Update CLI validation to require at least 10 input paths, defaulting to stdin (`-`) when the argument list is empty. Refactor the path iterator to explicitly recognize the stdin sentinel, bypassing extension validation and directory expansion to ensure direct passthrough to the file buffer without triggering `stat()` or recursive traversal.
Instrument index and scatter stages with `tracing::info` to log input file paths for better runtime observability. Additionally, optimize the path iterator by replacing redundant `is_dir()` checks with explicit `is_file()` validation and deferring metadata resolution, eliminating unnecessary `stat()` syscalls and improving traversal performance on high-latency network filesystems like Lustre and NFS.
Explicitly add `bzip2-sys` and `liblzma-sys` with the `static` feature to the `obiread` crate. This enforces static linking for BZ2 and LZMA/XZ backends, eliminating runtime dynamic library dependencies and ensuring consistent binary distribution.
This change introduces the `query` CLI command and its supporting infrastructure for sequence-to-genome mapping and k-mer matching. It adds a `QueryLayer` abstraction backed by MPHF and persistent matrices, exposes the index partition for direct querying, and implements `Hash`/`Eq` for `RoutableSuperKmer`. The command ingests sequence batches, deduplicates superkmers, routes them to index partitions for parallel exact or 1-mismatch matching, and outputs results as FASTA records annotated with JSON metadata. Includes `serde_json` dependency addition, module exports, and documentation updates.
- 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
- Introduce `obipipline` crate with multi-threaded data pipeline architecture
- Implement core types: SourceFn, SharedFun (Arc), SinkFN with biased scheduler and crossbeam channels
- Add macros: `make_source!`, `transform!/fallible`/sink!, and high-level DSL macro
- Replace old wrapper/error modules with unified scheduler module (renamed types, improved error variants)
- Update workspace: add `obipipeline` member to Cargo.toml and lockfile
- Document pipeline in docmd/implementation with full architecture, error handling & example
- Refactor sandbox_pipeline.rs to use new DSL instead of manual channel wiring
- 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
- Change `rope_tell()` return type from Option<usize> to usize, always returning cursor's absolute position (offset if unmoved).
- Update all call sites to remove `.unwrap_or(...)` around `rope_tell()`.
- Add new method `<Rope>::truncate(pos)`, replacing `split_off(...).map(|_| ())`.
- Refactor FASTA/FASTQ normalizers to use a single mutable write cursor (`wc`) and document the protocol.
- Simplify `end_segment()` logic: commit segment with 0x00 if length ≥ k, else reset.
- Improve documentation for write-cursor protocol and rope truncation semantics.
Eric Coissac