org.bdgenomics.adam.rdd.variant

ParquetUnboundGenotypeRDD

case class ParquetUnboundGenotypeRDD extends GenotypeRDD with Product with Serializable

Linear Supertypes
Product, Equals, GenotypeRDD, MultisampleAvroGenomicRDD[Genotype, Genotype, GenotypeRDD], MultisampleGenomicRDD[Genotype, GenotypeRDD], AvroGenomicRDD[Genotype, Genotype, GenotypeRDD], GenomicDataset[Genotype, Genotype, GenotypeRDD], GenomicRDD[Genotype, GenotypeRDD], ADAMRDDFunctions[Genotype], Logging, Serializable, Serializable, AnyRef, Any
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  1. ParquetUnboundGenotypeRDD
  2. Product
  3. Equals
  4. GenotypeRDD
  5. MultisampleAvroGenomicRDD
  6. MultisampleGenomicRDD
  7. AvroGenomicRDD
  8. GenomicDataset
  9. GenomicRDD
  10. ADAMRDDFunctions
  11. Logging
  12. Serializable
  13. Serializable
  14. AnyRef
  15. Any
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  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any
  3. final def ##(): Int

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

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

    Definition Classes
    Any
  6. def addHeaderLine(headerLineToAdd: VCFHeaderLine): GenotypeRDD

    Appends a new header line to the existing lines.

    Appends a new header line to the existing lines.

    headerLineToAdd

    A header line to add.

    returns

    A new RDD with the new header line added.

    Definition Classes
    GenotypeRDD
  7. def addHeaderLines(headerLinesToAdd: Seq[VCFHeaderLine]): GenotypeRDD

    Appends new header lines to the existing lines.

    Appends new header lines to the existing lines.

    headerLinesToAdd

    Zero or more header lines to add.

    returns

    A new RDD with the new header lines added.

    Definition Classes
    GenotypeRDD
  8. def addSample(sampleToAdd: Sample): GenotypeRDD

    Adds a single sample to the current RDD.

    Adds a single sample to the current RDD.

    sampleToAdd

    A single sample to add.

    returns

    Returns a new RDD with this sample added.

    Definition Classes
    MultisampleGenomicRDD
  9. def addSamples(samplesToAdd: Iterable[Sample]): GenotypeRDD

    Adds samples to the current RDD.

    Adds samples to the current RDD.

    samplesToAdd

    Zero or more samples to add.

    returns

    Returns a new RDD with samples added.

    Definition Classes
    MultisampleGenomicRDD
  10. def addSequence(sequenceToAdd: SequenceRecord): GenotypeRDD

    Appends metadata for a single sequence to the current RDD.

    Appends metadata for a single sequence to the current RDD.

    sequenceToAdd

    The sequence to add.

    returns

    Returns a new GenomicRDD with this sequence appended.

    Definition Classes
    GenomicRDD
  11. def addSequences(sequencesToAdd: SequenceDictionary): GenotypeRDD

    Appends sequence metadata to the current RDD.

    Appends sequence metadata to the current RDD.

    sequencesToAdd

    The new sequences to append.

    returns

    Returns a new GenomicRDD with the sequences appended.

    Definition Classes
    GenomicRDD
  12. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  13. def broadcast()(implicit tTag: ClassTag[Genotype]): Broadcast[IntervalArray[ReferenceRegion, Genotype]]

    Definition Classes
    GenomicRDD
  14. def broadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], txTag: ClassTag[(Genotype, X)]): GenericGenomicRDD[(Genotype, X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
    See also

    broadcastRegionJoinAgainst

  15. def broadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], txTag: ClassTag[(Genotype, X)]): GenericGenomicRDD[(Genotype, X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
    See also

    broadcastRegionJoinAgainst

  16. def broadcastRegionJoinAgainst[X](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenericGenomicRDD[(X, Genotype)]

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

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

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

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    Note

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

    See also

    broadcastRegionJoin

  17. def broadcastRegionJoinAgainstAndGroupByRight[X, Y <: GenomicRDD[X, Y]](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenericGenomicRDD[(Iterable[X], Genotype)]

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

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

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

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    Note

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

    See also

    broadcastRegionJoinAndGroupByRight

  18. def broadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Genotype], X)]): GenericGenomicRDD[(Iterable[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
    See also

    broadcastRegionJoinAgainstAndGroupByRight

  19. def broadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Genotype], X)]): GenericGenomicRDD[(Iterable[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
    See also

    broadcastRegionJoinAgainstAndGroupByRight

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

    Attributes
    protected
    Definition Classes
    GenotypeRDDGenomicRDD
  21. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. lazy val dataset: Dataset[Genotype]

  23. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  24. def filterByOverlappingRegion(query: ReferenceRegion): GenotypeRDD

    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 GenomicRDD containing only data that overlaps the query region.

