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Rotate by R bits at each step of NtHash #16

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Rotate by R bits at each step of NtHash #16

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28 changes: 15 additions & 13 deletions simd-minimizers/src/nthash.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,8 @@ const HASHES_F: [u32; 4] = [
0x2955_49f5_4be2_4456u64 as u32,
];

const R: u32 = 25;

type SeedHasher = BuildHasherDefault<DefaultHasher>;

pub trait CharHasher: Clone {
Expand Down Expand Up @@ -58,7 +60,7 @@ impl CharHasher for NtHasher {
fn new_with_seed<'s, SEQ: Seq<'s>>(k: usize, seed: Option<u32>) -> Self {
assert_eq!(SEQ::BITS_PER_CHAR, 2);

let rot = k as u32 - 1;
let rot = (k as u32 - 1) * R;
let hasher = SeedHasher::new();
let f = match seed {
None => HASHES_F,
Expand Down Expand Up @@ -132,7 +134,7 @@ const C: u32 = 0x517cc1b727220a95u64 as u32;
impl CharHasher for MulHasher {
fn new_with_seed<'s, SEQ: Seq<'s>>(k: usize, seed: Option<u32>) -> Self {
Self {
rot: (k as u32 - 1) % 32,
rot: ((k as u32 - 1) * R) % 32,
mul: match seed {
None => C,
Some(seed) => C ^ ((SeedHasher::new().hash_one(seed) as u32) << 1), // don't change parity,
Expand Down Expand Up @@ -190,12 +192,12 @@ pub fn nthash_kmer<'s, const RC: bool, H: CharHasher>(seq: impl Seq<'s>) -> u32
let mut hfw: u32 = 0;
let mut hrc: u32 = 0;
seq.iter_bp().for_each(|a| {
hfw = hfw.rotate_left(1) ^ hasher.f(a);
hfw = hfw.rotate_left(R) ^ hasher.f(a);
if RC {
hrc = hrc.rotate_right(1) ^ hasher.c(a);
hrc = hrc.rotate_right(R) ^ hasher.c(a);
}
});
hfw.wrapping_add(hrc.rotate_left(k as u32 - 1))
hfw.wrapping_add(hrc.rotate_left((k as u32 - 1) * R))
}

/// Returns a scalar iterator over the 32-bit NT hashes of all k-mers in the sequence.
Expand All @@ -214,16 +216,16 @@ pub fn nthash_seq_scalar<'s, const RC: bool, H: CharHasher>(
let mut add = seq.iter_bp();
let remove = seq.iter_bp();
add.by_ref().take(k - 1).for_each(|a| {
hfw = hfw.rotate_left(1) ^ hasher.f(a);
hfw = hfw.rotate_left(R) ^ hasher.f(a);
if RC {
hrc = hrc.rotate_right(1) ^ hasher.c_rot(a);
hrc = hrc.rotate_right(R) ^ hasher.c_rot(a);
}
});
add.zip(remove).map(move |(a, r)| {
let hfw_out = hfw.rotate_left(1) ^ hasher.f(a);
let hfw_out = hfw.rotate_left(R) ^ hasher.f(a);
hfw = hfw_out ^ hasher.f_rot(r);
if RC {
let hrc_out = hrc.rotate_right(1) ^ hasher.c_rot(a);
let hrc_out = hrc.rotate_right(R) ^ hasher.c_rot(a);
hrc = hrc_out ^ hasher.c(r);
hfw_out.wrapping_add(hrc_out)
} else {
Expand Down Expand Up @@ -273,18 +275,18 @@ pub fn nthash_mapper<'s, const RC: bool, SEQ: Seq<'s>, H: CharHasher>(
let mut fw = 0u32;
let mut rc = 0u32;
for _ in 0..k - 1 {
fw = fw.rotate_left(1) ^ hasher.f(0);
rc = rc.rotate_right(1) ^ hasher.c_rot(0);
fw = fw.rotate_left(R) ^ hasher.f(0);
rc = rc.rotate_right(R) ^ hasher.c_rot(0);
}

let mut h_fw = S::splat(fw);
let mut h_rc = S::splat(rc);

move |(a, r)| {
let hfw_out = ((h_fw << 1) | (h_fw >> 31)) ^ hasher.simd_f(a);
let hfw_out = ((h_fw << R) | (h_fw >> (32 - R))) ^ hasher.simd_f(a);
h_fw = hfw_out ^ hasher.simd_f_rot(r);
if RC {
let hrc_out = ((h_rc >> 1) | (h_rc << 31)) ^ hasher.simd_c_rot(a);
let hrc_out = ((h_rc >> R) | (h_rc << (32 - R))) ^ hasher.simd_c_rot(a);
h_rc = hrc_out ^ hasher.simd_c(r);
// Wrapping SIMD add
hfw_out + hrc_out
Expand Down
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