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bihealth / auto-acmg

Automatic classification of sequence variants and CNVs according to ACMG criteria.
GNU General Public License v3.0
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Adapt methods of `SeqVarPVS1Helper` to new annonars pydantic models #55

Closed gromdimon closed 6 months ago

gromdimon commented 7 months ago

Is your feature request related to a problem? Please describe. We need more consistency in such methods as _lof_is_frequent_in_population and _lof_removes_more_then_10_percent_of_protein after we implement real annonars pydantic models.

Describe the solution you'd like Migrate to new annonars models. Correct the counting of pathogenic variants in _critical4protein_function Correct the counting of LOF variants in _lof_is_frequent_in_population

Describe alternatives you've considered N/A

Additional context Good for implementation with #41

gromdimon commented 6 months ago

Should be implemented after #63

gromdimon commented 6 months ago

This methods were corrected in #63 since tests were failing otherwise. However, we have to increase code coverage for this methods