gtars-refget

Rust implementation of GA4GH refget sequence collection functions.

Features

• GA4GH refget protocol support
• Sequence digest computation (SHA512t24u and others)
• Sequence collection management
• FASTA file reading and writing
• Efficient sequence storage and retrieval

Modules

digest

Compute and verify sequence digests:

use gtars_refget::digest;

// Compute SHA512t24u digest for a sequence
let seq = b"ACGTACGTACGT";
let digest = digest::sha512t24u(seq);

collection

Manage sequence collections:

use gtars_refget::collection::SequenceCollection;

// Create and work with sequence collections
let mut collection = SequenceCollection::new();
// Add sequences, compute digests, etc.

store

Efficient sequence storage indexed by digest:

use gtars_refget::store::SequenceStore;

// Store and retrieve sequences by their digest
let store = SequenceStore::new();

fasta

Read and write FASTA files:

use gtars_refget::fasta;

// Parse FASTA files
// Write sequences to FASTA format

alphabet

Define sequence alphabets (DNA, protein, ASCII):

use gtars_refget::alphabet;

// Work with different sequence alphabets

Standards Compliance

Implements GA4GH refget specification for sequence collections and digests.

See also: the refget Python package builds on this crate. Its docs explain RefgetStore concepts and include tutorials: What is RefgetStore?