obitools4/autodoc/docmd/pkg/obikmer/minimizer_utils.md

Minimizer Size Utilities in obikmer

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).

Core Functions

• DefaultMinimizerSize(k)
  Returns a recommended minimizer size: ceil(k / 2.5), clamped to [1, k−1].
  → Ensures m is reasonably large for uniqueness while keeping window size (k − m + 1) manageable.

• MinMinimizerSize(nworkers)
  Computes the minimum m such that there are ≥ nworkers distinct minimizers:
  solves 4^m ≥ n_workers, i.e., ceil(log₄(nworkers)).
  → Guarantees enough diversity for parallelization (e.g., hashing-based distribution across workers).

• ValidateMinimizerSize(m, k, nworkers)
  Enforces constraints on m:

  • Lower bound: ≥ MinMinimizerSize(nworkers) (warns & adjusts if violated)
  • Hard bounds: 1 ≤ m < k
    → Prevents invalid or inefficient parameter choices.

Semantic Purpose

These functions ensure that minimizer-based workflows are:

• Theoretically sound (sufficient entropy for parallelism),
• Practically viable (avoiding degenerate cases like m = 0 or m ≥ k),
• User-friendly (providing sensible defaults + clear warnings on adjustment).