v2.1.3

Fixes for gbkToPkl to ensure functionality
Full Changelog: v2.1.2...v2.1.3

v2.1.2

Bump gumpy version to ensure bug fix

v2.1.1

What's Changed

• Add version flag by @JeremyWesthead in #29
• Added pushing to OCR as well as dockerhub for GPAS by @JeremyWesthead in #30
• Added s3fs req by @JeremyWesthead in #32
• gene_name --> gene in variants.csv for #33 by @JeremyWesthead in #34
• Added error handling to temporarily appease oxfordmmm/gumpy#24 by @JeremyWesthead in #35

Full Changelog: v2.1.0...v2.1.1

v2.1.0

What's Changed

• Fix pickled genome issue by @JeremyWesthead in #17
• Bug fixes by @JeremyWesthead in #20
• Ensure all values are properly converted to null by @JeremyWesthead in #21
• Fix for #22 by @JeremyWesthead in #24
• Fix for minor indel nc changes by @JeremyWesthead in #25

Full Changelog: v2.0.0...v2.1.0

v2.0.0

What's Changed

• Large deletions by @JeremyWesthead in #12
• Cicd docs by @JeremyWesthead in #14
• Minor aa fixes by @JeremyWesthead in #15

Full Changelog: v1.1.3...v2.0.0

v1.1.3

What's Changed

• Various improvements to tests. Now at 100% coverage by @JeremyWesthead in #7
• Fixed minority populations. Added extra tests for these by @JeremyWesthead in #8
• Add minor index parsing to the CLI script + various pandas index fixes by @JeremyWesthead in #9
• Explictly type cast pandas DataFrames to avoid FutureWarnings by @JeremyWesthead in #10

Full Changelog: v1.1.2...v1.1.3

v1.1.2

Bump gumpy version
This pulls in a bug fix which was causing erroneous InvaluidMutationException to be raised when a deletion started in a promoter and passed the gene end

v1.1.1

Updates to docker action to wait for PyPi to update before using it to build the new container

v1.1.0

Removal of an unused argument to populateEffects causing a non-backwards compatible API change.

v1.0.2

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.