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@JeremyWesthead JeremyWesthead released this 22 Sep 11:22
· 293 commits to main since this release

Due to changes to gumpy, this had to be updated to match.

When a synonymous mutation is found, there may be cases in which it is important to know specifically which nucleotides in the codon changed. For example, in the WHO catalogue, fabG1@L203L has three different predictions depending on which nucleotides are changed:
If the change is fabG1@g609a, it confers R
If the change is fabG1@c607t, it confers U
If the change is anything else, it should confer S due to the default rule gene@*= confers S

Therefore an update was made to include the nucleotide changes within each synonymous mutation. Within the WHO catalogue, this takes the form of all synonymous mutations being converted to multi-mutations with their nucleotide variants. This allows the above to be represented within single rows:
fabG1@L203L&fabG1@g609a confers R
fabG1@L203L&fabG1@c607t confers U
fabG1@L203L confers S

gumpy was then updated to match this logic - pulling out such nucleotide variants for all synonymous mutations.

Within gnomonicus then, this results in nucleotide variants being mixed into the MUTATIONS in such cases, but these are excluded from the EFFECTS in every case other than when the associated multi-mutation lies within the catalogue. The result is that the nucleotide is never considered as a stand-alone mutation for the sake of EFFECTS, but is included as part of a multi-mutation iff the catalogue specifies this.