org.bdgenomics.adam.rdd

ADAMSpecificRecordSequenceDictionaryRDDAggregator

class ADAMSpecificRecordSequenceDictionaryRDDAggregator[T] extends ADAMSequenceDictionaryRDDAggregator[T]

A class that provides functions to recover a sequence dictionary from a generic RDD of records that are defined in Avro. This class assumes that the reference identification fields are defined inside of the given type.

T

A type defined in Avro that contains the reference identification fields.

Note

Avro classes that have specific constraints around sequence dictionary contents should not use this class. Examples include ADAMRecords and ADAMNucleotideContigs

Linear Supertypes
ADAMSequenceDictionaryRDDAggregator[T], Logging, Serializable, Serializable, AnyRef, Any
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  1. ADAMSpecificRecordSequenceDictionaryRDDAggregator
  2. ADAMSequenceDictionaryRDDAggregator
  3. Logging
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  5. Serializable
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Instance Constructors

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

    rdd

    RDD over which aggregation is supported.

Value Members

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

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

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  3. final def ==(arg0: Any): Boolean

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  4. def adamGetSequenceDictionary(performLexSort: Boolean = false): SequenceDictionary

    Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.

    Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.

    returns

    A sequence dictionary describing the reference contigs in this dataset.

    Definition Classes
    ADAMSequenceDictionaryRDDAggregator
  5. final def asInstanceOf[T0]: T0

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  6. def clone(): AnyRef

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

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  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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

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  11. def getSequenceRecordsFromElement(elem: T): Set[SequenceRecord]

    For a single RDD element, returns 0+ sequence record elements.

    For a single RDD element, returns 0+ sequence record elements.

    elem

    Element from which to extract sequence records.

    returns

    A seq of sequence records.

    Definition Classes
    ADAMSpecificRecordSequenceDictionaryRDDAggregatorADAMSequenceDictionaryRDDAggregator
  12. def hashCode(): Int

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  13. final def isInstanceOf[T0]: Boolean

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  14. def isTraceEnabled(): Boolean

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  15. def log: Logger

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  16. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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  17. def logDebug(msg: ⇒ String): Unit

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  18. def logError(msg: ⇒ String, throwable: Throwable): Unit

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  19. def logError(msg: ⇒ String): Unit

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  20. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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  21. def logInfo(msg: ⇒ String): Unit

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  22. def logName: String

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  23. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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  24. def logTrace(msg: ⇒ String): Unit

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  25. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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  26. def logWarning(msg: ⇒ String): Unit

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  27. final def ne(arg0: AnyRef): Boolean

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  28. final def notify(): Unit

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  29. final def notifyAll(): Unit

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  30. lazy val sc: SparkContext

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

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  32. def toString(): String

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  33. final def wait(): Unit

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  34. final def wait(arg0: Long, arg1: Int): Unit

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  35. final def wait(arg0: Long): Unit

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