NEWS

Rminibwa 0.7.0-0.0.1.9000

Update vendored minibwa to exact upstream commit 74bdd485f2517fdd322faa1fd8eb36ecf297743d (MB_VERSION 0.7-r427-dirty; archive SHA256 292130071f72e2bcd8b792b888be6063986b8867176530027927602de6e8a6bf). This corrects mismatch counting when choosing gapped alignment, including the homopolymer-indel case in upstream issue #75. It also includes v0.7 and post-v0.7 fixes for paired-end metadata, option handling, short-read preset selection, CLI error status, paired-end diagnostics, and BWT prefetching.

Make Rduckhts the required htslib provider. Configure now validates and consumes its exact installed linking receipt on Unix and Windows, and rminibwa_htslib_info() verifies the linked version and build identity at runtime. This provides one verified htslib identity for future native alignment-format work without selecting its output architecture. Browser-wasm builds now omit the direct adapter explicitly because rwasm exposes only Rduckhts's host-native library to downstream configure scripts.
Add a Win32 file-mapping implementation for vendored minibwa so Windows and Rtools builds no longer require the unavailable POSIX sys/mman.h.
Add a versioned, lossless native FASTQ query-group stream for downstream native record consumers. The installed C API exposes bounded one-template views, typed CIGAR/tag data, header facts, cooperative cancellation, explicit ownership/lifetime rules, exact read-group preservation, and reason-coded paired FASTQ validation without a SAM-text or per-record-R-callback path.
Update vendored minibwa to the exact upstream v0.6 release commit ebc59eaff045898c6a9daed4689302547d1326cb (MB_VERSION 0.6-r416; archive SHA256 f84b42299923ccfcab19f46bfdb7fdb4562d87c95cb0fc591823458474870474). This includes the paired-end mapQ revision, memory-mapped index loading, --outs, BS-seq API support, and the corrected -I fixed insert-size distribution behavior from upstream v0.5 and v0.6.

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.

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 an optional external Python binding 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.