obikmer

OBIKmers/obikmer

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Commit Graph

Author	SHA1	Message	Date
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

Author

SHA1

Message

Date

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

3 Commits