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:

toml [dependencies] slow5 = "0.3.1"

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

Example

Getting record by id

rust 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

```rust use std::error::Error;

fn iteratingexample() -> Result<(), Box> { let filepath = "examples/example.slow5"; let mut slow5file = slow5::Builder::default() .picoamps(true) .open(filepath)?; let mut reciter = slow5file.seqreads(); while let Some(Ok(slow5rec)) = reciter.next() { // Iterate over every read for signal in slow5rec.signal_iter() { // Iterate over signal measurements in pA } } Ok(()) } ```

TODO

• [x] Read slow5 file
• [ ] Write slow5 file
• [x] Iterating over records
• [x] 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.