Crate cgdist 

cgdist - High-performance SNP/indel-level distance calculator for core genome MLST analysis

This library provides a high-performance implementation for calculating genetic distances between bacterial samples using core genome MLST (cgMLST) data. It supports multiple hashing algorithms and is compatible with chewBACCA allele calling.

Features

• High performance: Optimized parallel processing and caching
• Plugin system: Support for CRC32, SHA256, MD5, and custom hashers
• Multiple formats: TSV, CSV, PHYLIP, NEXUS output formats
• Flexible filtering: Sample and loci filtering with regex and file lists
• Quality control: Configurable thresholds for data completeness
• chewBACCA compatible: Full backward compatibility with existing workflows

Basic Usage

use cgdist::prelude::*;

// Load allelic profiles with CRC32 hasher (chewBACCA compatible)
let matrix = AllelicMatrix::from_file_with_hasher(
    std::path::Path::new("profiles.tsv"),
    "-",  // missing character
    "crc32",  // hasher type
    0.0,  // sample threshold
    0.0,  // locus threshold
    None, None, None, None,  // filters
    None, None, None, None,
)?;

// Calculate distances
let engine = DistanceEngine::new(AlignmentConfig::default(), "crc32".to_string());
let distances = calculate_distance_matrix(
    &matrix.samples,
    &matrix.loci_names,
    &engine,
    DistanceMode::SnpsOnly,
    0,  // min loci
    false,  // hamming fallback
);

Re-exports

pub use cli::Args;

pub use cli::ValidationResult;

pub use core::AlignmentConfig;

pub use core::DistanceEngine;

pub use core::DistanceMode;

pub use data::AllelicMatrix;

pub use data::AllelicProfile;

pub use data::SequenceDatabase;

pub use data::SequenceInfo;

pub use hashers::AlleleHash;

pub use hashers::AlleleHashPair;

pub use hashers::AlleleHasher;

pub use hashers::HasherRegistry;

Modules

cli

core

data

hashers

output

prelude

Constants

VERSION

Library version

Functions

get_info

Get library information