2 Commits

Author	SHA1	Message	Date
Eric Coissac	05de9ca58e	Add SuperKmer extraction functionality ... This commit introduces the ExtractSuperKmers function which identifies maximal subsequences where all consecutive k-mers share the same minimizer. It includes: - SuperKmer struct to represent the maximal subsequences - dequeItem struct for tracking minimizers in a sliding window - Efficient algorithm using monotone deque for O(1) amortized minimizer tracking - Comprehensive parameter validation - Support for buffer reuse for performance optimization - Extensive test cases covering basic functionality, edge cases, and performance benchmarks The implementation uses simultaneous forward/reverse m-mer encoding for O(1) canonical m-mer computation and maintains a monotone deque to track minimizers efficiently.	2026-02-04 16:04:06 +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