7 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	b7db3a33ed	docs: add coverage reference files and flag architectural drift ... These files catalog test coverage for Rust modules across architecture, implementation, and theory sections. They track recent structural changes, flag areas prone to documentation drift, and mandate verification of key parameters and routing logic to maintain alignment with the active codebase.	2026-05-23 13:44:23 +02:00
Eric Coissac	58391886a3	🔧 Replace degenerate minimizer logic with hash-based random ordering ... - Add `hash` field to MmerItem for stable, randomized minimizer ordering - Introduce hash_mMER() using mix64 with XOR seed to avoid fixed points (e.g., poly-A/T) - Remove is_degenerate() and minimizer_worse(), simplifying comparison to hash-only - Update push logic: compare hashes instead of canonical values with degeneracy checks	2026-04-27 20:19:43 +02:00
Eric Coissac	664d0216b5	📦 Add obipipeline crate and refactor path handling ... - Introduce new `obipackage` library with pipeline stages, scheduler and worker pool - Refactor path expansion in `obiread`: replace old list_of_files with new PathIter iterator - Add MIME type detection using `infer` crate (fastq/fasta) - Update dependencies in Cargo.lock: add bumpalo, byteorder, cfb (with deps), fnv, infer, js-sys/uuid/wasm-bindgen ecosystem - Fix formatting and improve tests in SuperKmer (canonical, revcomp) * Note: edition = "2024" in obipipeline/Cargo.toml is invalid; should be 2021	2026-04-23 21:06:11 +02:00
Eric Coissac	380b5a6f94	📖 Update super-kmer theory and implementation to prefer non-degenerate m-mers ... - 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.	2026-04-20 17:50:09 +02:00
Eric Coissac	de3f9b16cf	first implementation but far to be optimal	2026-04-19 12:17:16 +02:00