// the sg (synthetic genome) subcommand
the sg (synthetic genome) subcommand
the sg ( synthetic genome ) subcommand
fn sg_sc() -> App<'static, 'static> {
    SubCommand::with_name("sg")
        .about("Generate a synthetic reference genome without any transposons by removing ones found by the TE mapper")
        .arg(
            Arg::with_name("Reference")
                .long("ref")
                .takes_value(true)
                .value_name("FILE")
                .help("the path to the reference sequence FASTA file (relative or absolute)")
                .required(true),
        )
        .arg(
            Arg::with_name("Transposons File")
                .long("transposons")
                .takes_value(true)
                .value_name("FILE")
                .help("the path to the file containing the transposons found by the TE mapper")
        )
        .arg(
            Arg::with_name("Result Directory")
            .long("result")
            .takes_value(true)
            .value_name("DIR")
            .help("the path to the directory where results (a TSV file containing the found transposons as well as some intermediate files) will be stored (relative or absolute)")
            .required(true),
        )
}
fn sg_sc ( ) -> App < ' static , ' static > { SubCommand :: with_name ( " " ) . about ( " " ) . arg ( Arg :: with_name ( " " ) . long ( " " ) . takes_value ( true ) . value_name ( " " ) . help ( " " ) . required ( true ) , ) . arg ( Arg :: with_name ( " " ) . long ( " " ) . takes_value ( true ) . value_name ( " " ) . help ( " " ) ) . arg ( Arg :: with_name ( " " ) . long ( " " ) . takes_value ( true ) . value_name ( " " ) . help ( " " ) . required ( true ) , ) }
the sg (synthetic genome) subcommand
the sg ( synthetic genome ) subcommand