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Pathogen-Genomics-Cymru / lodestone

Mycobacterial pipeline
GNU Affero General Public License v3.0
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Bovis miscategorised as MTB #104

Open WhalleyT opened 1 week ago

WhalleyT commented 1 week ago

Sample Mycobacterium_bovis_BCG_Danish_1331_r250_e0_m0_24070812 is being flagged as MTB because Afanc identifies this sample as Bovis, however, the top hit is named Mycobacterium tuberculosis variant bovis BCG therefore the regex is ID-ing it as MTB

WhalleyT commented 1 week ago

see also use of lineage names e.g. La1 being bovis

WhalleyT commented 1 week ago

Testing. Added in a lineage dictionary for the La1 example. 520d757, then extended regex for "variant bovis" in 599b88a

WhalleyT commented 6 days ago

Tentatively, this seems to work. Sorting a bug about ntm profiler when condition before PR