2026-06-09 08:28:21 +00:00
1 changed files with 23 additions and 0 deletions
@@ -140,6 +140,29 @@ Fractions are computed over the size of the classified group, not over total
 genome count. An empty group (no genome classified as ingroup/outgroup) never
 triggers a filter failure.
 ### Conservative rounding of fraction thresholds
 When a fraction threshold `F` is applied to a group of size `N`, the effective
 integer threshold is determined by the direction of the bound:
 | Bound | Effective count | Rounding | Rationale |
 |-------|----------------|----------|-----------|
 | `--min-frac F` | k-mer in ≥ ⌈F·N⌉ genomes | **ceil** | stricter — a kmer present in exactly ⌊F·N⌋ genomes does not meet the fraction |
 | `--max-frac F` | k-mer in ≤ ⌊F·N⌋ genomes | **floor** | stricter — a kmer present in ⌈F·N⌉ genomes already exceeds the fraction |
 The same rule applies symmetrically to `--min-outgroup-frac` (ceil) and
 `--max-outgroup-frac` (floor). The outgroup direction is not inverted: the
 conservative rounding depends only on whether the bound is a minimum or a
 maximum, not on which group it applies to.
 **Example** — `--min-frac 0.5` with an ingroup of 3 genomes:
 `⌈0.5 × 3⌉ = ⌈1.5⌉ = 2` → at least 2 of 3 ingroup genomes must carry the k-mer.
 **Implementation note** — the filter evaluates `n / denom < min_frac` directly
 (integer `n`, float comparison) rather than pre-computing `⌈F·N⌉`. This is
 mathematically equivalent for integer counts: `n / N < F` ↔ `n < F·N` ↔
 `n ≤ ⌈F·N⌉ − 1` ↔ `n < ⌈F·N⌉`. No explicit rounding is needed.
 ## Examples
 Keep k-mers specific to *Betula nana* — present in at least 2 *B. nana* genomes