Extracts streaming entropy logic and sliding-window frequency tracking from obiskbuilder into a dedicated obikentropy crate. Introduces an EntropyTracker accumulator for O(1) per-base normalized Shannon entropy, replaces inline rolling statistics with delegated state management, and updates workspace dependencies across obikindex, obikpartitionner, and obiskbuilder. Adds criterion benchmarks to validate the refactored pipeline throughput.
Introduce the `obiread` crate with a streaming byte normalizer that processes FASTA, FASTQ, and GenBank files using a 64 KiB ring buffer for O(1) memory usage. Integrate this crate into `obiskbuilder` to provide `SuperKmerStreamIter`, enabling memory-efficient superkmer traversal with rolling entropy and minimizer-based cut conditions.
Centralize k-mer and minimizer configuration using a thread-safe global module, and replace manual bit-packing with a memory-efficient `PackedSeq` type. Refactor core sequence and k-mer types to use compile-time length enforcement and centralized hashing. Introduce a new De Bruijn graph implementation with compact node encoding and traversal iterators. Update I/O, partitioning, and builder modules to align with the new architecture, and add the `xxhash-rust` dependency.
- 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