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 = "0.8.0"
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(())
}
```
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
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.