    Definition Classes
    GenomicRDD
  25. def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): GenotypeRDD

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

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

    querys

    The regions to query for.

    returns

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

    Definition Classes
    GenomicRDD
  26. def finalize(): Unit

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

    Attributes
    protected
    Definition Classes
    GenomicRDD
  28. def fullOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Genotype], Option[X])]): GenericGenomicRDD[(Option[Genotype], Option[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  29. def fullOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otoxTag: ClassTag[(Option[Genotype], Option[X])]): GenericGenomicRDD[(Option[Genotype], Option[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
  30. final def getClass(): Class[_]

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

    elem

    The genotype to get a reference region for.

    returns

    Returns the singular region this genotype covers.

    Attributes
    protected
    Definition Classes
    GenotypeRDDGenomicRDD
  32. val headerLines: Seq[VCFHeaderLine]

    Definition Classes
    ParquetUnboundGenotypeRDDGenotypeRDD
  33. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  34. def isSorted: Boolean

    Definition Classes
    GenomicRDD
  35. def isTraceEnabled(): Boolean

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

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicRDD
  37. def leftOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], toxTag: ClassTag[(Genotype, Option[X])]): GenericGenomicRDD[(Genotype, Option[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  38. def leftOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], toxTag: ClassTag[(Genotype, Option[X])]): GenericGenomicRDD[(Genotype, Option[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
  39. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], toxTag: ClassTag[(Genotype, Iterable[X])]): GenericGenomicRDD[(Genotype, Iterable[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  40. def leftOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], toxTag: ClassTag[(Genotype, Iterable[X])]): GenericGenomicRDD[(Genotype, Iterable[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
  41. def log: Logger

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  48. def logName: String

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

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

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    ParquetUnboundGenotypeRDDGenomicRDD
  57. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[Genotype, GenotypeRDD, V]](cmd: String, files: List[String], environment: Map[String, String], flankSize: Integer, tFormatter: Class[V], xFormatter: OutFormatter[X], convFn: Function2[GenotypeRDD, RDD[X], Y]): Y

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

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

    Java/PySpark friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicRDD containing X's.

    V

    The InFormatter to use for formatting the data being piped to the command.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicRDD of type Y.

    Definition Classes
    GenomicRDD
  58. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[Genotype, GenotypeRDD, V]](cmd: String, files: Seq[Any], environment: Map[Any, Any], flankSize: Double, tFormatter: Class[V], xFormatter: OutFormatter[X], convFn: Function2[GenotypeRDD, RDD[X], Y]): Y

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

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

    SparkR friendly variant.

    X

    The type of the record created by the piped command.

    Y

    A GenomicRDD containing X's.

    V

    The InFormatter to use for formatting the data being piped to the command.

    cmd

    Command to run.

    files

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

    environment

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

    flankSize

    Number of bases to flank each command invocation by.

    tFormatter

    Class of formatter for data going into pipe command.

    xFormatter

    Formatter for data coming out of the pipe command.

    convFn

    The conversion function used to build the final RDD.

    returns

    Returns a new GenomicRDD of type Y.

    Definition Classes
    GenomicRDD
  59. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[Genotype, GenotypeRDD, V]](cmd: String, files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0)(implicit tFormatterCompanion: InFormatterCompanion[Genotype, GenotypeRDD, V], xFormatter: OutFormatter[X], convFn: (GenotypeRDD, RDD[X]) ⇒ Y, tManifest: ClassTag[Genotype], xManifest: ClassTag[X]): Y

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

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

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

    Pipes require the presence of an InFormatterCompanion and an OutFormatter as implicit values. The InFormatterCompanion should be a singleton whose apply method builds an InFormatter given a specific type of GenomicRDD. 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 GenomicRDD containing X's.

