twitcher 0.1.8

Find template switch mutations in genomic data
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use std::{path::Path, pin::Pin};

use anyhow::Context;
use bstr::{BStr, ByteSlice};
use rust_htslib::bcf::Record;
use tokio::io::{AsyncWrite, AsyncWriteExt, BufWriter};

enum RegionsFormat {
    Bed,
    Tab,
}

pub struct RegionWriter {
    writer: Pin<Box<dyn AsyncWrite + Send>>,
    format: RegionsFormat,
}

impl RegionWriter {
    pub async fn from_parameter(param: Option<&str>) -> anyhow::Result<Option<Self>> {
        if let Some(param) = param {
            let rw = if param == "-" {
                let writer = Box::pin(tokio::io::stdout());
                RegionWriter {
                    writer,
                    format: RegionsFormat::Tab,
                }
            } else {
                let file = tokio::fs::File::create(param).await?;
                let writer = Box::pin(BufWriter::new(file));
                let format = if Path::new(param)
                    .extension()
                    .is_some_and(|ext| ext.eq_ignore_ascii_case("bed"))
                {
                    RegionsFormat::Bed
                } else {
                    RegionsFormat::Tab
                };
                RegionWriter { writer, format }
            };
            Ok(Some(rw))
        } else {
            Ok(None)
        }
    }

    pub async fn write<'a>(
        &mut self,
        records: impl DoubleEndedIterator<Item = &'a Record>,
    ) -> anyhow::Result<()> {
        let (reg, pos, end) = self
            .get_coordinates(records)
            .with_context(|| "Couldn't extract coordinates")?;
        eprintln!("Now writing regions ...");
        self.writer
            .write_all(format!("{reg}\t{pos}\t{end}\n").as_bytes())
            .await?;
        Ok(())
    }

    pub async fn flush(&mut self) -> std::io::Result<()> {
        self.writer.flush().await
    }

    fn get_coordinates<'a>(
        &self,
        mut records: impl DoubleEndedIterator<Item = &'a Record>,
    ) -> Option<(&'a BStr, i64, i64)> {
        let first = records.next()?;
        let header = first.header();
        let rstr = header.rid2name(first.rid()?).ok()?.as_bstr();
        let pos_0_incl = first.pos();
        let end_0_excl = records.next_back().unwrap_or(first).end();
        let (pos, end) = match self.format {
            RegionsFormat::Bed => (pos_0_incl, end_0_excl),
            RegionsFormat::Tab => (pos_0_incl + 1, end_0_excl /* + 1 - 1 */),
        };
        Some((rstr, pos, end))
    }
}