A rust FFI library for minimap2. In development! Feedback appreciated!
minimap2-sys is the library of the raw FFI bindings to minimap2. minimap2 is the most rusty version.
toml
minimap2 = "0.1.10"
Also see Features
Tested with rustc 1.64.0 and nightly. So probably a good idea to upgrade before running. But let me know if you run into pain points with older versions and will try to fix!
bash
rustup update
Create an Aligner
rust
let mut aligner = Aligner::builder()
.map_ont()
.with_threads(8)
.with_cigar()
.with_index("ReferenceFile.fasta", None)
.expect("Unable to build index");
Align a sequence:
rust
let seq: Vec<u8> = b"ACTGACTCACATCGACTACGACTACTAGACACTAGACTATCGACTACTGACATCGA";
let alignment = aligner
.map(&seq, false, false, None, None)
.expect("Unable to align");
All minimap2 presets should be available (see functions section):
rust
let aligner = map_ont();
let aligner = asm20();
MapOpts and IdxOpts can be customized with Rust's struct pattern, as well as applying mapping settings. Inspired by bevy.
rust
Aligner {
mapopt: MapOpt {
seed: 42,
best_n: 1,
..Default::default()
},
idxopt: IdxOpt {
k: 21,
..Default::default()
},
..map_ont()
}
There is a binary called "fakeminimap2" that I am using to test for memory leaks. You can follow the source code for an example. It also shows some helper functions for identifying compression types and FASTA vs FASTQ files. I used my own parsers as they are well fuzzed, but open to removing them or putting them behind a feature wall.
Alignment functions return a Mapping struct. The Alignment struct is only returned when the Aligner is created using .with_cigar().
A very simple example would be: ```rust let mut file = std::fs::File::open(queryfile); let mut reader = BufReader::new(reader); let mut fasta = Fasta::frombuffer(&mut reader)
for seq in reader {
let seq = seq.unwrap();
let alignment: Vec
There is a map_file function that works on an entire file, but it is not-lazy and thus not suitable for large files. It may be removed in the future or moved to a separate lib.
rust
let mappings: Result<Vec<Mapping>> = aligner.map_file("query.fa", false, false);
Multithreading is supported, for implementation example see fakeminimap2. Minimap2 also supports threading itself, and will use a minimum of 3 cores for building the index. Multithreading for mapping is left to the end-user.
rust
let mut aligner = Aligner::builder()
.map_ont()
.with_threads(8);
The following crate features are available:
* mm2-fast - Replace minimap2 with mm2-fast. This is likely not portable.
* htslib - Support output of bam/sam files using htslib.
* map-file - Convenience function for mapping an entire file. Caution, this is single-threaded.
* simde - Compile minimap2 / mm2-fast with simd-everywhere support.
Follow these instructions.
In brief, using bash shell:
bash
docker pull messense/rust-musl-cross:x86_64-musl
alias rust-musl-builder='docker run --rm -it -v "$(pwd)":/home/rust/src messense/rust-musl-cross:x86_64-musl'
rust-musl-builder cargo build --release
Please note minimap2 is only tested for x86_64. Other platforms may work, please open an issue if minimap2 compiles but minimap2-rs does not.
Probably not freeing C memory somewhere.... Not sure yet, if so it's just leaking a little... Need to do a large run to test it.
You should cite the minimap2 papers if you use this in your work.
Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. [doi:10.1093/bioinformatics/bty191][doi]
and/or:
Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2]
Do not require libclang for normal compilation.
Multithreading support (use less raw pointers, and treat more like rust Struct's)
use libc instead of std:ffi::c_int as well
Support slightly older versions of rustc by using libc:: rather than std::ffi for c_char (Thanks dwpeng!)
