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obitools4/pkg/obikmer
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.
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