ODGI-FFI

A safe, ergonomic, and high-performance Rust wrapper for the odgi pangenome graph tool.

Overview

odgi-ffi provides idiomatic Rust bindings to the powerful odgi C++ library. It allows Rust developers to safely and efficiently load, query, and manipulate pangenome variation graphs. The library handles the complexity of the C++/Rust boundary, offering a clean API that abstracts away unsafe FFI calls.

This crate is ideal for bioinformaticians and developers who want to build high-performance pangenome analysis tools in Rust while leveraging the mature, feature-rich odgi ecosystem.

Features

• Safe Graph Handling: Load .odgi files into a memory-safe Graph struct.
• Comprehensive Graph Queries:
  • Get node counts, sequences, and lengths.
  • List all path names within the graph.
  • Traverse the graph by finding node successors and predecessors.
  • Identify which paths step on a specific node.
• Coordinate Projection: Project nucleotide positions on a path to their corresponding graph node and offset.
• File Format Conversion: Includes utilities to convert between GFA and ODGI formats by leveraging the bundled odgi executable.
• Thread Safety: The Graph object is Send + Sync, allowing it to be safely shared across threads for parallel processing.

Getting Started

Prerequisites

This crate compiles the odgi C++ library from source. To successfully build odgi-ffi, you must have a C++ build environment installed on your system. This includes:

• A C++17 compliant compiler (e.g., g++ or clang++)
• CMake (version 3.10 or higher)
• make

On Debian/Ubuntu, you can install these with:

sudo apt-get update && sudo apt-get install build-essential cmake

Installation

Add odgi-ffi as a dependency in your Cargo.toml file:

[dependencies]
odgi-ffi = "1.0.8"

Ask the AI

The combined_file.txt file contains all the source code contained in the /src folder. Just copy paste the entire contents of this file in your favorite LLM and ask questions like "Explain how this system works." or "How can I make an interactive pangenome visualization tool using this crate?" etc.

Usage

The primary entry point of this library is the Graph struct. The typical workflow involves loading an .odgi file and then using the Graph methods to inspect it.

If your data is in GFA format, you can first convert it using the provided gfa_to_odgi function.

Complete Example

Here is a complete example that demonstrates converting a GFA file, loading the resulting ODGI graph, and performing several queries.

use odgi_ffi::{gfa_to_odgi, Graph};
use std::io::Write;
use tempfile::NamedTempFile;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    // 1. Create a temporary GFA file for demonstration.
    let mut gfa_file = NamedTempFile::new()?;
    writeln!(gfa_file, "H\tVN:Z:1.0")?;
    writeln!(gfa_file, "S\t1\tGATTACA")?;
    writeln!(gfa_file, "S\t2\tT")?;
    writeln!(gfa_file, "L\t1\t+\t2\t+\t0M")?;
    writeln!(gfa_file, "P\tx\t1+,2+\t*")?;
    let gfa_path = gfa_file.path();

    // 2. Define a path for the output ODGI file.
    let odgi_file = NamedTempFile::new()?;
    let odgi_path = odgi_file.path();

    // 3. Convert the GFA file to ODGI format.
    gfa_to_odgi(gfa_path.to_str().unwrap(), odgi_path.to_str().unwrap())?;
    println!("Successfully converted GFA to ODGI.");

    // 4. Load the ODGI graph into memory.
    let graph = Graph::load(odgi_path.to_str().unwrap())?;
    println!("Graph loaded successfully!");

    // 5. Perform queries on the graph.
    assert_eq!(graph.node_count(), 2);
    println!("Node count: {}", graph.node_count());

    let path_names = graph.get_path_names();
    assert_eq!(path_names, vec!["x"]);
    println!("Path names: {:?}", path_names);

    let seq = graph.get_node_sequence(1);
    assert_eq!(seq, "GATTACA");
    println!("Sequence of node 1: {}", seq);

    // Projecting position 7 on path "x" should land at the start of node 2 (0-based).
    let position = graph.project("x", 7).unwrap();
    assert_eq!(position.node_id, 2);
    assert_eq!(position.offset, 0);
    println!("Position 7 on path 'x' projects to node {} at offset {}", position.node_id, position.offset);
    
    Ok(())
}

API Reference

The core of the library is the odgi_ffi::Graph struct. Below is a summary of its main methods. For detailed information, please refer to the official documentation on docs.rs.

Conversion Utilities

• gfa_to_odgi(gfa_path, odgi_path): Converts a GFA file to an ODGI file.
• odgi_to_gfa(odgi_path, gfa_path): Converts an ODGI file back to a GFA file.

Building from Source

To build the project locally, clone the repository and use Cargo. Make sure you have the prerequisites installed.

# Clone the repository
git clone https://github.com/caelrith/odgi-ffi.git
cd odgi-ffi

# Build the project
cargo build --release

# Run tests
cargo test

The build script (build.rs) automatically handles the following:

1. Copies the vendored odgi C++ source code to a temporary build directory.
2. Invokes cmake to compile odgi and its dependencies.
3. Makes the odgi executable path available as an environment variable (ODGI_EXE).
4. Configures Cargo to link against the compiled static libraries.
5. Builds the C++ FFI wrapper code using cxx.

Contributing

Contributions are welcome! If you find a bug, have a feature request, or want to contribute code, please open an issue or a pull request on our GitHub repository.

License

This project is licensed under the MIT License.