- Add new obiskio crate for high-performance SuperKmer serialization/deserialization
- Implement binary codec with 2-bit packed sequence encoding and raw header format (32 bits)
- Add transparent compression support via niffler: Zstd, Gzip/Bgzf/Lz4
- Implement SKFilePool with LRU-based fd management, max-concurrent-fd limiting (75% of ulimit)
- Add SKFileWriter with batched writes, configurable flush threshold (8 KiB default), and two-phase locking
- Add SKFileReader with sequential access, LRU recovery via reopen_and_seek()
+ New obikpartitionner crate: basic header/seq handling for binary super-kmer format
- Bump niffler from 2.7 to v3, add dependencies: allocator-api2, bitflags(>=1), errno/fastrand/rustix/tempfile/lru/hashbrown/bzip2/thiserror
- Update workspace members to include obikpartitionner andobiskio
- Update super-kmer definition in `kmERS.md` to specify that non-degenerate m-mers are preferred over degenerate ones (degeneracy = homopolymer).
- Refactor `superkmer.rs`: change `.canonical()` to mutate in-place and return bool.
- Add `m` field & canonical-aware minimizer position calculation to SuperKmerIter in obiskbuilder.
- Add helper functions `is_degenerate` and minimizer comparison logic to rolling_stat.rs for consistent tie-breaking.
- Minor formatting cleanup in superkmer command and chunk processing.
- Introduce lazy_static dependency
- Refactor encoding: rename encode_base →encode_nuc and make it pub(crate)
- Add from_raw_right/raw Right methods to Kmer for right-aligned handling
- Improve error message formatting and code readability in kmod.rs tests
- Replace inline entropy computation with precomputed tables (entropy_table module)—using LazyLock for static lookup arrays
- Simplify EntropyFilter by removing redundant tables and delegating to new entropy_table API
- Add RollingStat module for real-time kmer statistics and minimizer tracking
- Reorganize modules: move iter, encoding to pub(crate), add entropy_table and rolling_stat
- Update imports across obiskbuilder crate accordingly
Eric Coissac