phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Adding the ability to handle "complex" point mutations #172

Closed emarinier closed 1 year ago

emarinier commented 1 year ago

Adds the ability for starAMR to handle "complex" point mutations. That is, mutations where several individual point mutations are simultaneously required to confer a phenotype.

The solution has been created for Enterococcus faecium, but the framework should allow other similar mutations to be added to the "complex_mutations.tsv" file and handled in the same way.

emarinier commented 1 year ago

Updated the changelog in 2c7307c.

apetkau commented 1 year ago

Can you merge in the latest development to fix merge conflicts?

emarinier commented 1 year ago

Merge conflict should be resolved now.

emarinier commented 1 year ago

Good catch, as always!

I think the issue was the complex mutation logic always assumed there would be existing results to extend, but sometimes there's no results. I added some logic to catch this.