     See also

       sortLexicographically

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

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

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

     partitions

       The number of partitions for the new genomic dataset.

     storePartitionMap

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

     storageLevel

       The level at which to persist the resulting genomic dataset.

     stringency

       The level of ValidationStringency to enforce.

     returns

       Returns a new genomic dataset containing sorted data.

     Definition Classes
       GenomicDataset
     Note

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

     See also

       sort

128. #### def sortLexicographically(): VariantContextDataset

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

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

     returns

       Returns a new genomic dataset containing sorted data.

     Definition Classes
       GenomicDataset
     See also

       sort

129. #### lazy val spark: SparkSession

     Definition Classes
       GenomicDataset

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

     Definition Classes
       AnyRef

131. #### def toDF(): DataFrame

     returns

       These data as a Spark SQL DataFrame.

     Definition Classes
       GenomicDataset

132. #### def toGenotypes(): GenotypeDataset

     returns

       Returns a GenotypeDataset containing the Genotypes in this genomic dataset.

133. #### def toString(): String

     Definition Classes
       MultisampleGenomicDataset → GenomicDataset → AnyRef → Any

134. #### def toVariants(): VariantDataset

     returns

       Returns the Variants in this genomic dataset.

135. #### def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

     Attributes
       protected
     Definition Classes
       Logging

136. #### def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

     Attributes
       protected
     Definition Classes
       Logging

137. #### def trace(msg: ⇒ Any): Unit

     Attributes
       protected
     Definition Classes
       Logging

138. #### def transform(tFn: Function[JavaRDD[VariantContext], JavaRDD[VariantContext]]): VariantContextDataset

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

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

     tFn

       A function that transforms the underlying RDD.

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

     tFn

       A function that transforms the underlying RDD.

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

     tFn

       A function that transforms the underlying DataFrame as a DataFrame.

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

     tFn

       A function that transforms the underlying data as a DataFrame.

     returns

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

     Definition Classes
       GenomicDataset

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

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

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

     tFn

       A function that transforms the underlying Dataset as a Dataset.

     returns

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

     Definition Classes
       VariantContextDataset → GenomicDataset

143. #### def transformDataset(tFn: (Dataset[VariantContext]) ⇒ Dataset[VariantContext]): VariantContextDataset

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

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

     tFn

       A function that transforms the underlying Dataset as a Dataset.

     returns

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

     Definition Classes
       VariantContextDataset → GenomicDataset

144. #### def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[JavaRDD[VariantContext], JavaRDD[X]], convFn: Function2[VariantContextDataset, RDD[X], Z]): Z

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

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

     tFn

       A function that transforms the underlying RDD.

     convFn

       The conversion function used to build the final RDD.

     returns

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

     Definition Classes
       GenomicDataset

145. #### def transmute[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (RDD[VariantContext]) ⇒ RDD[X])(implicit convFn: (VariantContextDataset, RDD[X]) ⇒ Z): Z

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

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

     tFn

       A function that transforms the underlying RDD.

     returns

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

     Definition Classes
       GenomicDataset

146. #### def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[VariantContext, VariantContext, VariantContextDataset, X, Y, Z]): Z

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

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

     tFn

       A function that transforms the underlying DataFrame.

     returns

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

     Definition Classes
       GenomicDataset

147. #### def transmuteDataFrame[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (DataFrame) ⇒ DataFrame)(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (VariantContextDataset, Dataset[Y]) ⇒ Z): Z

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

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

     tFn

       A function that transforms the underlying DataFrame.

     returns

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

     Definition Classes
       GenomicDataset

148. #### def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: Function[Dataset[VariantContext], Dataset[Y]], convFn: GenomicDatasetConversion[VariantContext, VariantContext, VariantContextDataset, X, Y, Z]): Z

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

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

     tFn

       A function that transforms the underlying Dataset.

     returns

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

     Definition Classes
       GenomicDataset

149. #### def transmuteDataset[X, Y <: Product, Z <: GenomicDataset[X, Y, Z]](tFn: (Dataset[VariantContext]) ⇒ Dataset[Y])(implicit yTag: scala.reflect.api.JavaUniverse.TypeTag[Y], convFn: (VariantContextDataset, Dataset[Y]) ⇒ Z): Z

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

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

     tFn

       A function that transforms the underlying Dataset.

     returns

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

     Definition Classes
       GenomicDataset

150. #### val uTag: scala.reflect.api.JavaUniverse.TypeTag[VariantContext]

     Definition Classes
       VariantContextDataset → GenomicDataset

151. #### def union(datasets: VariantContextDataset*): VariantContextDataset

     (Scala-specific) Unions together multiple genomic datasets.

     (Scala-specific) Unions together multiple genomic datasets.

     datasets

       Genomic datasets to union with this genomic dataset.

     Definition Classes
       VariantContextDataset → GenomicDataset

152. #### def union(datasets: List[VariantContextDataset]): VariantContextDataset

     (Java-specific) Unions together multiple genomic datasets.

     (Java-specific) Unions together multiple genomic datasets.

     datasets

       Genomic datasets to union with this genomic dataset.

     Definition Classes
       GenomicDataset

153. #### def unpersist(): VariantContextDataset

     Unpersists underlying RDD from memory or disk.

     Unpersists underlying RDD from memory or disk.

     returns

       Uncached GenomicDataset.

     Definition Classes
       GenomicDataset

154. #### val unproductFn: (VariantContext) ⇒ VariantContext

     Attributes
       protected
     Definition Classes
       VariantContextDataset → GenomicDataset

155. #### final def wait(): Unit

     Definition Classes
       AnyRef
     Annotations
       @throws( ... )

156. #### final def wait(arg0: Long, arg1: Int): Unit

     Definition Classes
       AnyRef
     Annotations
       @throws( ... )

157. #### final def wait(arg0: Long): Unit

     Definition Classes
       AnyRef
     Annotations
       @throws( ... )

158. #### def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

     Attributes
       protected
     Definition Classes
       Logging

159. #### def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

     Attributes
       protected
     Definition Classes
       Logging

160. #### def warn(msg: ⇒ Any): Unit

     Attributes
       protected
     Definition Classes
       Logging

161. #### def writeTextRdd[T](rdd: RDD[T], outputPath: String, asSingleFile: Boolean, disableFastConcat: Boolean, optHeaderPath: Option[String] = None): Unit

     Writes an RDD to disk as text and optionally merges.

     Writes an RDD to disk as text and optionally merges.

     rdd

       RDD to save.

     outputPath

       Output path to save text files to.

     asSingleFile

       If true, combines all partition shards.

     disableFastConcat

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

     optHeaderPath

       If provided, the header file to include.

     Attributes
       protected
     Definition Classes
       GenomicDataset

### Inherited from VCFSupportingGenomicDataset[VariantContext, VariantContext, VariantContextDataset]

### Inherited from MultisampleGenomicDataset[VariantContext, VariantContext, VariantContextDataset]

### Inherited from GenomicDataset[VariantContext, VariantContext, VariantContextDataset]

### Inherited from Logging

### Inherited from AnyRef

### Inherited from Any

### Ungrouped