Add write_uncompressed index generation and a validated end-to-end
mmap_reference workflow, with an explicit disk-space tradeoff and a clear
error when required uncompressed tables are absent.
Unmap each memory-mapped index file using its validated extent, preventing a teardown crash exposed by the package's small real mmap workflow.
Create static archives with portable ar options accepted by GNU and Darwin
toolchains.
Use a pthread mutex-and-condition counter for the hash compressor on Darwin instead of deprecated unnamed POSIX semaphores.
Stop forcing the POSIX limits header into every imported C source because its
Darwin NZERO macro conflicts with the hash generator under -Werror.
Probe GCC-only C tuning and warning flags separately from C++ tuning flags so
Apple Clang can compile imported hash-generation sources under -Werror.
Use the portable POSIX limits header for imported metrics compilation on macOS.
Fix Apple Clang compilation for imported alignment extent and iterator initialization.
Build against the R-universe macOS Boost bundle and use POSIX and Darwin facilities where the imported Linux implementation was not portable.
Add a source-built R wrapper that owns and resolves dragen-os without
searching PATH.
Add typed S7 results, operational error values, and contract conditions for reference generation and FASTQ to SAM alignment.
Add a reproducible native source archive, configure-time build, tinytest coverage, and tarball-based package Makefile workflow.