Package: Rpgen 0.1.0

Rpgen: Vendored 'PLINK 2' pgenlib with a C-Callable Genotype Reader API

Vendors the read subset of 'PLINK 2's pgenlib library (<https://github.com/chrchang/plink-ng>), the same subset the CRAN package 'pgenlibr' vendors and builds, as a static library and exposes it through 'R_RegisterCCallable' C-callable entry points. Also vendors plink2's own import closure ('VcfToPgen', 'BcfToPgen', 'OxBgenToPgen', 'OxGenToPgen', 'OxHapslegendToPgen', 'Plink1DosageToPgen') so a VCF, BCF, BGEN, Oxford .gen, Oxford .haps/.legend, or legacy PLINK 1 --import-dosage file can be converted to a '.pgen' and read back through this package's own reader, without a separate 'htslib'-based parser. This is a carrier package: it has no high-level R modeling API of its own beyond a milestone smoke test that opens a '.pgen' file and reports its sample and variant counts. Other R packages link to it ('LinkingTo') to read 'PLINK 2' genotype files natively from their own C or C++ code, which 'pgenlibr' does not expose, since it only offers an R-level interface.

Authors:Sounkou Mahamane Toure [aut, cre], Christopher Chang [cph], Shaun Purcell [cph], Eric Biggers [cph], Yann Collet [cph], Meta Platforms, Inc. [cph], Evan Nemerson [cph], Mutsuo Saito [cph], Makoto Matsumoto [cph]