1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
extern crate regex;
extern crate statistical;
extern crate getopts;
use std::env;
use std::path::Path;
use getopts::Options;
pub mod io;
pub fn ross_base_options() -> Options{
let mut opts = Options::new();
opts.optflag("h", "help", "Print this help menu.");
opts.optopt("n","numcpus","Number of CPUs (default: 1)","INT");
opts.optflag("p","paired-end","The input reads are interleaved paired-end");
opts.optflag("v","verbose","Print more status messages");
return opts;
}
pub fn logmsg(msg: &str) {
let args: Vec<_> = env::args().collect();
let program = Path::file_name(Path::new(&args[0])).unwrap().to_str().unwrap();
eprintln!("{}: {}", &program, &msg);
}