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@jermp jermp released this 01 Jul 14:52
· 96 commits to master since this release
v3.0.0
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Learn about vigilant mode.

This release of the library features a restructured public API for the dictionary and its supported queries.

  • "Advanced" lookup queries now include, besides the usual absolute kmer_id: contig information (contig_id and contig_size of the contig where the k-mer lies in), the relative (within the contig) identifier of the k-mer (named kmer_id_in_contig), and the orientation of the k-mer in the contig. For any positive query, 0 <= kmer_id_in_contig < contig_size holds true.
  • Streaming queries are now general, not just streaming membership queries as they were in the previous releases, and return advanced lookup information by default.
  • Support for Navigational queries has been added. Given a k-mer g[1..k], a navigational query determines if g[2..k]+x is present (forward neighbourhood) and if x+g[1..k-1] is present (backward neighbourhood) in the dictionary, for x = A, C, G, T ('+' here means string concatenation).
    If a contig identifier is specified for a navigational query (rather than a k-mer), then the backward neighbourhood of the first k-mer and the forward neighbourhood of the last k-mer in the contig are returned.
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