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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

Semantic Description of `obikmer` Package

The obikmer package provides efficient k-mer encoding and comparison utilities for biological sequences, optimized for DNA analysis.

Core Functionalities

Nucleotide Encoding
- EncodeNucleotide(b byte): Maps DNA bases (A, C, G, T/U) to 2-bit values:
  0→A, 1→C, 2→G, 3→T/U.
  Ambiguous or non-standard characters (e.g., N, R, Y) default to A (0).
  Uses a lookup table for O(1) performance.
4-mer Encoding
- Encode4mer(seq, buffer): Converts a biological sequence into overlapping 4-mers.
  Each k-mer is encoded as an unsigned byte (0–255), where each nucleotide contributes 2 bits.
  Supports optional buffer reuse for memory efficiency.
4-mer Indexing
- Index4mer(seq, index, buffer): Builds an inverted index mapping each 4-mer code (0–255) to all its occurrence positions in the sequence.
  Returns [][]int, where rows correspond to k-mer codes and columns list positions.
Fast Sequence Comparison
- FastShiftFourMer(...): Compares two sequences using a FASTA-like shift-scoring algorithm.
  - Uses precomputed 4-mer index of a reference sequence and encodes the query.
  - Counts co-occurring 4-mers across all possible shifts (refpos − queryPos).
  - Computes raw and relative scores (normalized by alignment length).
  - Returns optimal shift, count of matching 4-mers, and maximum score (raw or relative).

Memory-aware: Supports buffer reuse to minimize allocations.
Robustness: Non-canonical bases handled gracefully (defaulting to A).
Performance-oriented: O(n) encoding and indexing; efficient hash-based shift counting.

Intended for rapid alignment-free sequence comparison in metabarcoding or metagenomic workflows.