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

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