fix: suppress unknown consequence errors

[holtgrewe]

Summary by CodeRabbit

• New Features

  • Enhanced query functionality for structural and sequence variants, improving error handling and data processing.
  • Added new utility functions for computing transcript effects and managing gene information.
  • Introduced a smoke test to validate query functionality.

• Bug Fixes

  • Improved logging levels for better clarity during record processing.

• Refactor

  • Cleaned up code for better readability and maintainability, including restructuring function calls and removing unnecessary comments.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The pull request introduces several enhancements to the seqvars and strucvars modules, focusing on the ingest and query subcommands. Key changes include adjustments to logging levels, improvements in functionality and error handling, updates to the ResultPayload structure, and the encapsulation of database loading logic. Additionally, new utility functions and a smoke test have been added, alongside general code cleanup for better readability and maintainability.

Changes

File Path	Change Summary
src/seqvars/ingest/mod.rs	No significant changes reported.
src/seqvars/query/mod.rs	- Logging level changed from debug to trace in run_query. - Updated write_header for filtering and error handling. - Struct Args updated, function signatures modified for write_header and create_and_write_record.
src/strucvars/query/mod.rs	- Logging level changed from debug to trace in run_query. - Enhanced overlap logic in run_query. - Added InMemoryDbs struct. - New functions: load_databases, translate_genes. - Function signature of run updated. - Smoke test added.
src/strucvars/query/mod.rs	- Various utility functions added or modified for transcript effects and gene information management. - Code cleanup performed.

Possibly related PRs

• fix: suppress unknown consequence errors #491: This PR modifies the write_header function in src/seqvars/query/mod.rs, which is also updated in the main PR to enhance filtering logic, indicating a direct relationship in functionality and code changes.

Poem

In the burrow where code does play,
New functions hop and dance today.
With logs that trace and queries bright,
We enhance the code, oh what a sight!
Through tunnels of logic, we swiftly glide,
In the world of data, we take great pride! 🐇✨

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[codecov]

Codecov Report

Attention: Patch coverage is 22.22222% with 7 lines in your changes missing coverage. Please review.

Project coverage is 74%. Comparing base (501e6e0) to head (3197b96).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/seqvars/query/mod.rs	0%	7 Missing ⚠️

Additional details and impacted files

@@         Coverage Diff         @@
##           main   #492   +/-   ##
===================================
- Coverage    74%    74%   -1%     
===================================
  Files        42     42           
  Lines      7365   7366    +1     
===================================
  Hits       5470   5470           
- Misses     1895   1896    +1     

Files with missing lines	Coverage Δ
src/seqvars/ingest/mod.rs	88% <100%> (ø)
src/strucvars/query/mod.rs	54% <100%> (ø)
src/seqvars/query/mod.rs	15% <0%> (-1%)	⬇️