Files
obitools4/pkg
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
..
2025-11-06 15:43:13 +01:00
2025-11-18 15:30:20 +01:00
2024-05-14 08:16:12 +02:00
2025-01-27 17:23:07 +01:00
2025-06-17 09:06:42 +02:00
2025-06-04 09:48:10 +02:00
2023-12-05 15:28:29 +01:00
2025-11-18 15:30:20 +01:00
2025-12-18 14:11:11 +01:00
2025-11-18 15:30:20 +01:00