Development

Useful checks

Run Rust tests:

cargo test --workspace

Run command matrix validation:

python3 tools/verify_command_matrix.py

Run documentation locally:

python3 -m venv .venv-docs
. .venv-docs/bin/activate
pip install -r docs/requirements.txt
sphinx-build -b html docs docs/_build/html

Documentation rules of thumb

Write for computational biologists and bioinformaticians first:

  • show real Picard-style commands;

  • name file formats directly, such as BAM, SAM, FASTQ, VCF, FASTA, and interval lists;

  • separate native coverage from fallback coverage;

  • connect performance claims to parity evidence;

  • avoid requiring Rust knowledge for normal user workflows.