refactor!: more protobuf cleaning

[holtgrewe]

Release-As: 0.16.0

Summary by CodeRabbit

• New Features

  • Enhanced clarity in frequency settings with renamed fields for maximum counts and frequencies in both Nuclear and Mitochondrial Frequency Settings.

• Bug Fixes

  • Updated frequency filtering logic to utilize new field names for improved consistency and clarity.

• Tests

  • Adjusted test cases to reflect the new field names, ensuring accurate assertions in frequency settings.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The changes in this pull request focus on renaming fields in the NuclearFrequencySettings and MitochondrialFrequencySettings messages across three files: query.proto, frequency.rs, and query.rs. The renaming aims to enhance clarity by changing field names such as heterozygous to max_het, homozygous to max_hom, and frequency to max_af. These changes are reflected in the respective structures, function parameters, and logic for filtering frequency data, while the overall functionality remains unchanged.

Changes

File Path	Change Summary
protos/varfish/v1/seqvars/query.proto	Renamed fields in NuclearFrequencySettings and MitochondrialFrequencySettings for clarity: heterozygous to max_het, homozygous to max_hom, hemizygous to max_hemi, and frequency to max_af.
src/seqvars/query/interpreter/frequency.rs	Updated passes function and related test functions to use renamed fields: max_het, max_hom, and max_af.
src/seqvars/query/schema/query.rs	Renamed fields in structs NuclearFrequencySettings and MitochondrialFrequencySettings for clarity: heterozygous to max_het, homozygous to max_hom, and frequency to max_af.

Possibly related PRs

• feat: add mode of inheritance from HPO #493: The changes in this PR involve renaming fields in the NuclearFrequencySettings and MitochondrialFrequencySettings structs, which directly relate to the renaming of fields in the same messages in the main PR.

🐰 In the meadow where changes bloom,
Fields renamed to lift the gloom.
Max counts now clear, no need to fret,
Clarity shines, a safe bet!
With every hop, we celebrate,
New names bring joy, oh, isn't it great? 🌼

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71%. Comparing base (0edcf98) to head (28da9b4).
Report is 1 commits behind head on main.

Additional details and impacted files

@@          Coverage Diff          @@
##            main    #511   +/-   ##
=====================================
- Coverage     71%     71%   -1%     
=====================================
  Files         43      43           
  Lines      11834   11831    -3     
=====================================
- Hits        8504    8501    -3     
  Misses      3330    3330           

Files with missing lines	Coverage Δ
src/seqvars/query/interpreter/frequency.rs	85% <100%> (-1%)	⬇️
src/seqvars/query/schema/query.rs	96% <100%> (ø)