NEWS

---

Rminibwa 0.0.0.9000

• Bootstrap Rminibwa as a GPL (>= 2) R package wrapping pinned upstream lh3/minibwa C sources.
• Add native bindings for index build/load, raw-vector query mapping, native external-pointer alignment batches, ALTREP column views, and packed CIGAR accessors.
• Install inst/include/Rminibwa.h and register C-callable accessors so downstream packages can consume alignment batches directly from C.
• Add staged KSW SIMD dispatch following the RsimdDispatch pattern: portable scalar/SIMDe fallback, SSE4, and AVX2 backends are compiled as separate objects and selected at runtime without global ISA compiler flags.
• Add AVX2 dual-gap extd2 support from the minibwa binding work and keep it as an optional runtime-dispatched backend.
• Vendor minibwa at commit f0fd108456d459e5da3755f29c8700dc7f6fe0df with a patch queue and provenance metadata.
• Add Rtinycc inline downstream-C examples in the README, vignette, and tests.
• Build and install a package-provided minibwa executable from vendored sources; CLI wrappers now use it by default.
• Add developer-only benchmarks comparing internal staged backends and optional external Python/Rust bindings from an explicit local checkout.
• Add make asm / tools/check-assembly.R to audit generated SIMD instruction families in staged objects and shared libraries.
• Add pkgdown configuration and GitHub Actions workflows for standard R CMD check, Fedora/R-devel CRAN-style check, and GitHub Pages deployment.