A library for interacting with SLOW5/BLOW5 files in the Rust programming language.

For more information check out the main slow5lib repository or the paper.

This repository provides two crates:

• slow5lib-sys: Bindings to the C library using bindgen
• slow5: Rust API built on-top of slow5lib-sys

The interface for slow5 is largely stable and now updated primarily to follow new versions slow5lib. If there is additional functionality you'd like to see, please file a Github Issue.

Add the following to your Cargo.toml:

[dependencies]
slow5 = "0.12"

If you'd like to download the git version, use the following command to download the repo

git clone --recursive https://github.com/bsaintjo/slow5-rs.git

use slow5::{FileReader, RecordExt};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let mut slow5 = FileReader::open("examples/example.slow5").unwrap();
    for record in slow5.records() {
        for signal in record?.picoamps_signal_iter() {
            // Do stuff
        }
    }
    Ok(())
}

use std::error::Error;
use slow5::{FileWriter, SignalCompression, Record};

fn main() -> Result<(), Box<dyn Error>> {
    let tmp_dir = std::env::temp_dir();
    let output = tmp_dir.join("test.blow5");
    let mut writer = FileWriter::options()
        .signal_compression(SignalCompression::StreamVByte)
        .attr("attribute", "value", 0)
        .create(output)?;
    let rec = Record::builder()
        .read_id("test_id")
        .read_group(0)
        .digitisation(4096.0)
        .offset(4.0)
        .range(12.0)
        .sampling_rate(4000.0)
        .raw_signal(&[0, 1, 2, 3])
        .build()?;
    writer.add_record(&rec)?;
    writer.close();
    Ok(())
}

For more example code, see the test code. Several examples from the original library have been ported to rust and can be found in the examples directory.

• zstd: Enable zstd-based compression
  • enabled by default
• zlib-ng: Enable usage of high performance zlib-ng
  • adds cmake dependency
• serde: Enable serde dependency
  • Mainly for serializing Record into serde-compatible formats

Licensed under either of

• Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
• MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)

at your option.

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.