rustynetics 0.1.4

// Copyright (C) 2024 Philipp Benner
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the “Software”), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.

use std::error::Error;
use std::process;

use clap::{Arg, Command};

use rustynetics::bigwig::BigWigFile;
use rustynetics::track_statistics::{bin_summary_statistics_from_string, BinSummaryStatistics};

/* -------------------------------------------------------------------------- */

fn query(
    filename_in: &str,
    chrom: &str,
    from: usize,
    to: usize,
    bin_size: usize,
    bin_overlap: usize,
    summary: BinSummaryStatistics,
    verbose: bool,
) -> Result<(), Box<dyn Error>> {
    if verbose {
        eprintln!("Opening bigWig file {}", filename_in);
    }

    // Open BigWig file
    let mut reader = BigWigFile::new_reader(filename_in).unwrap_or_else(|err| {
        eprintln!("Error opening file: {}", err);
        process::exit(1);
    });

    // Query BigWig file
    let result = reader.query_slice(chrom, from, to, summary, bin_size, bin_overlap, f64::NAN)?;

    println!("{:?}", result.0);

    Ok(())
}

/* -------------------------------------------------------------------------- */

fn main() {
    let matches = Command::new("BigWig Query")
        .version("1.0")
        .about("Query BigWig files")
        .arg(
            Arg::new("input")
                .help("The input BigWig file")
                .required(true),
        )
        .arg(
            Arg::new("chrom")
                .help("The chromosome to query")
                .required(true),
        )
        .arg(Arg::new("from").help("The start position").required(true))
        .arg(Arg::new("to").help("The end position").required(true))
        .arg(
            Arg::new("binsize")
                .help("The bin size for the query")
                .required(true),
        )
        .arg(
            Arg::new("bin-overlap")
                .long("bin-overlap")
                .default_value("0")
                .help("Number of overlapping bins when computing the summary"),
        )
        .arg(
            Arg::new("bin-summary")
                .long("bin-summary")
                .default_value("mean")
                .help("Bin summary statistic [mean, max, min]"),
        )
        .arg(
            Arg::new("verbose")
                .short('v')
                .long("verbose")
                .action(clap::ArgAction::SetTrue)
                .help("Be verbose"),
        )
        .get_matches();

    let filename_in = matches.get_one::<String>("input").unwrap();
    let chrom = matches.get_one::<String>("chrom").unwrap();
    let from = matches
        .get_one::<String>("from")
        .unwrap()
        .parse::<usize>()
        .unwrap_or_else(|_| {
            eprintln!("Invalid start position");
            process::exit(1);
        });
    let to = matches
        .get_one::<String>("to")
        .unwrap()
        .parse::<usize>()
        .unwrap_or_else(|_| {
            eprintln!("Invalid end position");
            process::exit(1);
        });
    let bin_size = matches
        .get_one::<String>("binsize")
        .unwrap()
        .parse::<usize>()
        .unwrap_or_else(|_| {
            eprintln!("Invalid bin size");
            process::exit(1);
        });
    let bin_overlap = matches
        .get_one::<String>("bin-overlap")
        .unwrap()
        .parse::<usize>()
        .unwrap();
    let summary_str = matches.get_one::<String>("bin-summary").unwrap();
    let verbose = matches.get_flag("verbose");

    let summary = bin_summary_statistics_from_string(summary_str).unwrap_or_else(|| {
        eprintln!("Invalid bin summary statistic. Choose from: mean, max, min");
        process::exit(1);
    });

    if let Err(e) = query(
        filename_in,
        chrom,
        from,
        to,
        bin_size,
        bin_overlap,
        summary,
        verbose,
    ) {
        eprintln!("{}", e);
        process::exit(1);
    }
}