Class

org.bdgenomics.adam.rdd.variation

VariantContextRDD

Related Doc: package variation

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case class VariantContextRDD(rdd: RDD[VariantContext], sequences: SequenceDictionary, samples: Seq[Sample]) extends MultisampleGenomicRDD[VariantContext, VariantContextRDD] with Logging with Product with Serializable

An RDD containing VariantContexts attached to a reference and samples.

rdd

The underlying RDD of VariantContexts.

sequences

The genome sequence these variants were called against.

samples

The genotyped samples in this RDD of VariantContexts.

Linear Supertypes
Serializable, Serializable, Product, Equals, Logging, MultisampleGenomicRDD[VariantContext, VariantContextRDD], GenomicRDD[VariantContext, VariantContextRDD], AnyRef, Any
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  1. VariantContextRDD
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Logging
  7. MultisampleGenomicRDD
  8. GenomicRDD
  9. AnyRef
  10. Any
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Instance Constructors

  1. new VariantContextRDD(rdd: RDD[VariantContext], sequences: SequenceDictionary, samples: Seq[Sample])

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    rdd

    The underlying RDD of VariantContexts.

    sequences

    The genome sequence these variants were called against.

    samples

    The genotyped samples in this RDD of VariantContexts.

Value Members

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

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

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

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    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  5. def broadcastRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(VariantContext, X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(VariantContext, X), Z]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  6. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  7. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  8. def filterByOverlappingRegion(query: ReferenceRegion): VariantContextRDD

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    Definition Classes
    GenomicRDD
  9. def finalize(): Unit

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

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    Attributes
    protected
    Definition Classes
    GenomicRDD
  11. def fullOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[VariantContext], Option[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(Option[VariantContext], Option[X]), Z]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

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

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

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    elem

    The variant context to get a reference region for.

    returns

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

    Attributes
    protected
    Definition Classes
    VariantContextRDDGenomicRDD
  14. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  15. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  16. def joinDatabaseVariantAnnotation(ann: DatabaseVariantAnnotationRDD): VariantContextRDD

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    Left outer join database variant annotations.

    Left outer join database variant annotations.

    ann

    Annotation RDD to join against.

    returns

    Returns a VariantContextRDD where annotations have been filled in.

  17. lazy val jrdd: JavaRDD[VariantContext]

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    Definition Classes
    GenomicRDD
  18. def leftOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(VariantContext, Option[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(VariantContext, Option[X]), Z]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  19. def log: Logger

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

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

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

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

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  26. def logName: String

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

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

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

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

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

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

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

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

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

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

    Files are substituted in to the command with a $x syntax. E.g., to invoke a command that uses the first file from the files Seq, use $0.

    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
  35. val rdd: RDD[VariantContext]

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    The underlying RDD of VariantContexts.

    The underlying RDD of VariantContexts.

    Definition Classes
    VariantContextRDDGenomicRDD
  36. def replaceRdd(newRdd: RDD[VariantContext]): VariantContextRDD

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    newRdd

    The RDD of VariantContexts to replace the underlying RDD.

    returns

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

    Attributes
    protected
    Definition Classes
    VariantContextRDDGenomicRDD
  37. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[VariantContext], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(Option[VariantContext], X), Z]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  38. def rightOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[VariantContext], X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(Option[VariantContext], X), Z]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  39. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[VariantContext], Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(Option[VariantContext], Iterable[X]), Z]

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    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
  40. val samples: Seq[Sample]

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    The genotyped samples in this RDD of VariantContexts.

    The genotyped samples in this RDD of VariantContexts.

    Definition Classes
    VariantContextRDDMultisampleGenomicRDD
  41. def saveAsVcf(filePath: String, sortOnSave: Boolean = false, asSingleFile: Boolean = false): Unit

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

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

    filePath

    The filepath to save to.

    sortOnSave

    Whether to sort before saving. Default is false (no sort).

  42. def saveAsVcf(args: SaveArgs, sortOnSave: Boolean): Unit

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

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

    sortOnSave

    Whether to sort before saving.

  43. val sequences: SequenceDictionary

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    The genome sequence these variants were called against.

    The genome sequence these variants were called against.

    Definition Classes
    VariantContextRDDGenomicRDD
  44. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(VariantContext, X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(VariantContext, X), Z]

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    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
  45. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(VariantContext, Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[VariantContext], xTag: ClassTag[X]): GenomicRDD[(VariantContext, Iterable[X]), Z]

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

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

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

    genomicRdd

    The right RDD in the join.

    returns

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

    Definition Classes
    GenomicRDD
  46. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  47. def toDatabaseVariantAnnotationRDD: DatabaseVariantAnnotationRDD

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    returns

    Returns a DatabaseVariantAnnotationRDD containing the variant annotations attached to this VariantContextRDD.

  48. def toGenotypeRDD: GenotypeRDD

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    returns

    Returns a GenotypeRDD containing the Genotypes in this RDD.

  49. def toVariantRDD: VariantRDD

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    returns

    Returns the Variants in this RDD.

  50. def transform(tFn: (RDD[VariantContext]) ⇒ RDD[VariantContext]): VariantContextRDD

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

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    Annotations
    @throws( ... )
  52. final def wait(arg0: Long, arg1: Int): Unit

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

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    Definition Classes
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    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from AnyRef

Inherited from Any

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