slow5 0.8.1

Library for interacting with slow5
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111

# slow5-rs

[![License][license-badge]][license-url]
[![Crates.io][crates-badge]][crates-url]
[![docs.rs][docs-badge]][docs-url]
[![Rust][ci-badge]][ci-url]
![Stability][stability-badge]
[![codecov][codecov-badge]][codecov-url]

[license-badge]: https://img.shields.io/crates/l/slow5?style=flat-square
[license-url]: https://github.com/bsaintjo/slow5-rs#license
[crates-badge]: https://img.shields.io/crates/v/slow5?style=flat-square
[crates-url]: https://crates.io/crates/slow5
[docs-badge]: https://img.shields.io/docsrs/slow5?style=flat-square
[docs-url]: https://docs.rs/slow5
[ci-badge]: https://github.com/bsaintjo/slow5-rs/actions/workflows/rust.yml/badge.svg
[ci-url]: https://github.com/bsaintjo/slow5-rs/actions/workflows/rust.yml
[codecov-badge]: https://codecov.io/gh/bsaintjo/slow5-rs/branch/main/graph/badge.svg?token=MODXRVRNQ0
[codecov-url]: https://codecov.io/gh/bsaintjo/slow5-rs
[stability-badge]: https://img.shields.io/badge/stability-experimental-orange.svg

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 = "0.8"
```

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<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(())
}
```

### Writing a compressed BLOW5 file with attributes

```rust
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(())
}
```

## TODO

- [ ] Allow optional dependency on zlib and zstd
- [ ] Handle string, array and enum auxiliary fields
- [ ] Allow for configuring slow5lib log level
- [ ] Check for thread safety

## License

Licensed under either of

- Apache License, Version 2.0, ([LICENSE-APACHE](LICENSE-APACHE) or <http://www.apache.org/licenses/LICENSE-2.0>)
- MIT license ([LICENSE-MIT](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.