feat: adding more annotations to output (#504)

[holtgrewe]

Summary by CodeRabbit

• New Features

  • Introduced new enumerations for TranscriptType and VariantLocation, enhancing data granularity related to transcript types and variant locations.
  • Updated the GeneRelatedConsequences message with new fields for transcript accession, version, and variant location.

• Improvements

  • Enhanced variant annotation and query processing with new logic for determining variant consequences and improved score handling.
  • Expanded score types and refined output structure for better clarity and consistency.

• Bug Fixes

  • Improved error handling in annotation and score querying processes.

[codecov]

Codecov Report

Attention: Patch coverage is 0.46948% with 212 lines in your changes missing coverage. Please review.

Project coverage is 71%. Comparing base (a9a2ae3) to head (ecf0f35).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
src/seqvars/query/mod.rs	0%	212 Missing ⚠️

Additional details and impacted files

@@          Coverage Diff           @@
##            main    #505    +/-   ##
======================================
- Coverage     73%     71%    -2%     
======================================
  Files         43      43            
  Lines      11648   11844   +196     
======================================
  Hits        8514    8514            
- Misses      3134    3330   +196     

Files with missing lines	Coverage Δ
src/seqvars/query/hpo.rs	97% <100%> (ø)
src/seqvars/query/mod.rs	9% <0%> (-2%)	⬇️

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📥 Commits

Files that changed from the base of the PR and between bce728e and ecf0f35.

Walkthrough

The pull request introduces significant enhancements to the protocol buffer definitions in output.proto, adding two new enumerations: TranscriptType and VariantLocation, which categorize transcript types and variant locations, respectively. Additionally, the GeneRelatedConsequences message is updated with new optional fields for transcript accession, version, and variant location. Changes in hpo.rs involve a minor adjustment in function parameter passing. The mod.rs file sees extensive updates to variant annotation processing, including new logic for handling variant consequences and score collection.

Changes

File Path	Change Summary
protos/varfish/v1/seqvars/output.proto	- Added enum TranscriptType with three types: unspecified, coding, non-coding. - Added enum VariantLocation with locations: upstream, exonic, intronic, downstream. - Updated GeneRelatedConsequences message to include new optional fields: tx_accession, tx_version, location, rank_ord, rank_total.
src/seqvars/query/hpo.rs	- Modified test_load_ncbi_to_hgnc function to pass path directly instead of &path.
src/seqvars/query/mod.rs	- Enhanced consequences function to determine variant locations and extract additional information. - Updated SingleValueCollector struct to include optional parameters for separator and max value computation. - Expanded VariantScoreColumn definitions to include new score types and refined output structure. - Improved error handling and updated test cases.

Possibly related PRs

• feat: add mode of inheritance from HPO #493: This PR adds a new enumeration ModeOfInheritance to the output.proto file, which is directly related to the changes made in the main PR that also modifies the output.proto file by adding new enumerations and fields related to genetic variants.

🐰 In the meadow, changes bloom,
New enums sprout, dispelling gloom.
With transcripts clear and scores refined,
Our data's richer, well-defined.
Hooray for variants, let’s all cheer,
For better insights, year by year! 🌼

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[coderabbitai]

Actionable comments posted: 7

🧹 Outside diff range and nitpick comments (1)

protos/varfish/v1/seqvars/output.proto (1)

197-200: Clarify the base index in documentation.

Please specify whether rank_ord is 0-based or 1-based in the field documentation. While the comment suggests it's 1-based, it's better to be explicit in the documentation.

-  // Exon/intron number (1-based).
+  // Exon/intron number (1-based, e.g., first exon has rank_ord=1).
   optional int32 rank_ord = 7;
   // Exon/intron total count.
   optional int32 rank_total = 8;

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 6b2d193 and bce728e.

📒 Files selected for processing (3)

• protos/varfish/v1/seqvars/output.proto (2 hunks)
• src/seqvars/query/hpo.rs (1 hunks)
• src/seqvars/query/mod.rs (9 hunks)

🔇 Additional comments (3)

src/seqvars/query/hpo.rs (1)

307-307: LGTM! Good improvement in ownership semantics.

The change from &path to path aligns with the function's signature which takes ownership via AsRef<std::path::Path>. This removes unnecessary borrowing while maintaining the same functionality, as the test doesn't need the path after the function call.

protos/varfish/v1/seqvars/output.proto (1)

159-167: LGTM! Well-structured enum definition.

The TranscriptType enum follows protobuf best practices with clear naming, proper documentation, and complete coverage of basic transcript types.

src/seqvars/query/mod.rs (1)

789-793: Ensure all fields are correctly initialized in GeneRelatedConsequences.

While constructing GeneRelatedConsequences, make sure that all optional fields are properly handled to avoid potential None values where not intended.

Please verify that all fields—tx_accession, tx_version, location, rank_ord, and rank_total—are correctly populated and that their optionality aligns with the protobuf definitions.