Core library lives in src/, organized by domain: collection (sample discovery), pipes and runners (pipeline orchestration), callers (tool interfaces), annotation and variant (VEP parsing, variant models), commands (external tool wrappers), io/helpers/functions (utilities), modkit, and math.
jq_filters/ holds jq modules used by the JSON post-processing examples in README.md.
pandora-config.example.toml documents runtime settings; copy and adapt for local runs. Build outputs land in target/.
Build, Test, and Development Commands
cargo build — compile the library; ensure system deps like minimap2, samtools, dorado, bcftools, modkit, and VEP are available for runtime pipelines.
cargo test -- --nocapture — run tests with stdout; set RUST_LOG=debug when debugging pipelines.
cargo fmt and cargo clippy -- -D warnings — format and lint; run before sending a PR.
cargo doc --open — generate local docs to understand module APIs.
Coding Style & Naming Conventions
Rust 2021 edition; use 4-space indentation and snake_case for functions/vars, PascalCase for types, SCREAMING_SNAKE_CASE for consts.
Prefer anyhow::Result with the ? operator; avoid unwrap() in pipeline code—propagate errors with context.
Keep modules focused (e.g., orchestration in runners, IO logic in io, stats in math/variant). Add small comments when wiring external tools or Docker/Slurm behaviors.
Testing Guidelines
Existing integration tests expect access to shared test data at the path in TEST_DIR (see src/lib.rs). If unavailable, skip or point to local fixtures when adding new tests.
Co-locate unit tests with their modules using Rust’s #[cfg(test)] blocks; name tests after the behavior under check (e.g., loads_bam_metadata, filters_low_quality_variants).
Before proposing changes, run cargo test and note any environment-specific assumptions (e.g., tool availability, data paths).
Commit & Pull Request Guidelines
Commit messages are short and imperative (e.g., add somatic stats export, fix dorado pod5 paths).
PRs should include: purpose, key changes, commands run (build/test), and any pipeline outputs or log snippets that validate tool integration.
Document new external tool requirements or config keys in README.md and update pandora-config.example.toml when adding settings.
Keep changes atomic: separate refactors from functional changes, and prefer small, reviewable diffs.
