Changes in version 0.4.0-0.0.1.9000                   

  - Update the bundled minibwa sources to upstream v0.4 / MB_VERSION
    0.4-r400 at commit b2dcea9b43c02cef47556f993fbd54bc0002cd4a.
  - Include upstream's heavily clipped alignment rescoring improvement
    and SAM PG-CL subcommand fix.

                  Changes in version 0.3.0-0.0.1.9000                   

  - Add a MinGW/Rtools-only kthread.c dead-return guard after
    pthread_exit() to avoid -Wreturn-type install warnings on Windows.
  - Make kseq.h's kroundup64() width-safe on 32-bit targets such as
    wasm32, avoiding Emscripten -Wshift-count-overflow diagnostics.
  - Add mb_map_batch() for native columnar mapping of many query
    sequences in one call, plus mb_map_pair_batch() for explicit
    two-batch paired-end input.
  - Add native FASTX iterators and mb_map_fastx_batch() so file-backed
    batches can be mapped without materializing sequence strings in R.
  - Add a read-level sidecar to alignment batches with read IDs, query
    lengths, fragment/mate fields, and per-read hit offsets/counts,
    exposed through ALTREP read columns and the C API.
  - Add a concise print method for native alignment batches.
  - Return simd_info() as a classed rminibwa_simd_info object with a
    concise print method for dispatch diagnostics.
  - Fold in upstream minibwa v0.3 / MB_VERSION 0.3-r391 at commit
    a679d17cb822c6cca67ab78c439f9c9826f1b07d.
  - Switch package versions to the <minibwa-version>-<Rminibwa-version>
    scheme; development builds now use 0.3.0-0.0.1.9000.
  - Add a MinGW/Rtools-only kalloc.c format-string guard for size_t
    diagnostics while leaving the non-MinGW upstream code path
    unchanged.

                     Changes in version 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.