libsfasta 0.3.4

Better FASTA sequence compression and querying
Documentation 
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
29
30
31
32
33

use std::fs::{metadata, File};
use std::io::{BufReader, Read};

#[inline]
pub fn generic_open_file(filename: &str) -> (usize, bool, Box<dyn Read + Send>) {
    let filesize = metadata(filename)
        .unwrap_or_else(|_| panic!("{}", &format!("Unable to open file: {}", filename)))
        .len();

    let file = match File::open(filename) {
        Err(why) => panic!("Couldn't open {}: {}", filename, why),
        Ok(file) => file,
    };

    let file = BufReader::new(file);
    let mut compressed: bool = false;

    let fasta: Box<dyn Read + Send> = if filename.ends_with("gz") {
        compressed = true;
        Box::new(flate2::read::GzDecoder::new(file))
    } else if filename.ends_with("snappy") || filename.ends_with("sz") || filename.ends_with("sfai")
    {
        compressed = true;
        Box::new(snap::read::FrameDecoder::new(file))
    } else {
        Box::new(file)
    };

    (filesize as usize, compressed, fasta)
}

#[cfg(test)]
mod tests {}