Commit Graph

4 Commits

Author SHA1 Message Date
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