unum

unum is a pure-Rust HLA/KIR genotyper — a port of T1K that rebuilds its kmer-based genotyping pipeline in Rust. It started as a byte-identical port, validated by differential-testing against the original C++ implementation, but has since diverged from T1K with deliberate bug fixes and improvements. Owning the port lets us correct T1K's latent bugs and improve behavior where unum can do better; every such divergence is tracked in docs/DIVERGENCES.md. Much of the original byte-for-byte parity remains frozen into self-contained golden/unit tests, and unum has no C++ dependency.

Visit us at Fulcrum Genomics to learn more about how we can power your bioinformatics with unum and beyond.

Note: the badge/logo URLs above point at fg-labs/unum; adjust them if the repository lands under a different path.

Subcommands

• unum build — build reference FASTAs from an IPD-IMGT/HLA or IPD-KIR .dat database and a genome GTF.
• unum extract — extract candidate reads from FASTQ or BAM/CRAM input against a reference.
• unum genotype — call a genotype from candidate reads against a reference.

Building

cargo build

The build is pure Rust with no C++ dependency — unum-core and unum never invoke a C++ compiler.

Development

CI runs three gates, each wired to a cargo alias in .cargo/config.toml so they are identical locally and in CI (both under the toolchain pinned in rust-toolchain.toml):

cargo ci-fmt    # rustfmt --check
cargo ci-lint   # clippy with -D warnings and the project's pedantic set
cargo ci-test   # the nextest suite

To catch format/lint failures before they reach CI, enable the shared pre-push hook once per clone:

git config core.hooksPath .githooks

This runs cargo ci-fmt and cargo ci-lint on every git push (bypass a single push with git push --no-verify). Worktrees inherit the setting, but core.hooksPath is per-clone, so run the command again in any freshly cloned checkout.

Divergences from T1K

unum began as a byte-identical port but intentionally diverges from T1K where it can be more correct or robust. Each divergence — what changed, why, and the T1K source it departs from — is recorded in docs/DIVERGENCES.md.

License

MIT — see LICENSE.

This project is a Rust port of, and derives from, T1K (MIT, © Li Song, Bo Li, Heng Li).