twitcher 0.1.8

Find template switch mutations in genomic data
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use crate::{
    common::{list_of_regions::Regions, reference::ReferenceReader},
    vcf::pipeline::{clusterizer::ClusterSettings, message::Message},
};
use std::fmt::Debug;

use clusterizer::Clusterizer;
use tokio::sync::mpsc;
use writer::Writer;

use crate::vcf::pipeline::{
    reader::VCFReader,
    writer::{OutputWriter, region_writer::RegionWriter},
};

pub mod clusterizer;
mod message;
pub mod reader;
pub mod writer;

#[derive(clap::Args, Debug)]
pub struct PipelineSettings {
    #[command(flatten)]
    pub cluster: clusterizer::ClusterSettings,

    #[arg(long = "buffer", default_value_t = 8192)]
    pub buffer_size: usize,
}

impl Default for PipelineSettings {
    fn default() -> Self {
        Self {
            cluster: ClusterSettings::default(),
            buffer_size: 8192,
        }
    }
}

pub async fn run(
    input: VCFReader,
    output: OutputWriter,
    reference: ReferenceReader,
    targets: Option<Regions>,
    region_output: Option<RegionWriter>,
    settings: PipelineSettings,
    bam_f: Option<rust_htslib::bam::IndexedReader>,
) -> anyhow::Result<()> {
    // TODO do some pre-checks on the input
    // 1. Is there more than one sample?
    // 2. Is the GT generally diploid?

    let aligner_settings = settings.cluster;

    let (tx, rx) = mpsc::channel(settings.buffer_size);
    tokio::spawn(async move {
        let c = Clusterizer::new(input, reference, targets, bam_f, tx, aligner_settings);
        c.run().await;
    });

    // We run the writer on the main thread, as when it completes we can exit.
    let w = Writer::new(rx, output, region_output);
    w.run().await?;

    Ok(())
}