slow5-rs

A library for interacting with SLOW5 files in rust. Not official.

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 = "0.10"

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

Git

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

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

Getting started

Reading signal from SLOW5 file

```rust use slow5::{FileReader, RecordExt};

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

Writing a compressed BLOW5 file with attributes

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

fn main() -> Result<(), Box> { let tmpdir = std::env::tempdir(); let output = tmpdir.join("test.blow5"); let mut writer = FileWriter::options() .signalcompression(SignalCompression::StreamVByte) .attr("attribute", "value", 0) .create(output)?; let rec = Record::builder() .readid("testid") .readgroup(0) .digitisation(4096.0) .offset(4.0) .range(12.0) .samplingrate(4000.0) .rawsignal(&[0, 1, 2, 3]) .build()?; writer.addrecord(&rec)?; writer.close(); Ok(()) } ```

Feature flags

• 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)

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.