Eric Coissac
036d044291
Refactor `Kmer`, `SuperKmer`, and chunk reader into optimized, generic representations with compile-time length parameters and bitwise operations. Update the pipeline and scheduler to support batch processing, 1→N flat transformations, and multi-source merging. Introduce an approximate evidence mode using b-bit fingerprints and `.idx` files, alongside existing exact mode. Update CLI documentation, minimizer selection, and query output schema accordingly.
43 lines
1.8 KiB
Markdown
43 lines
1.8 KiB
Markdown
# DNA encoding
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## 2-bit nucleotide encoding
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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:
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| Base | Encoding |
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|------|----------|
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| A | `00` |
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| C | `01` |
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| G | `10` |
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| T | `11` |
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The Watson-Crick complement of any base is its bitwise NOT on 2 bits: `complement(base) = ~base & 0b11`.
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## Kmer encoding
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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`.
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Reverse complement is computed by **bit manipulation in four steps**, with no lookup table:
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!!! abstract "Algorithm — Kmer reverse complement"
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```text
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procedure KmerRevcomp(kmer, k):
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x ← ~kmer -- complement all bases
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x ← swap_bytes(x) -- reverse byte order
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x ← ((x >> 4) & 0x0F0F0F0F0F0F0F0F)
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| ((x & 0x0F0F0F0F0F0F0F0F) << 4) -- swap nibbles within each byte
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x ← ((x >> 2) & 0x3333333333333333)
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| ((x & 0x3333333333333333) << 2) -- swap 2-bit pairs within each nibble
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return x << (64 - 2*k) -- re-align to MSB
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```
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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.
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The **canonical form** is the lexicographic minimum of the kmer and its reverse complement:
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```
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canonical(kmer) = min(kmer, revcomp(kmer))
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```
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This halves the kmer space and ensures strand-independent counting.
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