ref_solver/core/mod.rs
1//! Core data types for reference genome identification.
2//!
3//! This module provides the fundamental types used throughout the library:
4//!
5//! - [`contig::Contig`]: Represents a single sequence/chromosome with name, length, and optional MD5
6//! - [`header::QueryHeader`]: A sequence dictionary extracted from a BAM/SAM/CRAM file
7//! - [`reference::KnownReference`]: A reference genome definition from the catalog
8//! - [`types::ReferenceId`], [`types::Assembly`], [`types::ReferenceSource`]: Reference metadata types
9//! - [`types::MatchType`], [`types::Confidence`]: Result classification types
10//!
11//! ## Contig Naming
12//!
13//! Different reference sources use different naming conventions:
14//!
15//! | Source | Chromosome 1 | Mitochondrial |
16//! |--------|--------------|---------------|
17//! | UCSC | chr1 | chrM |
18//! | NCBI | 1 | MT |
19//! | Ensembl| 1 | MT |
20//!
21//! Matching uses **exact names** - name equivalence is defined only through explicit
22//! aliases (from SAM AN tag or NCBI assembly reports).
23
24pub mod assembly;
25pub mod contig;
26pub mod header;
27pub mod reference;
28pub mod types;