Rust 2024 edition. Standard Cargo commands:
cargo build # debug build
cargo build --release # release build
cargo test # run all tests
cargo clippy # lint (zero warnings expected)
cargo fmt --check # formatting checkCI runs on Linux (x86_64, x86-64-v3, aarch64), macOS (aarch64), and Windows (x86_64). PRs must pass all CI checks before merging.
Small synthetic and yeast test data lives in test/. Integration tests in tests/ use the synthetic genome. Differential testing against STAR reference outputs is done via test/compare_sam.py and test/compare_pe.py.
rustar-aligner was written as a faithful port of STAR by Alexander Dobin. Up to the initial release, the goal was behavioral parity with STAR — matching its algorithms, thresholds, and output formats as closely as possible. Notes from that development phase are in docs-old/ (docs-old/dev/ and the phase*.md files).
Future development is not bound by that constraint. Adding STARsolo, new features, or diverging from STAR behavior is entirely welcome.
The user-facing docs site is an Astro Starlight project under docs/:
cd docs
pnpm install
pnpm dev # local dev server
pnpm build # production build into docs/dist/Content lives under docs/src/content/docs/ as Markdown / MDX files with YAML frontmatter (title, description). Sidebar order is configured in docs/astro.config.mjs. Site-wide design tokens (colours, fonts, graph-paper background, wave dividers) live in docs/src/styles/custom.css and can be tuned in one place.
MIT, matching the original STAR license.