Module catalog 

Reference genome catalog storage and indexing.

The catalog contains definitions of known human reference genomes with their contigs, MD5 checksums, and metadata. An embedded catalog is compiled into the binary, but custom catalogs can also be loaded from JSON files.

Embedded Catalog

The default catalog includes common reference genomes:

• GRCh38/hg38: UCSC, NCBI, Broad analysis set, DRAGEN, hs38, hs38DH
• GRCh37/hg19: UCSC, NCBI, Broad b37, hs37d5
• T2T-CHM13: Complete telomere-to-telomere assembly

Example

use ref_solver::ReferenceCatalog;
use ref_solver::core::types::ReferenceId;

// Load embedded catalog
let catalog = ReferenceCatalog::load_embedded().unwrap();

// List all references
for reference in &catalog.references {
    println!("{}", reference.id);
}

// Get a specific reference
let hg38 = catalog.get(&ReferenceId::new("hg38_ucsc"));

Custom Catalogs

Custom catalogs can be created by exporting and modifying the embedded catalog:

use ref_solver::ReferenceCatalog;
use std::path::Path;

// Export to JSON
let catalog = ReferenceCatalog::load_embedded().unwrap();
let json = catalog.to_json().unwrap();

// Load from custom file
let custom = ReferenceCatalog::load_from_file(Path::new("my_catalog.json")).unwrap();

Modules

builder

Reference builder for creating catalog entries from multiple input sources.

hierarchical

Hierarchical catalog structure for assemblies and distributions.

index

store