slow5-rs

A library for interacting with SLOW5 files in rust.

Usage

Add the following to your Cargo.toml:

[dependencies]
slow5 = "0.1.0"

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)?;
    for slow5_read in slow5_file.seq_reads() {
        // Iterate over every read
        if let Ok(result) = slow5_read {
            for signal in result.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