org.bdgenomics.adam.rdd

AvroReadGroupGenomicRDD

abstract class AvroReadGroupGenomicRDD[T, U <: AvroReadGroupGenomicRDD[T, U]] extends AvroGenomicRDD[T, U]

An abstract class describing a GenomicRDD where:

* The data are Avro IndexedRecords. * The data are associated to read groups (i.e., they are reads or fragments).

Linear Supertypes
AvroGenomicRDD[T, U], GenomicRDD[T, U], ADAMRDDFunctions[T], Logging, Serializable, Serializable, AnyRef, Any
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  1. AvroReadGroupGenomicRDD
  2. AvroGenomicRDD
  3. GenomicRDD
  4. ADAMRDDFunctions
  5. Logging
  6. Serializable
  7. Serializable
  8. AnyRef
  9. Any
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Instance Constructors

  1. new AvroReadGroupGenomicRDD()(implicit arg0: (T) ⇒ IndexedRecord, arg1: Manifest[T])

Abstract Value Members

  1. abstract def buildTree(rdd: RDD[(ReferenceRegion, T)])(implicit tTag: ClassTag[T]): IntervalArray[ReferenceRegion, T]

    Attributes
    protected
    Definition Classes
    GenomicRDD
  2. abstract def getReferenceRegions(elem: T): Seq[ReferenceRegion]

    Attributes
    protected
    Definition Classes
    GenomicRDD
  3. abstract val rdd: RDD[T]

    The RDD of genomic data that we are wrapping.

    The RDD of genomic data that we are wrapping.

    Definition Classes
    GenomicRDD
  4. abstract val recordGroups: RecordGroupDictionary

    A dictionary describing the read groups attached to this GenomicRDD.

  5. abstract def replaceRdd(newRdd: RDD[T]): U

    Attributes
    protected
    Definition Classes
    GenomicRDD
  6. abstract val sequences: SequenceDictionary

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

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

    Definition Classes
    GenomicRDD

Concrete 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[(T, X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(T, 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 broadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Iterable[T], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(Iterable[T], 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
  9. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef → Any
  12. def filterByOverlappingRegion(query: ReferenceRegion): U

    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
  13. def filterByOverlappingRegions(querys: List[ReferenceRegion]): U

    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
  14. def finalize(): Unit

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

    Attributes
    protected
    Definition Classes
    GenomicRDD
  16. def fullOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[T], Option[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(Option[T], 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
  17. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  18. def hashCode(): Int

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

    Definition Classes
    Any
  20. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging
  21. lazy val jrdd: JavaRDD[T]

    The underlying RDD of genomic data, as a JavaRDD.

    The underlying RDD of genomic data, as a JavaRDD.

    Definition Classes
    GenomicRDD
  22. def leftOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(T, Option[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(T, 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
  23. def log: Logger

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

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

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

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

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

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

    Attributes
    protected
    Definition Classes
    Logging
  30. def logName: String

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

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

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

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

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

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

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

    Definition Classes
    AnyRef
  38. def pipe[X, Y <: GenomicRDD[X, Y], V <: InFormatter[T, U, V]](cmd: String, files: Seq[String] = Seq.empty, environment: Map[String, String] = Map.empty, flankSize: Int = 0)(implicit tFormatterCompanion: InFormatterCompanion[T, U, V], xFormatter: OutFormatter[X], convFn: (U, RDD[X]) ⇒ Y, tManifest: ClassTag[T], 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
  39. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[T], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(Option[T], 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
  40. def rightOuterBroadcastRegionJoinAndGroupByRight[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Iterable[T], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(Iterable[T], 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[T], X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(Option[T], 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[T], Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(Option[T], 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 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
    AvroReadGroupGenomicRDDAvroGenomicRDD
  49. 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
  50. def saveRddAsParquet(args: SaveArgs): Unit

    Attributes
    protected
    Definition Classes
    ADAMRDDFunctions
  51. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(T, X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(T, 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
  52. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(T, Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[T], xTag: ClassTag[X]): GenomicRDD[(T, 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
  53. def sort(): U

    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

  54. def sortLexicographically(): U

    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

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

    Definition Classes
    AnyRef
  56. def toString(): String

    Definition Classes
    AnyRef → Any
  57. def transform(tFn: (RDD[T]) ⇒ RDD[T]): U

    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
  58. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from AvroGenomicRDD[T, U]

Inherited from GenomicRDD[T, U]

Inherited from ADAMRDDFunctions[T]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped