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pub type BitKmerSeq = u64;
pub type BitKmer = (BitKmerSeq, u8);
const NUC2BIT_LOOKUP: [Option<u8>; 256] = {
let mut lookup = [None; 256];
lookup[b'A' as usize] = Some(0);
lookup[b'C' as usize] = Some(1);
lookup[b'G' as usize] = Some(2);
lookup[b'T' as usize] = Some(3);
lookup[b'a' as usize] = Some(0);
lookup[b'c' as usize] = Some(1);
lookup[b'g' as usize] = Some(2);
lookup[b't' as usize] = Some(3);
lookup
};
fn nuc2bti_lookup_nocheck(nuc: u8) -> Option<u8> {
unsafe { *NUC2BIT_LOOKUP.get_unchecked(nuc as usize) }
}
fn extend_kmer(kmer: &mut BitKmer, new_char: u8) -> bool {
if let Some(new_char_int) = nuc2bti_lookup_nocheck(new_char) {
let new_kmer = (kmer.0 << 2) + new_char_int as BitKmerSeq;
kmer.0 = new_kmer & (BitKmerSeq::pow(2, u32::from(2 * kmer.1)) - 1) as BitKmerSeq;
true
} else {
false
}
}
fn update_position(
start_pos: &mut usize,
kmer: &mut BitKmer,
buffer: &[u8],
initial: bool,
) -> bool {
if *start_pos + kmer.1 as usize > buffer.len() {
return false;
}
let (mut kmer_len, stop_len) = if initial {
(0, (kmer.1 - 1) as usize)
} else {
((kmer.1 - 1) as usize, kmer.1 as usize)
};
let cur_kmer = kmer;
while kmer_len < stop_len {
if extend_kmer(cur_kmer, buffer[*start_pos + kmer_len]) {
kmer_len += 1;
} else {
kmer_len = 0;
*cur_kmer = (0u64, cur_kmer.1);
*start_pos += kmer_len + 1;
if *start_pos + cur_kmer.1 as usize > buffer.len() {
return false;
}
}
}
true
}
pub struct BitNuclKmer<'a> {
start_pos: usize,
cur_kmer: BitKmer,
buffer: &'a [u8],
canonical: bool,
}
impl<'a> BitNuclKmer<'a> {
pub fn new(slice: &'a [u8], k: u8, canonical: bool) -> BitNuclKmer<'a> {
let mut kmer = (0u64, k);
let mut start_pos = 0;
update_position(&mut start_pos, &mut kmer, slice, true);
BitNuclKmer {
start_pos,
cur_kmer: kmer,
buffer: slice,
canonical,
}
}
}
impl<'a> Iterator for BitNuclKmer<'a> {
type Item = (usize, BitKmer, bool);
fn next(&mut self) -> Option<(usize, BitKmer, bool)> {
if !update_position(&mut self.start_pos, &mut self.cur_kmer, self.buffer, false) {
return None;
}
self.start_pos += 1;
if self.canonical {
let (kmer, was_rc) = canonical(self.cur_kmer);
Some((self.start_pos - 1, kmer, was_rc))
} else {
Some((self.start_pos - 1, self.cur_kmer, false))
}
}
}
pub fn reverse_complement(kmer: BitKmer) -> BitKmer {
let mut new_kmer = kmer.0;
new_kmer = (new_kmer >> 2 & 0x3333_3333_3333_3333) | (new_kmer & 0x3333_3333_3333_3333) << 2;
new_kmer = (new_kmer >> 4 & 0x0F0F_0F0F_0F0F_0F0F) | (new_kmer & 0x0F0F_0F0F_0F0F_0F0F) << 4;
new_kmer = (new_kmer >> 8 & 0x00FF_00FF_00FF_00FF) | (new_kmer & 0x00FF_00FF_00FF_00FF) << 8;
new_kmer = (new_kmer >> 16 & 0x0000_FFFF_0000_FFFF) | (new_kmer & 0x0000_FFFF_0000_FFFF) << 16;
new_kmer = (new_kmer >> 32 & 0x0000_0000_FFFF_FFFF) | (new_kmer & 0x0000_0000_FFFF_FFFF) << 32;
new_kmer ^= 0xFFFF_FFFF_FFFF_FFFF;
new_kmer >>= 2 * (32 - kmer.1);
(new_kmer, kmer.1)
}
pub fn canonical(kmer: BitKmer) -> (BitKmer, bool) {
let rc = reverse_complement(kmer);
if kmer.0 > rc.0 {
(rc, true)
} else {
(kmer, false)
}
}
pub fn minimizer(kmer: BitKmer, minmer_size: u8) -> BitKmer {
let mut new_kmer = kmer.0;
let mut lowest = !0;
let bitmask = (BitKmerSeq::pow(2, u32::from(2 * minmer_size)) - 1) as BitKmerSeq;
for _ in 0..=(kmer.1 - minmer_size) {
let cur = bitmask & new_kmer;
if cur < lowest {
lowest = cur;
}
let cur_rev = reverse_complement((bitmask & new_kmer, kmer.1));
if cur_rev.0 < lowest {
lowest = cur_rev.0;
}
new_kmer >>= 2;
}
(lowest, kmer.1)
}
pub fn bitmer_to_bytes(kmer: BitKmer) -> Vec<u8> {
let mut new_kmer = kmer.0;
let mut new_kmer_str = Vec::new();
let offset = (kmer.1 - 1) * 2;
let bitmask = BitKmerSeq::pow(2, u32::from(2 * kmer.1 - 1))
+ BitKmerSeq::pow(2, u32::from(2 * kmer.1 - 2));
for _ in 0..kmer.1 {
let new_char = (new_kmer & bitmask) >> offset;
new_kmer <<= 2;
new_kmer_str.push(match new_char {
0 => b'A',
1 => b'C',
2 => b'G',
3 => b'T',
_ => panic!("Mathematical impossibility"),
});
}
new_kmer_str
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn can_kmerize() {
let mut i = 0;
for (_, k, _) in BitNuclKmer::new(b"AGCT", 1, false) {
match i {
0 => assert_eq!(k.0, 0b00 as BitKmerSeq),
1 => assert_eq!(k.0, 0b10 as BitKmerSeq),
2 => assert_eq!(k.0, 0b01 as BitKmerSeq),
3 => assert_eq!(k.0, 0b11 as BitKmerSeq),
_ => unreachable!("Too many kmers"),
}
i += 1;
}
i = 0;
for (_, k, _) in BitNuclKmer::new(b"ACNGT", 2, false) {
match i {
0 => assert_eq!(k.0, 0b0001 as BitKmerSeq),
1 => assert_eq!(k.0, 0b1011 as BitKmerSeq),
_ => unreachable!("Too many kmers"),
}
i += 1;
}
i = 0;
for (_, k, _) in BitNuclKmer::new(b"ACNG", 2, false) {
match i {
0 => assert_eq!(k.0, 0x0001 as BitKmerSeq),
_ => unreachable!("Too many kmers"),
}
i += 1;
}
i = 0;
for (_, k, _) in BitNuclKmer::new(b"AC", 2, false) {
match i {
0 => assert_eq!(k.0, 0x0001 as BitKmerSeq),
_ => unreachable!("Too many kmers"),
}
i += 1;
}
}
#[test]
fn test_iterator() {
let seq = b"ACGTA";
let mut kmer_iter = BitNuclKmer::new(seq, 3, false);
assert_eq!(kmer_iter.next(), Some((0, (6, 3), false)));
assert_eq!(kmer_iter.next(), Some((1, (27, 3), false)));
assert_eq!(kmer_iter.next(), Some((2, (44, 3), false)));
assert_eq!(kmer_iter.next(), None);
let seq = b"TA";
let mut kmer_iter = BitNuclKmer::new(seq, 3, false);
assert_eq!(kmer_iter.next(), None);
}
#[test]
fn test_reverse_complement() {
assert_eq!(reverse_complement((0b00_0000, 3)).0, 0b11_1111);
assert_eq!(reverse_complement((0b11_1111, 3)).0, 0b00_0000);
assert_eq!(reverse_complement((0b0000_0000, 4)).0, 0b1111_1111);
assert_eq!(reverse_complement((0b0001_1011, 4)).0, 0b0001_1011);
}
#[test]
fn test_minimizer() {
assert_eq!(minimizer((0b00_1011, 3), 2).0, 0b0010);
assert_eq!(minimizer((0b00_1011, 3), 1).0, 0b00);
assert_eq!(minimizer((0b1100_0011, 4), 2).0, 0b0000);
assert_eq!(minimizer((0b11_0001, 3), 2).0, 0b0001);
}
#[test]
fn test_bytes_to_bitkmer() {
let mut ikmer: BitKmer = bytes_to_bitmer(b"C");
assert_eq!(ikmer.0, 1 as BitKmerSeq);
ikmer = bytes_to_bitmer(b"TTA");
assert_eq!(ikmer.0, 60 as BitKmerSeq);
ikmer = bytes_to_bitmer(b"AAA");
assert_eq!(ikmer.0, 0 as BitKmerSeq);
}
#[test]
fn test_bitmer_to_bytes() {
assert_eq!(bitmer_to_bytes((1 as BitKmerSeq, 1)), b"C".to_vec());
assert_eq!(bitmer_to_bytes((60 as BitKmerSeq, 3)), b"TTA".to_vec());
assert_eq!(bitmer_to_bytes((0 as BitKmerSeq, 3)), b"AAA".to_vec());
}
pub fn bytes_to_bitmer(kmer: &[u8]) -> BitKmer {
let k = kmer.len() as u8;
let mut bit_kmer = (0u64, k);
for i in 0..k {
extend_kmer(&mut bit_kmer, kmer[i as usize]);
}
bit_kmer
}
}