Eric Coissac a016ad5b8a Refactor kmer index to disk-based partitioning with minimizer ...

Refactor kmer index package to use disk-based partitioning with minimizer

- Replace roaring64 bitmaps with disk-based kmer index
- Implement partitioned kmer sets with delta-varint encoding
- Add support for frequency filtering during construction
- Introduce new builder pattern for index construction
- Add streaming operations for set operations (union, intersect, etc.)
- Add support for super-kmer encoding during construction
- Update command line tool to use new index format
- Remove dependency on roaring bitmap library

This change introduces a new architecture for kmer indexing that is more memory efficient and scalable for large datasets.

2026-02-09 17:52:37 +01:00

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