pandora_lib_promethion/src/io/gff.rs

use anyhow::Context;
use noodles_gff as gff;

use crate::{config::Config, positions::GenomeRange};

use super::readers::get_gz_reader;

pub fn features_ranges(feature_type: &str, config: &Config) -> anyhow::Result<Vec<GenomeRange>> {
    let path = &config.refseq_gff;
    let mut reader = get_gz_reader(path)
        .map(gff::io::Reader::new)
        .with_context(|| format!("Error while creating the reader of {path}"))?;

    let mut res = Vec::new();
    for result in reader.record_bufs() {
        let record = result?;
        let ty = record.ty();
        if ty != feature_type {
            continue;
        }

        res.push(GenomeRange::from_1_inclusive(
            record.reference_sequence_name(),
            record.start().get() as u32,
            record.end().get() as u32,
        ));
    }
    Ok(res)
}