- Remove `entropy.rs`, `minimizer.rs` and `window.rs`; consolidate logic into new module
- Introduce unified state management in RollingStat with incremental entropy tracking and canonical minimizer computation via monotone deque
- Update SuperKmerIter to use RollingStat instead of separate components, simplifying iteration and state transitions
- Add `*.fasta` to .gitignore for generated FASTA outputs
Introduce static precomputed lists of canonical k-mers (K1– K6) via build_canonical_list and expose them through a canonical_kmers() helper. Update RollingStat to accept entropy_max_k parameter, remove obsolete shift_left field and fix minimizer window condition. Refactor normalized_entropy() to use entropy_max_k instead of hardcoded 1..=6, and optimize count-based loop in compute_entropy() to iterate only over canonical indices.
Fix incorrect nucleotide encoding in `rolling_k` update, correct shift amount for reverse complement k-mer (`self.k - 1`, not `k`), and rename method to match semantics. Also add proper windowed minimizer cleanup when received length exceeds k.
- 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
- Change `rope_tell()` return type from Option<usize> to usize, always returning cursor's absolute position (offset if unmoved).
- Update all call sites to remove `.unwrap_or(...)` around `rope_tell()`.
- Add new method `<Rope>::truncate(pos)`, replacing `split_off(...).map(|_| ())`.
- Refactor FASTA/FASTQ normalizers to use a single mutable write cursor (`wc`) and document the protocol.
- Simplify `end_segment()` logic: commit segment with 0x00 if length ≥ k, else reset.
- Improve documentation for write-cursor protocol and rope truncation semantics.
- Introduce SeekMode::Rope for absolute rope-index positioning
- Add CursorState.offset field to support local coordinate systems per cursor
- Implement ForwardCursor.cursor() and BackwardCursor(cursor()) to create sub-cursors with independent offsets
- Update tell(), get(i), set i, len() to use local coordinates (relative offset)
- Add rope_tell(), reset()—deprecate old absolute behavior in favor of offset-aware API
- Add comprehensive tests for sub-cursor semantics, including write/reset and bounds checking
Eric Coissac