noodles-util 0.79.0

//! Queries an alignment file with the given region.
//!
//! The input must have an associated index in the same directory.
//!
//! The result matches the output of `samtools view [--reference <fasta-src>] <src> <region>`.

use std::{
    env,
    io::{self, BufWriter},
};

use noodles_fasta as fasta;
use noodles_sam::{self as sam, alignment::io::Write};
use noodles_util::alignment;

const UNMAPPED: &str = "*";

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let mut args = env::args().skip(1);

    let src = args.next().expect("missing src");
    let raw_region = args.next().expect("missing region");
    let fasta_src = args.next();

    let mut builder = alignment::io::indexed_reader::Builder::default();

    if let Some(fasta_src) = fasta_src {
        let repository = fasta::io::indexed_reader::Builder::default()
            .build_from_path(fasta_src)
            .map(fasta::repository::adapters::IndexedReader::new)
            .map(fasta::Repository::new)?;

        builder = builder.set_reference_sequence_repository(repository);
    }

    let mut reader = builder.build_from_path(src)?;
    let header = reader.read_header()?;

    let query: Box<dyn Iterator<Item = io::Result<Box<dyn sam::alignment::Record>>>> =
        if raw_region == UNMAPPED {
            reader.query_unmapped(&header).map(Box::new)?
        } else {
            let region = raw_region.parse()?;
            reader.query(&header, &region).map(Box::new)?
        };

    let stdout = io::stdout().lock();
    let mut writer = sam::io::Writer::new(BufWriter::new(stdout));

    for result in query {
        let record = result?;
        writer.write_alignment_record(&header, &record)?;
    }

    Ok(())
}