NucleotideContigFragmentRDDFunctions

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

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4. final def ==(arg0: AnyRef): Boolean

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6. def adamGetReferenceString(region: ReferenceRegion): String

   From a set of contigs, returns the base sequence that corresponds to a region of the reference.

   From a set of contigs, returns the base sequence that corresponds to a region of the reference.

   region

   Reference region over which to get sequence.

   returns

   String of bases corresponding to reference sequence.

   Exceptions thrown

   UnsupportedOperationException

   Throws exception if query region is not found.

7. def adamGetSequenceDictionary(): 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

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

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14. def getSequenceRecordsFromElement(elem: NucleotideContigFragment): 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

    NucleotideContigFragmentRDDFunctions → ADAMSequenceDictionaryRDDAggregator

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

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34. def toReads(): RDD[AlignmentRecord]

    Converts an RDD of nucleotide contig fragments into reads.

    Converts an RDD of nucleotide contig fragments into reads. Adjacent contig fragments are combined.

    returns

    Returns an RDD of reads.

35. def toString(): String

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36. final def wait(): Unit

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