intspan 0.7.0

Command line tools for IntSpan related bioinformatics operations
Documentation 
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use clap::*;
use intspan::*;
use serde_yaml::Value;
use std::collections::BTreeMap;
use std::ffi::OsStr;
use std::path::Path;

// Create clap subcommand arguments
pub fn make_subcommand<'a>() -> Command<'a> {
    Command::new("merge")
        .about("Merge runlist yaml files")
        .arg(
            Arg::new("infiles")
                .help("Sets the input file to use")
                .required(true)
                .min_values(1)
                .index(1),
        )
        .arg(
            Arg::new("all")
                .long("all")
                .help("All parts of file_stem (aka basename), except the last one"),
        )
        .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 out_yaml: BTreeMap<String, Value> = BTreeMap::new();

    let is_all = args.is_present("all");

    for infile in args.values_of("infiles").unwrap() {
        let yaml = read_yaml(infile);

        let key = if is_all {
            Path::new(infile)
                .file_stem()
                .and_then(OsStr::to_str)
                .unwrap()
                .to_string()
        } else {
            Path::new(infile)
                .file_stem()
                .and_then(OsStr::to_str)
                .unwrap()
                .split('.')
                .next()
                .unwrap()
                .to_string()
        };
        out_yaml.insert(key, serde_yaml::to_value(yaml).unwrap());
    }

    //----------------------------
    // Output
    //----------------------------
    write_yaml(args.value_of("outfile").unwrap(), &out_yaml)?;

    Ok(())
}