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ga4gh / vrs-python

GA4GH Variation Representation Python Implementation
https://github.com/ga4gh/vrs
Apache License 2.0
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feat: refactor hgvsTools and support `c.` translation #366

Closed larrybabb closed 8 months ago

larrybabb commented 8 months ago

Address #365

Begin refactoring the Translator logic to aggregate the functions and logic related to hgvs and provide support for c. from and to translation. This should be step in the direction of re-thinking the organization of how the Translators are architected.

jsstevenson commented 8 months ago

It would be nice, albeit out of scope here, if the generic dataproxy interface that's redefined (copied?) in VRS-Python from seqrepo was located in a more central package so that we don't do any damage by making these changes here without mirroring them back to their origin

korikuzma commented 8 months ago

@larrybabb can you pull in changes from main branch and resolve conflicts first?

larrybabb commented 8 months ago

@korikuzma @jsstevenson @ahwagner could you please try to prioritize reviewing this PR? The primary purpose of it was to get support for the c. nomenclature working. I also reverted the hgvs branch dependency that we introduced and will localize our version of it until that hgvs branch is officially merged and a new release is created. I started to consolidate all the hgvs-related logic in the hgvs_tools class, but deferred making any larger strategic design changes until we can meet as a team and agree on what and when we need to do there.

korikuzma commented 8 months ago

@larrybabb I am in the middle of reviewing 😄 James is PTO today, but he did an initial review already

jsstevenson commented 8 months ago

@larrybabb as Kori said, I'm out for at least today (which will probably entail some frantic catch-up once I'm back) but for the sake of pragmatism, we can assume my approval once Kori's additional notes above are addressed