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biocommons / hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
https://hgvs.readthedocs.io/
Apache License 2.0
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`Normalizer.normalize()` is performing sequence position validation which cannot be skipped #705

Open mihaitodor opened 11 months ago

mihaitodor commented 11 months ago

The code here tests whether the sequence position actually exists, but there isn't any way to skip this test which requires fetching sequence data. Would it not make sense to skip it when the validate parameter is set to False? Also, I see there's a TODO in there which I guess should also be addressed (but not sure how):

# tests whether the sequence position actually exists
# This is *way* janky.
# TODO: push functionality to hdp which can implement differently
# based on capabilities of sequence backend
github-actions[bot] commented 10 months ago

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

mihaitodor commented 10 months ago

Bump

github-actions[bot] commented 7 months ago

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

github-actions[bot] commented 6 months ago

This issue was closed because it has been stalled for 7 days with no activity.