cgDist v0.1.2

Maintenance release focused on installation, documentation, and reproducibility — making cgDist easier to install on current toolchains and its validation suite easier to reproduce from a fresh clone. The distance algorithms and their numerical results are unchanged from 0.1.1.

Changed

• Clarified the minimum supported Rust version and install guidance (latest stable Rust; cargo install cgdist --locked).
• Documented the recombination-candidate workflow through its supported path: an enriched cache (--enrich-lengths) analysed by recombination_candidate_analyzer; cache inspection via cgdist --inspector.
• Hardened CLI input validation, error messages, and detailed-alignment output (--save-alignments).

Added

• A self-contained validation suite that runs in CI on every push — covering distance-mode correctness, cache consistency, the recombination-candidate workflow, filtering / missing-data / output-format behaviour, and a smoke-test over every CLI argument.

Install

docker pull ghcr.io/genpat-it/cgdist:0.1.2
# or from source (needs Rust >= 1.88):
cargo install --git https://github.com/genpat-it/cgDist --tag v0.1.2 --locked cgdist

cgDist v0.1.1

Highlights

• Default --threads is now 1 (previously implementation-defined). Pass --threads 0 for auto-detect.
• Hamming fallback is now opt-in via --hamming-fallback.
• CLI flag rename, with deprecated aliases for backward compatibility:
  • --recombination-log → --candidate-recombination-log
  • --recombination-threshold → --candidate-recombination-threshold
• Binary rename, with a deprecation shim for the old name:
  • recombination_analyzer → recombination_candidate_analyzer
• README rewritten: new badges (MSRV, Zenodo concept DOI, bioRxiv); the recombination section is reframed as Recombination-Candidate Flagging with an explicit disclaimer that cgDist is not a recombination detector and that confirmation requires phylogeny-aware tools (Gubbins, ClonalFrameML, fastGEAR).
• Validation suite reproducible from a fresh clone.
• New GitHub Actions workflow runs cargo fmt --check, cargo clippy -D warnings, cargo test, a four-mode validation smoke test, and Docker image build/push to GHCR.
• Wide round of cargo clippy autofixes (no behaviour change).
• Cargo.toml metadata extended (MSRV, homepage, documentation, keywords, categories).
• New CHANGELOG.md (Keep a Changelog format).

Install

cargo install --git https://github.com/genpat-it/cgDist --tag v0.1.1 cgdist

See CHANGELOG.md for the full list of changes.

cgDist v0.1.0

Archived release of cgDist for scientific publication.

cgDist: Nucleotide-Level Distance Calculation from cgMLST Allelic Profiles

This release corresponds to the implementation described in our manuscript.

Key Features

• SNP and InDel-level distance calculation from cgMLST allelic profiles
• Unified cache architecture for incremental surveillance
• Multi-mode distance calculations (SNPs-only, SNPs+InDel-events, SNPs+InDel-bases)
• Integrated recombination detection

Citation

bioRxiv preprint: https://doi.org/10.1101/2025.10.16.682749

Links

• GitHub repository: https://github.com/genpat-it/cgDist
• Documentation: See README.md