Commit Graph

2 Commits

Author SHA1 Message Date
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 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