`veff.py` has no unit tests

[RajdeepKushwaha5]

I noticed veff.py (~620 lines) has zero unit tests — everything else in the codebase is well covered.

I'd like to add tests for the Annotator.get_effects() method covering the main effect categories (synonymous/non-synonymous SNPs, frameshifts, in-frame indels, UTR, splice sites). The tests would use small synthetic genes with zarr genomes so they run fast and don't need GCS access.

Would this be a useful contribution? And should I avoid the two TODO branches (#916, #1132) since those are being worked on separately?

[Tanisha127]

Hi @jonbrenas, I'd like to work on this. I've looked through veff.py and plan to add tests for Annotator.get_effects() covering synonymous/non-synonymous SNPs, frameshifts, in-frame indels, UTR, and splice site variants using synthetic fixtures (no GCS access needed). I'll skip the TODO branches (#916, #1132) since those are being handled separately.
Happy to coordinate with @RajdeepKushwaha5 if needed. Would you be okay for me to proceed?

[jonbrenas]

Hi @RajdeepKushwaha5, @Tanisha127, you can certainly add unit tests for veff.py, if you want.

[RajdeepKushwaha5]

hi @jonbrenas -thanks for the update!
Since I'm not working on this for GSoC and i'm currently focused on another organisation.
I'm happy to step back and let @Tanisha127 proceed.
I'll keep an eye on the PR and offer help if needed, but no need to coordinate with me for now.
Good luck!

[kunal-10-cloud]

Hi @jonbrenas, I have raised a PR(#1188) for this issue. Whenever you are available, please review it and let me know if any changes are required.