3 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	fd2c23e7df	refactor: remove equivalence class folding from entropy pipeline ... Removes circular-reverse complement machinery and explicit k-mer canonicalization across the entropy pipeline. Frequency tallying and Shannon entropy computation now operate directly on raw k-mer values, eliminating prior score inflation and alignment-dependent artifacts while preserving orientation invariance. Updates build scripts to generate normalized lookup tables for k-mer lengths 1–6, restricts the public API to `EntropyTracker`, and bumps crate versions. Documentation is updated to reflect the simplified raw-value approach and revised module structure.	2026-07-08 19:36:30 +02:00
Eric Coissac	036d044291	refactor: update core types and add approximate evidence support ... Refactor `Kmer`, `SuperKmer`, and chunk reader into optimized, generic representations with compile-time length parameters and bitwise operations. Update the pipeline and scheduler to support batch processing, 1→N flat transformations, and multi-source merging. Introduce an approximate evidence mode using b-bit fingerprints and `.idx` files, alongside existing exact mode. Update CLI documentation, minimizer selection, and query output schema accordingly.	2026-05-26 10:04:25 +02:00
Eric Coissac	de3f9b16cf	first implementation but far to be optimal	2026-04-19 12:17:16 +02:00