org.bdgenomics.adam.rdd.variant

VariantRDD

case class VariantRDD(rdd: RDD[Variant], sequences: SequenceDictionary, headerLines: Seq[VCFHeaderLine] = ...) extends AvroGenomicRDD[Variant, VariantRDD] with Product with Serializable

An RDD containing variants called against a given reference genome.

rdd

Variants.

sequences

A dictionary describing the reference genome.

headerLines

The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of Variants.

Linear Supertypes
Product, Equals, AvroGenomicRDD[Variant, VariantRDD], GenomicRDD[Variant, VariantRDD], ADAMRDDFunctions[Variant], Logging, Serializable, Serializable, AnyRef, Any
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  1. VariantRDD
  2. Product
  3. Equals
  4. AvroGenomicRDD
  5. GenomicRDD
  6. ADAMRDDFunctions
  7. Logging
  8. Serializable
  9. Serializable
  10. AnyRef
  11. Any
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Instance Constructors

  1. new VariantRDD(rdd: RDD[Variant], sequences: SequenceDictionary, headerLines: Seq[VCFHeaderLine] = ...)

    rdd

    Variants.

    sequences

    A dictionary describing the reference genome.

    headerLines

    The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of Variants.

Value Members

  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. final def asInstanceOf[T0]: T0

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

    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
  8. def clone(): AnyRef

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

    Definition Classes
    AnyRef
  10. def filterByOverlappingRegion(query: ReferenceRegion): VariantRDD

    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
  11. def filterByOverlappingRegions(querys: List[ReferenceRegion]): VariantRDD

    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
  12. def finalize(): Unit

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

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

    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
  15. final def getClass(): Class[_]

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

    elem

    The variant to get a reference region for.

    returns

    Returns the singular region this variant covers.

    Attributes
    protected
    Definition Classes
    VariantRDDGenomicRDD
  17. val headerLines: Seq[VCFHeaderLine]

    The VCF header lines that cover all INFO/FORMAT fields needed to represent this RDD of Variants.

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  19. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging
  20. lazy val jrdd: JavaRDD[Variant]

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

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

    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
  22. def log: Logger

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  29. def logName: String

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

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

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

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

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

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

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

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

    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
  38. val rdd: RDD[Variant]

    Variants.

    Variants.

    Definition Classes
    VariantRDDGenomicRDD → ADAMRDDFunctions
  39. def replaceRdd(newRdd: RDD[Variant]): VariantRDD

    newRdd

    An RDD to replace the underlying RDD with.

    returns

    Returns a new VariantRDD with the underlying RDD replaced.

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

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

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

    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
  43. def save(filePath: String): Unit

    Java-friendly method for saving to Parquet.

    Java-friendly method for saving to Parquet.

    filePath

    Path to save to.

  44. 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
  45. 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
  46. 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
  47. 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
  48. def saveAvro[U <: SpecificRecordBase](filename: 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.

    filename

    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
  49. 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.

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

    Saves an RDD of Avro data to Parquet.

    Saves an RDD of Avro data to Parquet.

    filePath

    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.

    compressCodec

    The compression codec to apply to pages.

    disableDictionaryEncoding

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

    schema

    The schema to set.

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

    Attributes
    protected
    Definition Classes
    ADAMRDDFunctions
  52. val sequences: SequenceDictionary

    A dictionary describing the reference genome.

    A dictionary describing the reference genome.

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

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

    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
  55. def sort(): VariantRDD

    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
    Note

    Does not support data that is unaligned or where objects align to multiple positions.

    See also

    sortLexicographically

  56. def sortLexicographically(): VariantRDD

    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
    Note

    Does not support data that is unaligned or where objects align to multiple positions.

    See also

    sort

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

    Definition Classes
    AnyRef
  58. def transform(tFn: (RDD[Variant]) ⇒ RDD[Variant]): VariantRDD

    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
  59. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from AvroGenomicRDD[Variant, VariantRDD]

Inherited from GenomicRDD[Variant, VariantRDD]

Inherited from ADAMRDDFunctions[Variant]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped