refactor: moving all variant coordinates to GnomAD

[DSuveges]

✨ Context

The variant mapping of the curated GWAS Catalog dataset is done via the REST API of Ensembl. This process uses +1 based numbering for indels, however GnomAD uses 0 based numbering. As we don't have complete allele set for the curated data, we only know if an associated variant is an indel if it is grounded to GnomAD.

So far the current implementation contained logic to permanently change the indel coordinates to Ensembl of the GnomAD variant annotation. This also affected the LD index generation. All this causing a series of complications across the board. More context here: #3274

🛠 What does this PR implement

• Removing gnomadVariantId column from variant annotation. gnomadVariantId is the variant id.
• utils.convert_gnomad_position_to_ensembl moved to datasource/gwas_catalog/associations.py as that function is no longer universal. (doctest updated)
• Logic to change coordinates in the variant annotation step removed.
• Logic to change coordinates in the LD index step removed.

🙈 Missing

These steps were not yet re-run. Also the LD index generation needs to be refactored to not do liftover but use the provided variant b38 mapping.

🚦 Before submitting

• Do these changes cover one single feature (one change at a time)?
• Did you read the contributor guideline?
• Did you make sure to update the documentation with your changes?
• Did you make sure there is no commented out code in this PR?
• Did you follow conventional commits standards in PR title and commit messages?
• Did you make sure the branch is up-to-date with the dev branch?
• Did you write any new necessary tests?
• Did you make sure the changes pass local tests (make test)?
• Did you make sure the changes pass pre-commit rules (e.g poetry run pre-commit run --all-files)?

[d0choa]

Code looks more clear than the alternative coordinate system.
We shouldn't forget about the "missing" section regarding LD index. cc @Daniel-Considine
Thanks

[d0choa]

Suggested change

# ensemblPosition column is dropped. Only the GnomAD position is kept.