slow5-rs

A library for interacting with SLOW5 files in rust.

Note: Library design is in flux and care should be taken in upgrading this crate.

Installation

Add the following to your Cargo.toml:

[dependencies]
slow5 = "0.3.1"

Note: version does not directly translate to version of slow5lib.

Example

Getting record by id

fn get_by_read_id() {
    let file_path = "examples/example.slow5";
    let mut slow5_file = slow5::Builder::default().open(file_path).unwrap();
    let record = slow5_file.get_read(b"r3").unwrap();
    assert_eq!(b"r3", record.read_id());
}

Iterating over records sequentially

use std::error::Error;

fn iterating_example() -> Result<(), Box<dyn Error>> {
    let file_path = "examples/example.slow5";
    let mut slow5_file = slow5::Builder::default()
        .picoamps(true)
        .open(file_path)?;
    let mut rec_iter = slow5_file.seq_reads();
    while let Some(Ok(slow5_rec)) = rec_iter.next() {
        // Iterate over every read
        for signal in slow5_rec.signal_iter() {
            // Iterate over signal measurements in pA
        }
    }
    Ok(())
}

TODO

• Read slow5 file
• Write slow5 file
• Iterating over records
• Iterating over raw or picoamp measurements
• Parity with pyslow5
• Read blow5 file (haven't tested)
• Reading headers
• Reading aux info

License

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.

Contribution

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.