ADAMNucleotideContigFragmentRDDFunctions

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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

8. def adamRewriteContigIds(sequenceDict: SequenceDictionary): RDD[ADAMNucleotideContigFragment]

   Rewrites the contig IDs of a FASTA reference set to match the contig IDs present in a different sequence dictionary.

   Rewrites the contig IDs of a FASTA reference set to match the contig IDs present in a different sequence dictionary. Sequences are matched by name.

   sequenceDict

   A sequence dictionary containing the preferred IDs for the contigs.

   returns

   New set of contigs with IDs rewritten.

   Note

   Contigs with names that aren't present in the provided dictionary are filtered out of the RDD.

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15. def getSequenceRecordsFromElement(elem: ADAMNucleotideContigFragment): 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

    ADAMNucleotideContigFragmentRDDFunctions → ADAMSequenceDictionaryRDDAggregator

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