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reverse_complement: Pre-allocate a buffer based on input size #44

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Merged
merged 1 commit into from
Feb 24, 2017
Merged

reverse_complement: Pre-allocate a buffer based on input size #44

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14 changes: 11 additions & 3 deletions src/reverse_complement.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
// http://benchmarksgame.alioth.debian.org/
//
// contributed by the Rust Project Developers
// contributed by Matt Brubeck
// contributed by TeXitoi

//extern crate libc;
Expand All @@ -20,6 +21,8 @@ mod libc {
use std::io::{Read, Write};
use std::ptr::copy;
use std::thread;
use std::fs::File;
use std::os::unix::io::FromRawFd;

struct Tables {
table8: [u8;1 << 8],
Expand Down Expand Up @@ -187,10 +190,15 @@ fn parallel<'a, I, T, F>(iter: I, ref f: F)
for jh in jhs { jh.join().unwrap(); }
}

fn file_size(f: &mut File) -> std::io::Result<usize> {
Ok(f.metadata()?.len() as usize)
}

fn main() {
let stdin = std::io::stdin();
let mut data = Vec::with_capacity(1024 * 1024);
stdin.lock().read_to_end(&mut data).unwrap();
let mut stdin = unsafe { File::from_raw_fd(0) };
let size = file_size(&mut stdin).unwrap_or(1024 * 1024);
let mut data = Vec::with_capacity(size + 1);
stdin.read_to_end(&mut data).unwrap();
let tables = &Tables::new();
parallel(mut_dna_seqs(&mut data), |seq| reverse_complement(seq, tables));
let stdout = std::io::stdout();
Expand Down