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BrucellaID 2.1.1

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@duceppemo duceppemo released this 08 Nov 20:42
· 14 commits to main since this release

The quality assurance report no longer shows the biovars recorded for a sample's sequence type. The
Biovars of its isolates row is gone from each sample's evidence block, in both the HTML and the PDF.

The reason is the shape of the data rather than the idea. Of the 118 sequence types in the shipped table,
42 have a single biovar on record and 59 have none, so on about a third of samples the row rendered one
bare value — 2:60 — beside that sample's own species and sequence type. That reads as a biovar call,
which is how the reference-genome biovar column came to be misread before 1.1.0 removed it. The 17 sequence
types that record several biovars did convey the ambiguity well, but they were the minority.

Nothing measured is lost. The counts stay in the packaged mlst_st_species.tsv, in a custom
--st-species table, and in brucellaid.json. The reference genomes' own biovars stay in
brucellaid_mash.tsv, where they are facts about the references rather than calls about the sample. The
report's methods section still sets out why no biovar can be measured — 7 of the 432 references carry one,
the two B. suis biovar 2 genomes sit further apart than the biovar 3 genome is from one of them, and the
best any sequence-type-to-biovar rule manages over the isolate database is 66% — and now says plainly that
this is why it shows none at all.

Also in this release:

  • The wiki's biovar explanation is cut to one short treatment under
    How it works, where it had grown
    to seven places and about forty lines of argument for something the tool does not do.
  • 393 tests, 100% statement and branch coverage. One is new, and asserts the row is absent from both
    reports while the fixture still carries biovars, so it cannot come back unnoticed.

No identification changes: the species call, the sequence type, the distances and the shared-hash counts
are all as in 2.1.0.