2 Commits

Author	SHA1	Message	Date
Eric Coissac	00c8be6b48	docs: add architecture documentation for OBITools commands ... Ajout d'une documentation détaillée sur l'architecture des commandes OBITools, incluant la structure modulaire, les patterns architecturaux et les bonnes pratiques pour la création de nouvelles commandes.	2026-02-07 12:26:35 +01:00
Eric Coissac	500144051a	Add jj Makefile targets and k-mer encoding utilities ... Add new Makefile targets for jj operations (jjnew, jjpush, jjfetch) to streamline commit workflow. Introduce k-mer encoding utilities in pkg/obikmer: - EncodeKmers: converts DNA sequences to encoded k-mers - ReverseComplement: computes reverse complement of k-mers - NormalizeKmer: returns canonical form of k-mers - EncodeNormalizedKmers: encodes sequences with normalized k-mers Add comprehensive tests for k-mer encoding functions including edge cases, buffer reuse, and performance benchmarks. Document k-mer index design for large genomes, covering: - Use cases and objectives - Volume estimations - Distance metrics (Jaccard, Sørensen-Dice, Bray-Curtis) - Indexing options (Bloom filters, sorted sets, MPHF) - Optimization techniques (k-2-mer indexing) - MinHash for distance acceleration - Recommended architecture for presence/absence and counting queries	2026-02-04 14:27:10 +01:00