Introduces `CommonArgs::validate()` to enforce strict constraints on `--kmer-size` (odd, 11–31), `--minimizer-size` (odd, 3–k−1), and `z` (strictly less than k). This validation is applied at the entry point of the `superkmer` and `index` commands to prevent invalid configurations, avoid palindromes, prevent u64 overflow, and ensure positive effective indexing sizes. Documentation is updated to reflect these runtime checks and immediate termination on invalid input.
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.
- 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
Eric Coissac