DNA encoding

2-bit nucleotide encoding

All nucleotides are encoded on 2 bits, MSB-first within each word. Nucleotides are numbered 0-based from the 5′ end across all sequence types:

Base	Encoding
A	00
C	01
G	10
T	11

The Watson-Crick complement of any base is its bitwise NOT on 2 bits: complement(base) = ~base & 0b11.

Kmer encoding

A kmer fits in a single u64. Nucleotide 0 occupies bits 63–62, nucleotide i occupies bits 63−2i and 62−2i, and the low 64−2k bits are zero. Extraction of nucleotide i (0 ≤ i < k): (kmer >> (62 - 2*i)) & 0b11.

Reverse complement is computed by bit manipulation in four steps, with no lookup table:

Algorithm — Kmer reverse complement

procedure KmerRevcomp(kmer, k):
    x ← ~kmer                                           -- complement all bases
    x ← swap_bytes(x)                                   -- reverse byte order
    x ← ((x >> 4) & 0x0F0F0F0F0F0F0F0F)
       | ((x & 0x0F0F0F0F0F0F0F0F) << 4)               -- swap nibbles within each byte
    x ← ((x >> 2) & 0x3333333333333333)
       | ((x & 0x3333333333333333) << 2)                -- swap 2-bit pairs within each nibble
    return x << (64 - 2*k)                              -- re-align to MSB

The three reorder passes together reverse the order of all 2-bit base codes across the 64-bit word. The bitwise NOT in the first step complements each base (A↔T, C↔G). The final left shift clears the low 64−2k padding bits.

The canonical form is the lexicographic minimum of the kmer and its reverse complement:

canonical(kmer) = min(kmer, revcomp(kmer))

This halves the kmer space and ensures strand-independent counting.