NEWS

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Rsassy 0.2.1-0.1.0.9000

• Added experimental sassy_fastx_iter() / sassy_fastx_next() chunked FASTA/FASTQ iteration backed by vendored needletail, with ALTREP character record IDs and raw ALTREP sequence/quality slices over immutable native batch buffers.
• Added committed R Markdown/Markdown conformance and performance reports under benchmarks/, with upstream sassy CLI baselines and threaded Rsassy runs.
• Added a webR/WebAssembly package check in CI.
• Built webR packages with static Rust FFI symbols and wasm_simd128.
• Added native package-level SIMD backends:
  • x86_64: scalar, AVX2, AVX-512.
  • arm64/aarch64: scalar, NEON.
• Added one-shot backend selection:
  • automatic best-backend selection on first native call;
  • explicit sassy_set_backend() before first native call.
• Added sassy_features() fields for installed backends, selected backend, compiled features, and CPU/runtime capabilities.
• Added CRAN-style Rust vendoring with an offline Cargo vendor tarball.
• Added CRAN-safe default Cargo parallelism and local fast Makefile targets.
• Added list-based bulk search support for sassy_searcher_search() and sassy_search(): pattern and text are now lists of raw vectors or character scalars, so each raw vector is one byte sequence and callers can mix raw, character, and ALTREP-backed string elements.
• Added bulk search strategies "pairwise", "batch_texts", "batch_patterns", and "encoded_patterns"/"v2".
• Added native Rust/Rayon threading for bulk search; wasm32 remains serial.
• Improved threaded strategy = "pairwise" scheduling to split Cartesian pattern/text tasks, which helps one-pattern-many-text workloads.
• Ordered returned matches by input text, then start/end coordinate, then pattern index, matching record-oriented CLI expectations.
• Added match_region = TRUE; reverse-strand regions are returned in pattern direction.
• Added class sassy_matches and print.sassy_matches().
• Added optional ANSI coloring for printed match regions.
• Added SAM-compatible reverse-strand formatting with sam = TRUE and sassy_as_sam().
• Added pattern_id and text_id mapping in the C data-frame construction path.
• Added native C/Rust CRISPR search support for in-memory guide/target lists.
• Added committed upstream sassy CLI fixtures under inst/extdata/ and tests that compare Rsassy output against those generated ground-truth tables.
• Removed the raw R connection stream API before release; FASTA/FASTQ input will use an explicit record-oriented file API rather than stream-relative text coordinates.
• Added result columns pattern_idx, text_idx, text_start, text_end, pattern_start, pattern_end, cost, strand, and cigar.
• Added the R API functions sassy_searcher(), sassy_searcher_search(), and sassy_search().
• Added configure checks for Cargo and rustc >= 1.91.0.
• Added bundled Rust crate authorship and license notes.