    V

    The InFormatter to use for formatting the data being piped to the command.

    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.

    returns

    Returns a new GenomicRDD of type Y.

    Definition Classes
    GenomicRDD
  60. lazy val rdd: RDD[Genotype]

    Definition Classes
    ParquetUnboundGenotypeRDDGenomicRDD → ADAMRDDFunctions
  61. def replaceHeaderLines(newHeaderLines: Seq[VCFHeaderLine]): GenotypeRDD

    Replaces the header lines attached to this RDD.

    Replaces the header lines attached to this RDD.

    newHeaderLines

    The new header lines to attach to this RDD.

    returns

    A new RDD with the header lines replaced.

    Definition Classes
    ParquetUnboundGenotypeRDDGenotypeRDD
  62. def replaceRdd(newRdd: RDD[Genotype], newPartitionMap: Option[Array[Option[(ReferenceRegion, ReferenceRegion)]]] = None): GenotypeRDD

    newRdd

    An RDD to replace the underlying RDD with.

    returns

    Returns a new GenotypeRDD with the underlying RDD replaced.

    Attributes
    protected
    Definition Classes
    GenotypeRDDGenomicRDD
  63. def replaceSamples(newSamples: Iterable[Sample]): GenotypeRDD

    Replaces the sample metadata attached to the RDD.

    Replaces the sample metadata attached to the RDD.

    newSamples

    The new sample metadata to attach.

    returns

    A GenomicRDD with new sample metadata.

    Definition Classes
    ParquetUnboundGenotypeRDDMultisampleGenomicRDD
  64. def replaceSequences(newSequences: SequenceDictionary): GenotypeRDD

    Replaces the sequence dictionary attached to a GenomicRDD.

    Replaces the sequence dictionary attached to a GenomicRDD.

    newSequences

    The new sequence dictionary to attach.

    returns

    Returns a new GenomicRDD with the sequences replaced.

    Definition Classes
    ParquetUnboundGenotypeRDDGenomicRDD
  65. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otxTag: ClassTag[(Option[Genotype], X)]): GenericGenomicRDD[(Option[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoin

  66. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otxTag: ClassTag[(Option[Genotype], X)]): GenericGenomicRDD[(Option[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoin

  67. def rightOuterBroadcastRegionJoinAgainst[X](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenericGenomicRDD[(Option[X], Genotype)]

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

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

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

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    Note

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

    See also

    rightOuterBroadcastRegionJoin

  68. def rightOuterBroadcastRegionJoinAgainstAndGroupByRight[X, Y <: GenomicRDD[X, Y]](broadcastTree: Broadcast[IntervalArray[ReferenceRegion, X]])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenericGenomicRDD[(Iterable[X], Genotype)]

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

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

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

    broadcastTree

    The data on the left side of the join.

    returns

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

    Definition Classes
    GenomicRDD
    Note

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

    See also

    rightOuterBroadcastRegionJoinAndGroupByRight

  69. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Genotype], X)]): GenericGenomicRDD[(Iterable[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  70. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], itxTag: ClassTag[(Iterable[Genotype], X)]): GenericGenomicRDD[(Iterable[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
    See also

    rightOuterBroadcastRegionJoinAgainstAndGroupByRight

  71. def rightOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otxTag: ClassTag[(Option[Genotype], X)]): GenericGenomicRDD[(Option[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  72. def rightOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otxTag: ClassTag[(Option[Genotype], X)]): GenericGenomicRDD[(Option[Genotype], X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
  73. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otixTag: ClassTag[(Option[Genotype], Iterable[X])]): GenericGenomicRDD[(Option[Genotype], Iterable[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  74. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], otixTag: ClassTag[(Option[Genotype], Iterable[X])]): GenericGenomicRDD[(Option[Genotype], Iterable[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
  75. val samples: Seq[Sample]

    The samples who have data contained in this GenomicRDD.

    The samples who have data contained in this GenomicRDD.

    Definition Classes
    ParquetUnboundGenotypeRDDMultisampleGenomicRDD
  76. def saveAsParquet(filePath: String): Unit

    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    Definition Classes
    AvroGenomicRDD
  77. def saveAsParquet(filePath: String, blockSize: Integer, pageSize: Integer, compressCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit

    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

    Whether or not to disable bit-packing.

