large refactoring

DevDocMD/kmers.md

@@ -0,0 +1,34 @@
+# Kmers and super-kmers
+
+## Kmers
+
+A **kmer** is a DNA subsequence of fixed length k. Two constraints govern the choice of k:
+
+- **k ∈ [11, 31]**: the range ensures the kmer is long enough to be specific and short enough to fit in a single machine word (u64 at 2 bits/base requires k ≤ 32; k < 11 yields insufficient specificity).
+- **k is odd**: an odd-length sequence cannot equal its own reverse complement (no palindromes). This guarantees that the canonical form `min(kmer, revcomp(kmer))` is always strictly defined — the two orientations are always distinct — which is required for strand-independent counting.
+
+Both constraints are **enforced at CLI entry** by `CommonArgs::validate()` in `superkmer` and `index`. Passing an invalid k exits immediately with an error message.
+
+## Super-kmers
+
+A **super-kmer** is a maximal run of consecutive kmers from a DNA read, each overlapping the next by k−1 nucleotides, sharing the same **canonical minimizer**. The **canonical minimizer** of a kmer is the m-mer (m < k) whose canonical hash `hash_kmer(min(m-mer, revcomp(m-mer)))` is smallest over all m-mers in the kmer window. The hash function is a `mix64`-based bijection; selection is purely hash-ordered with no degeneracy filter. A super-kmer is capped at 256 nucleotides; a longer run is split at that boundary.
+
+### Canonical super-kmers
+
+A **canonical super-kmer** is the lexicographic minimum of a super-kmer and its reverse complement:
+
+```
+canonical(super-kmer) = min(super-kmer, revcomp(super-kmer))
+```
+
+When a read and its reverse-complement are both sequenced, they produce super-kmers that are reverse complements of each other. Both map to the same canonical form: the same genomic region is represented by a single canonical super-kmer regardless of which strand was read.
+
+### Expected length of a super-kmer
+
+For a random minimizer of length m over k-mers of length k, the density of minimizer positions is approximately 2/(k−m+2) [@Zheng2020-ji; @Golan2025-xf], so the expected number of consecutive k-mers per super-kmer is (k−m+2)/2. A run of n k-mers spans n + k − 1 nucleotides, giving:
+
+$$L_{\text{nt}} = \frac{k-m+2}{2} + k - 1$$
+
+For k=31, m=13: expected ≈ 40 nt. In practice super-kmers rarely exceed a few dozen nucleotides.[^superkmer_length]
+
+[^superkmer_length]: The expected length formula and the density approximation 2/(k−m+2) should be verified against the values reported in [@Zheng2020-ji] and [@Golan2025-xf].