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|
// xfail-pretty
// xfail-test
use core::cast::transmute;
use core::libc::{STDOUT_FILENO, c_int, fdopen, fgets, fopen, fputc, fwrite};
use core::libc::{size_t};
use core::ptr::null;
use core::vec::{capacity, reserve, reserve_at_least};
use core::vec::raw::set_len;
static LINE_LEN: u32 = 80;
static COMPLEMENTS: [u8, ..256] = [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0,
'T' as u8,
'V' as u8,
'G' as u8,
'H' as u8,
0,
0,
'C' as u8,
'D' as u8,
0,
0,
'M' as u8,
0,
'K' as u8,
'N' as u8,
0,
0,
0,
'Y' as u8,
'S' as u8,
'A' as u8,
'A' as u8,
'B' as u8,
'W' as u8,
0,
'R' as u8,
0,
0,
0,
0,
0,
0,
0,
'T' as u8,
'V' as u8,
'G' as u8,
'H' as u8,
0,
0,
'C' as u8,
'D' as u8,
0,
0,
'M' as u8,
0,
'K' as u8,
'N' as u8,
0,
0,
0,
'Y' as u8,
'S' as u8,
'A' as u8,
'A' as u8,
'B' as u8,
'W' as u8,
0,
'R' as u8,
0,
0,
0,
0,
0,
0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
];
#[fixed_stack_segment]
fn main() {
unsafe {
let mode = "r";
//let stdin = fdopen(STDIN_FILENO as c_int, transmute(&mode[0]));
let path = "reversecomplement-input.txt";
let stdin = fopen(transmute(&path[0]), transmute(&mode[0]));
let mode = "w";
let stdout = fdopen(STDOUT_FILENO as c_int, transmute(&mode[0]));
let mut out: ~[u8] = ~[];
reserve(&mut out, 12777888);
let mut pos = 0;
loop {
let needed = pos + (LINE_LEN as uint) + 1;
if capacity(&out) < needed {
reserve_at_least(&mut out, needed);
}
let mut ptr = out.unsafe_mut_ref(pos);
if fgets(transmute(ptr), LINE_LEN as c_int, stdin) == null() {
break;
}
// Don't change lines that begin with '>' or ';'.
let first = *ptr;
if first == ('>' as u8) {
while *ptr != 0 {
ptr = ptr.offset(1);
}
*ptr = '\n' as u8;
pos = (ptr as uint) - (out.unsafe_ref(0) as uint);
fwrite(transmute(out.unsafe_ref(0)),
1,
pos as size_t,
stdout);
pos = 0;
loop;
}
// Complement other lines.
loop {
let ch = *ptr;
if ch == 0 {
break;
}
*ptr = COMPLEMENTS.unsafe_get(ch as uint);
ptr = ptr.offset(1);
}
*ptr = '\n' as u8;
pos = (ptr as uint) - (out.unsafe_ref(0) as uint);
}
fwrite(transmute(out.unsafe_ref(0)), 1, pos as size_t, stdout);
}
}
|
