OBIKmers/obikmer
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22951fb0e868aedbd12962d34348e5c885b9606b
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4 Commits

Author SHA1 Message Date
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