ross 0.1.7

A set of scripts to run basic analysis on fastq files
Documentation 
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extern crate getopts;
extern crate ross;
use std::fs::File;
use std::io::BufReader;

use ross::ross_base_options;
use ross::io::fastq;
use ross::io::seq::Cleanable;
use ross::logmsg;

use std::env;

#[test]
/// Test to see whether we read the challenge dataset correctly
fn challenge_dataset () {
    // Open the difficult file
    let challenge_file = File::open("testdata/four_reads.gt_16_lines.fastq").expect("Could not open testdata/four_reads.gt_16_lines.fastq");
    let challenge_buffer=BufReader::new(challenge_file);
    let challenge_reader=fastq::FastqReader::new_careful(challenge_buffer);
    let mut challenge_string = String::new();
    for seq_obj in challenge_reader {
        challenge_string.push_str(&seq_obj.to_string());
    }

    // Open the easy file
    let easy_file  = File::open("testdata/four_reads.fastq").expect("Could not open testdata/four_reads.fastq");
    let easy_buffer= BufReader::new(easy_file);
    let easy_reader=fastq::FastqReader::new(easy_buffer);
    let mut easy_string = String::new();
    for seq_obj in easy_reader {
        easy_string.push_str(&seq_obj.to_string());
    }
    
    assert_eq!(challenge_string,easy_string);
}


fn main(){
    let args: Vec<String> = env::args().collect();
    let opts = ross_base_options();
    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
    if matches.opt_present("help") {
        println!("Convert a fastq file to a standard 4-lines-per-entry format\n{}", opts.usage(&opts.short_usage(&args[0])));
        std::process::exit(0);
    }
    if matches.opt_present("paired-end") {
        logmsg("WARNING: --paired-end is not utilized in this script");
    }

    let my_file = File::open("/dev/stdin").expect("Could not open file");
    let my_buffer=BufReader::new(my_file);
    let fastq_reader=fastq::FastqReader::new_careful(my_buffer);
    for seq in fastq_reader {
        seq.print();
    }
}