Function read_fasta

src/plot.rs:73–85

Reads the given region from the given fasta file and returns it as a vec of the bases as chars

(path: P, region: &Region)

/// Reads the given region from the given fasta file and returns it as a vec of the bases as chars
fn read_fasta<P: AsRef<Path> + std::fmt::Debug>(path: P, region: &Region) -> Result<Vec<char>> {
    let mut reader = fasta::IndexedReader::from_file(&path).unwrap();
    let index =
        fasta::Index::with_fasta_file(&path).context("error reading index file of input FASTA")?;
    let _sequences = index.sequences();

    let mut seq: Vec<u8> = Vec::new();

    reader.fetch(&region.target, region.start as u64, region.end as u64)?;
    reader.read(&mut seq)?;

    Ok(seq.iter().map(|u| char::from(*u)).collect_vec())
}

/// A Read containing all relevant information for being plotted in a read plot
#[derive(Serialize, Debug, PartialEq, Eq)]