Upgrade amrfinderplus to 4.0.3 #96
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
zwets
force-pushed
the
upgrade-amrfinderplus
branch
from
37dffac to
5a6d274
Compare
This was referenced Dec 30, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.