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varfish-org / varfish-server-worker

Rust-based background worker for varfish-server
MIT License
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feat: adding more annotations to output (#504) #505

Closed holtgrewe closed 1 month ago

holtgrewe commented 1 month ago

Summary by CodeRabbit

codecov[bot] commented 1 month ago

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 :warning:
Additional details and impacted files ```diff @@ 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](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/505?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org) | Coverage Δ | | |---|---|---| | [src/seqvars/query/hpo.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/505?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Fhpo.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvaHBvLnJz) | `97% <100%> (ø)` | | | [src/seqvars/query/mod.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/505?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Fmod.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvbW9kLnJz) | `9% <0%> (-2%)` | :arrow_down: |
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📥 Commits Files that changed from the base of the PR and between bce728ea5f9544f9d66b5a1d2e4748a15ea78912 and ecf0f35e275e08810533b0eaef93eed0e8598bd3.

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

🐰 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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