Package: Rpgen
Title: Vendored 'PLINK 2' pgenlib with a C-Callable Genotype Reader API
Version: 0.1.0
Authors@R: c(
    person(given = "Sounkou Mahamane", family = "Toure", email = "sounkoutoure@gmail.com", role = c("aut", "cre")),
    person(given = "Christopher", family = "Chang", role = "cph", comment = "Author of the vendored pgenlib library and plink2 program"),
    person(given = "Shaun", family = "Purcell", role = "cph", comment = "Co-author of the vendored plink2 program (VcfToPgen import closure)"),
    person(given = "Eric", family = "Biggers", role = "cph", comment = "Author of included libdeflate library"),
    person(given = "Yann Collet", family = "", role = "cph", comment = "Author of included Zstd library"),
    person(given = "Meta Platforms, Inc.", role = "cph", comment = "Zstd library"),
    person(given = "Evan", family = "Nemerson", role = "cph", comment = "Author of included SIMDe library"),
    person(given = "Mutsuo", family = "Saito", role = "cph", comment = "Co-author of included SFMT library"),
    person(given = "Makoto", family = "Matsumoto", role = "cph", comment = "Co-author of included SFMT library")
    )
Description: 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.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.4.0), Rfmalloc
Suggests: tinytest
Remotes: sounkou-bioinfo/Rfmalloc/packages/Rfmalloc
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://github.com/sounkou-bioinfo/Rfmalloc,
        https://sounkou-bioinfo.github.io/Rfmalloc/Rpgen/
BugReports: https://github.com/sounkou-bioinfo/Rfmalloc/issues
Config/pak/sysreqs: make
Repository: https://sounkou-bioinfo.r-universe.dev
Date/Publication: 2026-07-10 06:12:39 UTC
RemoteUrl: https://github.com/sounkou-bioinfo/Rfmalloc
RemoteRef: HEAD
RemoteSha: 921d01f6786a2db38d90a2629c39f56a244b7875
RemoteSubdir: packages/Rpgen
NeedsCompilation: yes
Packaged: 2026-07-10 10:09:41 UTC; root
Author: Sounkou Mahamane Toure [aut, cre],
  Christopher Chang [cph] (Author of the vendored pgenlib library and
    plink2 program),
  Shaun Purcell [cph] (Co-author of the vendored plink2 program
    (VcfToPgen import closure)),
  Eric Biggers [cph] (Author of included libdeflate library),
  Yann Collet [cph] (Author of included Zstd library),
  Meta Platforms, Inc. [cph] (Zstd library),
  Evan Nemerson [cph] (Author of included SIMDe library),
  Mutsuo Saito [cph] (Co-author of included SFMT library),
  Makoto Matsumoto [cph] (Co-author of included SFMT library)
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>