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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
28 lines
1.3 KiB
Markdown
28 lines
1.3 KiB
Markdown
# Minimizer Size Utilities in `obikmer`
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This Go package provides helper functions to compute and validate the **minimizer size** `m` in k-mer-based genomic algorithms (e.g., minimizer schemes for sequence comparison or indexing).
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## Core Functions
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- **`DefaultMinimizerSize(k)`**
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Returns a *recommended* minimizer size: `ceil(k / 2.5)`, clamped to `[1, k−1]`.
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→ Ensures `m` is reasonably large for uniqueness while keeping window size (`k − m + 1`) manageable.
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- **`MinMinimizerSize(nworkers)`**
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Computes the *minimum* `m` such that there are ≥ `nworkers` distinct minimizers:
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solves `4^m ≥ n_workers`, i.e., `ceil(log₄(nworkers))`.
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→ Guarantees enough diversity for parallelization (e.g., hashing-based distribution across workers).
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- **`ValidateMinimizerSize(m, k, nworkers)`**
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Enforces constraints on `m`:
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- Lower bound: ≥ `MinMinimizerSize(nworkers)` (warns & adjusts if violated)
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- Hard bounds: `1 ≤ m < k`
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→ Prevents invalid or inefficient parameter choices.
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## Semantic Purpose
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These functions ensure that minimizer-based workflows are:
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- **Theoretically sound** (sufficient entropy for parallelism),
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- **Practically viable** (avoiding degenerate cases like `m = 0` or `m ≥ k`),
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- **User-friendly** (providing sensible defaults + clear warnings on adjustment).
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