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

    Saves this RDD to disk as a Parquet file.

    Saves this RDD to disk as a Parquet file.

    filePath

    Path to save the file at.

    blockSize

    Size per block.

    pageSize

    Size per page.

    compressCodec

    Name of the compression codec to use.

    disableDictionaryEncoding

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

    Definition Classes
    AvroGenomicRDD
  79. def saveAsParquet(args: SaveArgs): Unit

    Saves RDD as a directory of Parquet files.

    Saves RDD as a directory of Parquet files.

    The RDD is written as a directory of Parquet files, with Parquet configuration described by the input param args. The provided sequence dictionary is written at args.outputPath/_seqdict.avro as Avro binary.

    args

    Save configuration arguments.

    Definition Classes
    AvroGenomicRDD
  80. 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
    ADAMRDDFunctions
  81. def saveMetadata(filePath: String): Unit

    Called in saveAsParquet after saving RDD to Parquet to save metadata.

    Called in saveAsParquet after saving RDD to Parquet to save metadata.

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

    filePath

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

    Attributes
    protected
    Definition Classes
    GenotypeRDDMultisampleAvroGenomicRDDAvroGenomicRDD
  82. def savePartitionMap(filePath: String): Unit

    Save the partition map to disk.

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

    filePath

    The filepath where we will save the partition map.

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

    Saves an RDD of Avro data to Parquet.

    Saves an RDD of Avro data to Parquet.

    pathName

    The path to save the file to.

    blockSize

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

    pageSize

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

    compressCodec

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

    disableDictionaryEncoding

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

    optSchema

    The optional schema to set. Defaults to None.

    Attributes
    protected
    Definition Classes
    ADAMRDDFunctions
  84. def saveRddAsParquet(args: SaveArgs): Unit

    Attributes
    protected
    Definition Classes
    ADAMRDDFunctions
  85. def saveSamples(filePath: String): Unit

    Save the samples to disk.

    Save the samples to disk.

    filePath

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

    Attributes
    protected
    Definition Classes
    MultisampleAvroGenomicRDD
  86. def saveSequences(filePath: String): Unit

    Save the sequence dictionary to disk.

    Save the sequence dictionary to disk.

    filePath

    The filepath where we will save the sequence dictionary.

    Attributes
    protected
    Definition Classes
    AvroGenomicRDD
  87. def saveVcfHeaders(filePath: String): Unit

    Save the VCF headers to disk.

    Save the VCF headers to disk.

    filePath

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

    Definition Classes
    GenotypeRDD
  88. 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
    ParquetUnboundGenotypeRDDGenomicRDD
  89. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], txTag: ClassTag[(Genotype, X)]): GenericGenomicRDD[(Genotype, X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  90. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], txTag: ClassTag[(Genotype, X)]): GenericGenomicRDD[(Genotype, X)]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
  91. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], tixTag: ClassTag[(Genotype, Iterable[X])]): GenericGenomicRDD[(Genotype, Iterable[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  92. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y]](genomicRdd: GenomicRDD[X, Y], flankSize: Long)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X], tixTag: ClassTag[(Genotype, Iterable[X])]): GenericGenomicRDD[(Genotype, Iterable[X])]

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

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

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

    genomicRdd

    The right RDD in the join.

    flankSize

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

    returns

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

    Definition Classes
    GenomicRDD
  93. def sort(partitions: Int = rdd.partitions.length, stringency: ValidationStringency = ValidationStringency.STRICT)(implicit tTag: ClassTag[Genotype]): GenotypeRDD

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

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

    partitions

    The number of partitions for the new RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicRDD
    Note

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

    See also

    sortLexicographically

  94. def sort(): GenotypeRDD

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

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

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicRDD
    See also

    sortLexicographically

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

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

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

    partitions

    The number of partitions for the new RDD.

    storePartitionMap

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

    storageLevel

    The level at which to persist the resulting RDD.

    stringency

    The level of ValidationStringency to enforce.

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicRDD
    Note

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

    See also

    sort

  96. def sortLexicographically(): GenotypeRDD

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

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

    returns

    Returns a new RDD containing sorted data.

