agc-rs

Rust bindings for AGC (Assembled Genomes Compressor).

Overview

This crate provides safe Rust bindings to the AGC C++ library, allowing you to read compressed genome collections from Rust programs.

Features

• Read access to AGC archives
• List samples and contigs
• Fetch sequence regions
• Thread-safe operations

Usage

use agc_rs::AGCFile;

let mut agc = AGCFile::new();
agc.open("genomes.agc", true)?;

// List all samples
let samples = agc.list_samples();

// Get a sequence region
let sequence = agc.get_contig_sequence("sample1", "chr1", 100, 200)?;

Building

This crate includes vendored AGC source code and will build it automatically. Just run:

cargo build

The build process will:

1. Use the vendored AGC source in the agc/ directory
2. Build the AGC library if not already built
3. Link against the built library

Updating AGC source

To update the vendored AGC source code from upstream:

./vendor-agc.sh

This will download the latest AGC v3.2.1 release and all its dependencies.

Alternative build methods

If you have AGC installed elsewhere, you can:

1. Use a system-wide installation (if installed to /usr/local)
2. Set the AGC_DIR environment variable:

   export AGC_DIR=/path/to/agc
   cargo build

Requirements

• C++20 compatible compiler
• CMake
• zstd library

License

MIT License (same as AGC)