Commit Graph

5 Commits

Author SHA1 Message Date
Eric Coissac 75bf980046 (deps) Add regex crate and improve MIME type detection
- Added `regex` dependency to obiread crate
- Replaced manual byte checks with regex-based detection for FASTA/FASTQ formats in mimetype.rs
- Switched from `once_cell::sync::Lazy` to standard library's `std:: sync :: LazyLock`
- Added generic text/plain fallback detection for ASCII-compatible content
- Updated `MimeTypeGuesser::new` constructor call syntax and simplified API usage of PeekReader's header method
- Implemented `Read trait for MimeTypeGuesser to allow transparent passthrough reading
2026-04-24 17:16:17 +02:00
Eric Coissac 3f8880a7e5 📦 Add infer and new pipeline infrastructure
- Update Cargo.lock with dependency additions (bumpalo, byteorder, cfb, fnv, infer, js-sys, uuid wasm-bindgen)
- Refactor obikseq::superkmer: reorder imports and improve formatting
  - Add `obipipeline` crate with scheduler, error handling & macros (WIP)
- Replace obiread::expand_paths logic with PathIter and path_iterator module
  - Add mimetype detection using `infer` crate via PeekReader wrapper
2026-04-23 21:06:11 +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 0dcb5dd6c2 ♻️ refactor rope implementation to use obikrope
- rename `obirope` → `obikroper`
- replace legacy rope with new in-place, Cell-based implementation
  - add ForwardCursor/Backward Cursor & SeekMode support (no more BytesMut)
- update all dependents:
  - obiread: switch to Rope + cursors, remove tape.rs
    • chunk iterator yields `Rope` instead of Vec<Bytes>
  - obiskbuilder: use ForwardCursor over Rope
- remove bytes dependency from affected crates
2026-04-19 21:23:10 +02:00
Eric Coissac de3f9b16cf first implementation but far to be optimal 2026-04-19 12:17:16 +02:00