intspan 0.7.0

Command line tools for IntSpan related bioinformatics operations
Documentation 
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use clap::*;
use intspan::*;
use std::io::BufRead;

// Create clap subcommand arguments
pub fn make_subcommand<'a>() -> Command<'a> {
    Command::new("paf2ovlp")
        .about("Convert minimap .paf to overlaps")
        .arg(
            Arg::new("infiles")
                .help("Sets the input file to use")
                .required(true)
                .min_values(1)
                .index(1),
        )
        .arg(
            Arg::new("outfile")
                .short('o')
                .long("outfile")
                .takes_value(true)
                .default_value("stdout")
                .forbid_empty_values(true)
                .help("Output filename. [stdout] for screen"),
        )
}

// command implementation
pub fn execute(args: &ArgMatches) -> std::result::Result<(), Box<dyn std::error::Error>> {
    //----------------------------
    // Loading
    //----------------------------
    let mut writer = writer(args.value_of("outfile").unwrap());

    for infile in args.values_of("infiles").unwrap() {
        let reader = reader(infile);
        for line in reader.lines().filter_map(|r| r.ok()) {
            let ovlp = Overlap::from_paf(&line);

            //----------------------------
            // Output
            //----------------------------
            writer.write_all((ovlp.to_string() + "\n").as_ref())?;
        }
    }

    Ok(())
}