slow5 0.12.1

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

use anyhow::Result;
use assert_fs::TempDir;
use slow5::{FieldType, FileWriter, Record};

fn main() -> Result<()> {
    let persist = std::env::var_os("PERSIST").is_some();
    let tmp_dir = TempDir::new()?.into_persistent_if(persist);
    if persist {
        println!("{}", tmp_dir.path().display());
    }
    let file_path = tmp_dir.join("test.slow5");
    let mut slow5 = FileWriter::options()
        .attr("run_id", "run_0", 0)
        .attr("asic_id", "asic_id_0", 0)
        .aux("median", FieldType::Float)
        .create(file_path)?;

    let rec = set_record_fields(&mut slow5)?;
    slow5.add_record(&rec)?;
    slow5.close();

    println!("Success!");
    tmp_dir.close()?;
    Ok(())
}

fn set_record_fields(writer: &mut FileWriter) -> Result<Record> {
    let raw_signal = (0..10).collect::<Vec<_>>();
    let mut rec = Record::builder()
        .read_id("read_0")
        .read_group(0)
        .range(12.0)
        .digitisation(4096.)
        .offset(3.0)
        .sampling_rate(4000.)
        .raw_signal(&raw_signal)
        .build()?;
    rec.set_aux_field(writer, "median", 1.2f32)?;
    Ok(rec)
}

#[cfg(test)]
mod test {
    use super::*;

    #[test]
    fn test() {
        main().unwrap()
    }
}