cgdist 0.1.1

Ultra-fast SNP/indel-level distance calculator for core genome MLST analysis
Documentation 
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// mod.rs - Core logic module

pub mod alignment;
pub mod distance;
// pub mod recombination; // Disabled - pluggable system not needed for now

// Re-export main types for convenience
pub use alignment::{compute_alignment_stats, AlignmentConfig, DetailedAlignment, DistanceMode};
pub use distance::{calculate_distance_matrix, calculate_sample_distance, DistanceEngine};
// pub use recombination::{
//     RecombinationDetector, RecombinationResult, RecombinationDetectorConfig,
//     RecombinationDetectorFactory, ThresholdDetector, PhiTestDetector, RMRatioDetector
// };