fix: allow multiple references in mehari server run

[tedil]

Support multiple references in mehari server run, e.g.

mehari server run \
  --transcripts GRCh38-ensembl.bin.zst \
  --transcripts GRCh37-ensembl.bin.zst \
  --reference GCF_000001405.40_GRCh38.p14_genomic.fna \
  --reference GCF_000001405.25_GRCh37.p13_genomic.fna

Note that this relies on the strings "GRCh38" or "GRCh37" to be present in the file path (the check is done on lowercase strings) at the moment, i.e. there is no sophisticated logic for matching the --transcripts to the --reference (and also no cli based matching, e.g. something along the lines of --transcripts GRCh38=foo.bin.zst --transcripts GRCH37=bar.bin.zst --reference GRCh38=baz.fasta --reference GRCh37=etc).

Resolves #716

Summary by CodeRabbit

• New Features

  • Added support for specifying multiple reference genome files.
  • Improved informational logging to display loaded data sources and predictor build status.

• Bug Fixes

  • Enhanced validation to ensure the number of reference genomes matches supported genome releases, providing clearer error messages.

• Documentation

  • Clarified requirements for reference genome file names in user-facing documentation.

[coderabbitai[bot]]

Walkthrough

The changes update the handling of reference genome paths in the server's run module. The Args struct's reference field now accepts multiple paths instead of a single optional path, with added documentation specifying that paths must contain "GRCh37" or "GRCh38" for correct matching. The run function validates that the number of provided references matches supported genome releases or is zero, and matches each reference to its genome release by filename. Logging improvements and warnings are included for unmatched references, and the annotator construction now uses the matched reference path per genome release.

Changes

File(s)	Change Summary
src/server/run/mod.rs	Changed Args.reference from Option<PathBuf> to Vec<PathBuf>, updated documentation, implemented logic for matching multiple reference genome paths to genome releases, added validation, improved logging, and updated annotator construction to use per-release reference paths.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Server
    participant Annotator

    User->>Server: Start with Args (multiple reference paths)
    Server->>Server: Validate reference count vs genome releases
    Server->>Server: For each genome release, match reference path by name
    Server->>Annotator: Build ConsequenceAnnotator with matched reference path
    Server->>Server: Log loaded sources
    Server-->>User: Complete setup or return error

Possibly related PRs

• varfish-org/mehari#684: Adds support for specifying a single reference FASTA and in-memory loading, including changes to annotator construction and reference genome handling, directly related to the new multi-reference input logic.

Poem

A rabbit hopped through code so bright,
Matching genomes left and right—
With many paths now in its pack,
It finds the right one, never looks back.
Logs are clearer, warnings sound,
Genome releases all around!
🐇✨

✨ Finishing Touches

• [ ] 📝 Generate Docstrings

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