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500144051a
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