    Definition Classes
    GenomicRDD
    See also

    sort

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

    Definition Classes
    AnyRef
  98. def toDF(): DataFrame

    returns

    This data as a Spark SQL DataFrame.

    Definition Classes
    GenomicDataset
  99. def toString(): String

    Definition Classes
    MultisampleGenomicRDDGenomicRDD → AnyRef → Any
  100. def toVariantContexts(): VariantContextRDD

    returns

    Returns this GenotypeRDD squared off as a VariantContextRDD.

    Definition Classes
    GenotypeRDD
  101. def transform(tFn: Function[JavaRDD[Genotype], JavaRDD[Genotype]]): GenotypeRDD

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicRDD
  102. def transform(tFn: (RDD[Genotype]) ⇒ RDD[Genotype]): GenotypeRDD

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicRDD
  103. def transformDataFrame(tFn: Function[DataFrame, DataFrame]): GenotypeRDD

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

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

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

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

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

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

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

    tFn

    A function that transforms the underlying RDD as a DataFrame.

    returns

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

    Definition Classes
    GenomicDataset
  105. def transformDataset(tFn: (Dataset[Genotype]) ⇒ Dataset[Genotype]): GenotypeRDD

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

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

    tFn

    A function that transforms the underlying RDD as a Dataset.

    returns

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

    Definition Classes
    GenotypeRDDGenomicDataset
  106. def transmute[X, Y <: GenomicRDD[X, Y]](tFn: Function[JavaRDD[Genotype], JavaRDD[X]], convFn: Function2[GenotypeRDD, RDD[X], Y]): Y

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

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

    tFn

    A function that transforms the underlying RDD.

    convFn

    The conversion function used to build the final RDD.

    returns

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

    Definition Classes
    GenomicRDD
  107. def transmute[X, Y <: GenomicRDD[X, Y]](tFn: (RDD[Genotype]) ⇒ RDD[X])(implicit convFn: (GenotypeRDD, RDD[X]) ⇒ Y): Y

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicRDD
  108. def transmuteDataFrame[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: Function[DataFrame, DataFrame], convFn: GenomicDatasetConversion[Genotype, GenotypeRDD, X, Y]): Y

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  109. def transmuteDataFrame[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: (DataFrame) ⇒ DataFrame)(implicit xTag: scala.reflect.api.JavaUniverse.TypeTag[X], convFn: (GenotypeRDD, Dataset[X]) ⇒ Y): Y

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  110. def transmuteDataset[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: Function[Dataset[Genotype], Dataset[X]], convFn: GenomicDatasetConversion[Genotype, GenotypeRDD, X, Y]): Y

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  111. def transmuteDataset[X <: Product, Y <: GenomicDataset[_, X, Y]](tFn: (Dataset[Genotype]) ⇒ Dataset[X])(implicit xTag: scala.reflect.api.JavaUniverse.TypeTag[X], convFn: (GenotypeRDD, Dataset[X]) ⇒ Y): Y

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

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

    tFn

    A function that transforms the underlying RDD.

    returns

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

    Definition Classes
    GenomicDataset
  112. val uTag: scala.reflect.api.JavaUniverse.TypeTag[Genotype]

    Definition Classes
    GenotypeRDDGenomicDataset
  113. def union(rdds: GenotypeRDD*): GenotypeRDD

    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    GenotypeRDDGenomicRDD
  114. def union(rdds: List[GenotypeRDD]): GenotypeRDD

    Unions together multiple genomic RDDs.

    Unions together multiple genomic RDDs.

    rdds

    RDDs to union with this RDD.

    Definition Classes
    GenomicRDD
  115. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  118. 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
    GenomicRDD

Inherited from Product

Inherited from Equals

Inherited from GenotypeRDD

Inherited from MultisampleAvroGenomicRDD[Genotype, Genotype, GenotypeRDD]

Inherited from MultisampleGenomicRDD[Genotype, GenotypeRDD]

Inherited from AvroGenomicRDD[Genotype, Genotype, GenotypeRDD]

Inherited from GenomicDataset[Genotype, Genotype, GenotypeRDD]

Inherited from GenomicRDD[Genotype, GenotypeRDD]

Inherited from ADAMRDDFunctions[Genotype]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped