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Contributing to GenoLance

Thanks for your interest in GenoLance. This is a small, single-maintainer project that ships Apache-2.0 Rust tooling for fast, columnar multi-sample variant analysis on top of Lance.

Crates in this repo: genolance-core, genolance-variants, genolance-cli.

Before you open a PR

  • Open an issue first if the change is non-trivial (new API surface, schema change, new ingest/export semantics, dependency bump beyond a patch). For small fixes - typos, docs, minor bug fixes, additional tests - go straight to a PR.
  • Run cargo fmt --all and cargo clippy --all-targets -- -D warnings locally. CI will run them too.
  • Run cargo test --workspace.
  • Update CHANGELOG.md under ## [Unreleased] with a short bullet describing the user-visible change.
  • Keep commits small and prefer Conventional Commits (feat:, fix:, docs:, refactor:, test:, chore:).
  • Code is ASCII only and #![forbid(unsafe_code)].

Working with VCFs and ClinVar

GenoLance is validated against real DeepVariant WGS data (GRCh37, ~5.8M sites per sample) and several ClinVar builds. When changing ingest, query, or join semantics, please add a fixture-backed test that exercises the affected code path. Real-data smoke tests live under fixtures/ and tests/.

ClinVar VCFs are auto-detected by filename. Chromosome naming mismatch (chr1 vs 1) is normalized automatically, so GRCh37 sample VCFs join correctly against GRCh37 ClinVar builds - if you touch this, please test both directions.

Roundtrip guarantee

genolance export is verified byte-exact (modulo float QUAL trailing-zero formatting) on DeepVariant VCFs. If you change anything that touches the export path or per-row format_key_order storage, the roundtrip test in tests/ must continue to pass.

Security

Please report security vulnerabilities privately via GitHub Security Advisories - see SECURITY.md. Do not open public issues for vulnerabilities.

DCO

By submitting a contribution you certify that you have the right to submit the work under the project license (Apache-2.0) and agree to the Developer Certificate of Origin.

License

By submitting a PR you agree that your contribution is licensed under the Apache License 2.0, the same terms as the rest of the project.