mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 13:30:52 +00:00
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.