Module core 

Core data types for reference genome identification.

This module provides the fundamental types used throughout the library:

• contig::Contig: Represents a single sequence/chromosome with name, length, and optional MD5
• header::QueryHeader: A sequence dictionary extracted from a BAM/SAM/CRAM file
• reference::KnownReference: A reference genome definition from the catalog
• types::ReferenceId, types::Assembly, types::ReferenceSource: Reference metadata types
• types::MatchType, types::Confidence: Result classification types

Contig Naming

Different reference sources use different naming conventions:

Source	Chromosome 1	Mitochondrial
UCSC	chr1	chrM
NCBI	1	MT
Ensembl	1	MT

Matching uses exact names - name equivalence is defined only through explicit aliases (from SAM AN tag or NCBI assembly reports).

Modules

assembly

Hierarchical assembly types for the catalog.

contig

header

reference

types