Function create_plot_data

src/plot.rs:25–70

Generates the plot data for a given region of a bam file

(
    bam_path: P,
    ref_path: P,
    region: &Region,
    max_read_depth: usize,
    aux_tags: Option<Vec<String>>,
    mismatch_display_min_percent: f64,
)

/// Generates the plot data for a given region of a bam file
pub(crate) fn create_plot_data<P: AsRef<Path> + std::fmt::Debug>(
    bam_path: P,
    ref_path: P,
    region: &Region,
    max_read_depth: usize,
    aux_tags: Option<Vec<String>>,
    mismatch_display_min_percent: f64,
) -> Result<(Vec<EncodedRead>, Reference, usize, Coverage, usize)> {
    let mut bam = bam::IndexedReader::from_path(&bam_path)?;
    let tid = bam
        .header()
        .tid(region.target.as_bytes())
        .context(format!(
            "bam header does not contain given region target {}",
            &region.target
        ))
        .unwrap() as i32;
    bam.fetch(FetchRegion(tid, region.start, region.end))?;
    let mut data = bam
        .records()
        .filter_map(|r| r.ok())
        .filter_map(|r| {
            Read::from_record(r, &ref_path, &region.target, &aux_tags)
                .context(format!(
                    "bam file does not contain given region target {}",
                    &region.target
                ))
                .unwrap()
        })
        .collect_vec();
    let coverage = Coverage::from_reads(&data, region, mismatch_display_min_percent);
    let total_read_count = data.len();
    data.order(max_read_depth)?;
    let retained_reads = data.len();
    let reference_data = Reference {
        start: region.start,
        reference: read_fasta(ref_path, region)?.iter().collect(),
    };
    Ok((
        vec![EncodedRead::from_reads(data)],
        reference_data,
        total_read_count,
        coverage,
        retained_reads,
    ))
}

/// 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>> {