Class

org.bdgenomics.adam.rdd.variation

GenotypeRDD

Related Doc: package variation

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case class GenotypeRDD(rdd: RDD[Genotype], sequences: SequenceDictionary, samples: Seq[Sample]) extends MultisampleAvroGenomicRDD[Genotype, GenotypeRDD] with Product with Serializable

An RDD containing genotypes called in a set of samples against a given reference genome.

rdd

Called genotypes.

sequences

A dictionary describing the reference genome.

samples

The samples called.

Linear Supertypes
Product, Equals, MultisampleAvroGenomicRDD[Genotype, GenotypeRDD], MultisampleGenomicRDD[Genotype, GenotypeRDD], AvroGenomicRDD[Genotype, GenotypeRDD], GenomicRDD[Genotype, GenotypeRDD], ADAMRDDFunctions[Genotype], Logging, Serializable, Serializable, AnyRef, Any
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Inherited
  1. GenotypeRDD
  2. Product
  3. Equals
  4. MultisampleAvroGenomicRDD
  5. MultisampleGenomicRDD
  6. AvroGenomicRDD
  7. GenomicRDD
  8. ADAMRDDFunctions
  9. Logging
  10. Serializable
  11. Serializable
  12. AnyRef
  13. Any
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Visibility
  1. Public
  2. All

Instance Constructors

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

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    rdd

    Called genotypes.

    sequences

    A dictionary describing the reference genome.

    samples

    The samples called.

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[(Genotype, X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenomicRDD[(Genotype, 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): GenotypeRDD

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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, Genotype)]

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

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    elem

    The genotype to get a reference region for.

    returns

    Returns the singular region this genotype covers.

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

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

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

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

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

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

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

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

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    Attributes
    protected
    Definition Classes
    Logging
  25. def logName: String

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

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

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

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

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

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

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

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    Definition Classes
    AnyRef
  33. 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

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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
  34. val rdd: RDD[Genotype]

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    Called genotypes.

    Called genotypes.

    Definition Classes
    GenotypeRDDGenomicRDD → ADAMRDDFunctions
  35. def replaceRdd(newRdd: RDD[Genotype]): GenotypeRDD

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    newRdd

    An RDD to replace the underlying RDD with.

    returns

    Returns a new GenotypeRDD with the underlying RDD replaced.

    Attributes
    protected
    Definition Classes
    GenotypeRDDGenomicRDD
  36. def rightOuterBroadcastRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[Genotype], X), Z]](genomicRdd: GenomicRDD[X, Y])(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenomicRDD[(Option[Genotype], 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
  37. def rightOuterShuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[Genotype], X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenomicRDD[(Option[Genotype], 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
  38. def rightOuterShuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Option[Genotype], Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenomicRDD[(Option[Genotype], 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
  39. val samples: Seq[Sample]

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    The samples called.

    The samples called.

    Definition Classes
    GenotypeRDDMultisampleGenomicRDD
  40. def save(args: SaveArgs): Boolean

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    Automatically detects the extension and saves to either VCF or Parquet.

    Automatically detects the extension and saves to either VCF or Parquet.

    args

    Arguments configuring how to save the output.

  41. def save(filePath: String): Unit

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    Java-friendly method for saving.

    Java-friendly method for saving.

    filePath

    Path to save file to. If ends in ".vcf", saves as VCF, else saves as Parquet.

  42. def saveAsParquet(filePath: String): Unit

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    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
  43. def saveAsParquet(filePath: String, blockSize: Integer, pageSize: Integer, compressCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit

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

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    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
  45. def saveAsParquet(args: SaveArgs): Unit

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    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
  46. def saveAsVcf(args: SaveArgs, sortOnSave: Boolean = false): Unit

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    Explicitly saves to VCF.

    Explicitly saves to VCF.

    args

    Arguments configuring how/where to save the output.

    sortOnSave

    Whether to sort when saving or not.

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

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    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

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    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
    MultisampleAvroGenomicRDDAvroGenomicRDD
  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

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

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    Attributes
    protected
    Definition Classes
    ADAMRDDFunctions
  51. val sequences: SequenceDictionary

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    A dictionary describing the reference genome.

    A dictionary describing the reference genome.

    Definition Classes
    GenotypeRDDGenomicRDD
  52. def shuffleRegionJoin[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Genotype, X), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenomicRDD[(Genotype, 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
  53. def shuffleRegionJoinAndGroupByLeft[X, Y <: GenomicRDD[X, Y], Z <: GenomicRDD[(Genotype, Iterable[X]), Z]](genomicRdd: GenomicRDD[X, Y], optPartitions: Option[Int] = None)(implicit tTag: ClassTag[Genotype], xTag: ClassTag[X]): GenomicRDD[(Genotype, 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
  54. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  55. def toVariantContextRDD: VariantContextRDD

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    returns

    Returns this GenotypeRDD squared off as a VariantContextRDD.

  56. def transform(tFn: (RDD[Genotype]) ⇒ RDD[Genotype]): GenotypeRDD

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

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from MultisampleAvroGenomicRDD[Genotype, GenotypeRDD]

Inherited from MultisampleGenomicRDD[Genotype, GenotypeRDD]

Inherited from AvroGenomicRDD[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