rust-yara

Rust FFI bindings for the YARA read mapper.

Overview

rust-yara provides safe Rust bindings for the YARA read mapper, a fast and accurate read mapper based on the SeqAn2 C++ library. The workspace supports both building FM indices from FASTA reference files and mapping paired-end reads against a pre-built index — all from Rust, without SAM serialization/deserialization overhead.

Crate Structure

Prerequisites

• Rust stable toolchain (see rust-toolchain.toml for the pinned version)
• zlib development headers
• OpenMP:
  • macOS: brew install libomp
  • Linux: libgomp (typically included with GCC; install libomp-dev if using Clang)

Quick Start

Add yara-mapper to your Cargo.toml:

cargo add yara-mapper

Build an index and map reads:

use yara_mapper::{IndexerOptions, MapperOptions, ReadBatch, YaraIndexer, YaraMapper};

// Build an index from a FASTA file.
let indexer = YaraIndexer::build("ref.fasta", "ref", &IndexerOptions::default()).unwrap();
println!("Indexed {} contigs", indexer.contig_count());

// Open the index and map reads.
let mapper = YaraMapper::open("ref", &MapperOptions::default()).unwrap();
let mut batch = ReadBatch::new();
batch.push("read1", b"ACGTACGT", b"IIIIIIII", b"TGCATGCA", b"IIIIIIII").unwrap();
let records = mapper.map_paired(&batch).unwrap();
for rec in &records {
    println!("contig={} pos={} mapq={}", rec.contig_id, rec.pos, rec.mapq);
}

Examples

Build an FM index from a FASTA reference:

cargo run --example build_index -- ref.fasta ref

Map reads against a pre-built index:

cargo run --example align -- ref

Building from Source

cargo build                  # debug build
cargo clippy --all-targets   # lint
cargo fmt --check            # format check

To use a local SeqAn2 checkout instead of the vendored headers, set SEQAN_DIR:

export SEQAN_DIR=/path/to/seqan

License

This project is licensed under the MIT License.

The vendored SeqAn2 headers and YARA application sources are licensed under the BSD 3-Clause License — see yara-seqan2-sys/vendor/include/seqan/LICENSE and yara-seqan2-sys/vendor/apps/yara/LICENSE.

Contributing

See CONTRIBUTING.md for development setup and guidelines.