obikmer/docmd/implementation/kmer.md

# Kmer — implementation

## Types and layout

`KmerOf<L>` is a `#[repr(transparent)]` newtype over `u64` parameterized by a `KmerLength` marker:

```rust
#[repr(transparent)]
pub struct KmerOf<L: KmerLength>(u64, PhantomData<L>);
```

Three marker types implement `KmerLength`:

| Marker | `len()` source | Used for |
|--------|---------------|---------|
| `KLen` | `params::k()` | k-mers |
| `MLen` | `params::m()` | minimizers |
| `ConstLen<N>` | const generic `N` | tests |

Public aliases:

```rust
pub type Kmer     = KmerOf<KLen>;         // k-mer, global k
pub type Minimizer = CanonicalKmerOf<MLen>; // canonical m-mer, global m
```

Nucleotides are packed 2 bits each, **left-aligned**, MSB-first. Nucleotide 0 occupies bits 63–62; nucleotide i occupies bits 63−2i and 62−2i. The low 64−2·len bits are always zero. The length is **not stored** — every operation reads it from `L::len()`.

| 63–62 | 61–60 | … | 63−2(k−1)−1 to 63−2(k−1) | 63−2k down to 0 |
|-------|-------|---|--------------------------|-----------------|
| nt 0  | nt 1  | … | nt k−1                   | zero padding    |

## Global parameters

`params::set_k(k)` / `params::k()` and `params::set_m(m)` / `params::m()` are backed by `OnceLock<usize>` in production (write-once, panic on conflict) and by `thread_local! { Cell<usize> }` in test builds (per-thread, freely writable). `params::init(k, m)` sets both in one call.

## Encoding

`KmerOf::<L>::from_ascii(ascii)` encodes the first `L::len()` bytes using the shared `ENC` table (see [SuperKmer — ASCII encoding](superkmer.md#ascii-encoding-and-decoding)):

```rust
for i in 0..k {
    val = (val << 2) | encode_base(ascii[i]) as u64;
}
KmerOf(val << (64 - 2 * k), PhantomData)
```

Zero allocation — result lives on the stack.

## Decoding

`write_ascii(writer)` writes k ASCII characters to any `W: Write` using the shared `DEC4` table: one lookup per 4 nucleotides, one partial lookup for the remainder. No allocation in the hot path.

`to_ascii()` is a convenience wrapper that allocates and returns a `Vec<u8>`; intended for tests and display only.

## Reverse complement

Computed as pure arithmetic — no lookup table, no memory access:

```rust
let x = !self.0;                                                               // complement
let x = x.swap_bytes();                                                        // reverse bytes
let x = ((x >> 4) & 0x0F0F0F0F0F0F0F0F) | ((x & 0x0F0F0F0F0F0F0F0F) << 4); // swap nibbles
let x = ((x >> 2) & 0x3333333333333333) | ((x & 0x3333333333333333) << 2);   // swap 2-bit groups
KmerOf(x << (64 - 2 * k), PhantomData)
```

After complementing, bytes are reversed (`swap_bytes`), then nibbles, then 2-bit groups — restoring 2-bit nucleotides to their correct positions in reverse order. A final left-shift realigns to MSB. Zero allocation — result lives on the stack.

## Canonical form and `CanonicalKmerOf`

`canonical()` returns a `CanonicalKmerOf<L>` — a distinct newtype that carries the same `u64` layout but enforces the invariant that the stored value equals `min(kmer, revcomp)`:

```rust
pub fn canonical(&self) -> CanonicalKmerOf<L> {
    let rc = self.revcomp();
    CanonicalKmerOf(if self.0 <= rc.0 { self.0 } else { rc.0 }, PhantomData)
}
```

Lexicographic minimum of forward and reverse-complement, comparing the raw `u64` values directly (left-aligned encoding makes this equivalent to nucleotide-wise comparison). Zero allocation — result lives on the stack.

`CanonicalKmerOf::from_raw_unchecked(raw)` is the only other public constructor, for trusted paths such as deserialisation.

## Sliding window helpers

`push_right(nuc)` / `push_left(nuc)` shift the window by one base in O(1). `is_overlapping(other)` checks whether the last k−1 nucleotides of `self` equal the first k−1 of `other`.

## Hashing

`hash_kmer(raw: u64) -> u64` computes `mix64(raw ^ 0x9e3779b97f4a7c15)`, the seeded splitmix64 finalizer. `CanonicalKmerOf::seq_hash()` delegates to `hash_kmer`.