Upgrade amrfinderplus to 4.0.3 #96
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This was referenced Dec 30, 2024
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This upgrades AFP to latest version (4.0.3) in Conda, closing #95, and likely also #91.
It converts both nucleotide and protein detections. These can be interspersed in a single report, so this needed a change to the way field mappings are handled. I've kept the change minimal, but we may want to refactor it later (see the TODO in the code).
Note a few ResFinder fixes had piggybacked onto this PR, now gone to another branch. I force pushed a rewind, so please re-pull if you already had this branch locally.