{
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  "Package": "RBCFTools",
  "Title": "Packaged 'BCFtools' and 'HTSlib' Command-Line Tools",
  "Version": "1.23-0.0.4.9000",
  "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\",\nemail = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Abiomix FZ LLC\", role = c(\"cph\", \"fnd\"),\ncomment = \"Copyright holder and funder of Abiomix contributions\"),\nperson( given = \"Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas Davies, Robert M, Pierre Lindenbaum\",  role = \"cph\",\ncomment = \"Authors of included htslib library and bcftools command line tools\"),\nperson(given = \"Zilong\", family = \"Li\", email = \"zilong.dk@gmail.com\", role = c(\"cph\"),\ncomment = \"Author of the vcfpp library from whom makefiles and configure strategy is borrowed\"),\nperson(given = \"Giulio\", family = \"Genovese\", email = \"giulio.genovese@gmail.com\", role = \"cph\", comment = \"Author of BCFTools munge plugin\"))",
  "Description": "Builds and installs pinned 'bcftools' and 'htslib'\ncommand-line tools, including packaged plugins such as liftover\nand score. Provides executable discovery, deterministic plugin\nenvironment configuration, version inspection, and structured\nprocess execution. Variant table, 'DuckDB', 'DuckLake', Arrow,\nParquet, and annotation APIs are intentionally owned by\n'Rduckhts' rather than duplicated here.",
  "License": "GPL (>= 3)",
  "Copyright": "See inst/AUTHORS",
  "SystemRequirements": "GNU make, pkg-config, libcurl, libgsl, libdeflate,\nlibbzip2, libzlib, libssl-dev (or other ssl library), liblzma,\nlibsuitesparse-dev/libcholmod5 (optional for pgs plugin)",
  "OS_type": "unix",
  "URL": "https://github.com/abiomix/abiomix-r-open,\nhttps://github.com/RGenomicsETL/RBCFTools,\nhttps://rgenomicsetl.github.io/RBCFTools/",
  "BugReports": "https://github.com/abiomix/abiomix-r-open/issues",
  "Config/abiomix/public-license": "GPL-3.0-or-later",
  "Config/abiomix/commercial-license": "Separate written agreement for\nAbiomix-owned contributions",
  "Config/abiomix/license-policy": "https://github.com/abiomix/abiomix-r-open/blob/main/LICENSES.md",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "make libgsl0-dev liblzma-dev pkg-config",
  "Repository": "https://abiomix.r-universe.dev",
  "Date/Publication": "2026-07-13 08:37:42 UTC",
  "RemoteUrl": "https://github.com/abiomix/abiomix-r-open",
  "RemoteRef": "HEAD",
  "RemoteSha": "dd82290ba296385fcc7d7dfed339886e9deb41a2",
  "RemoteSubdir": "packages/RBCFTools",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-13 11:47:46 UTC",
    "User": "root"
  },
  "Author": "Sounkou Mahamane Toure [aut, cre],\nAbiomix FZ LLC [cph, fnd] (Copyright holder and funder of Abiomix\ncontributions),\nBonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and\nOhan, Valeriu and Whitwham, Andrew and Keane, Thomas Davies, Robert\nM, Pierre Lindenbaum [cph] (Authors of included htslib library and\nbcftools command line tools),\nZilong Li [cph] (Author of the vcfpp library from whom makefiles and\nconfigure strategy is borrowed),\nGiulio Genovese [cph] (Author of BCFTools munge plugin)",
  "Maintainer": "Sounkou Mahamane Toure <sounkoutoure@gmail.com>",
  "_user": "abiomix",
  "_type": "src",
  "_file": "RBCFTools_1.23-0.0.4.9000.tar.gz",
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  "_expires": "2026-10-21T12:04:27.000Z",
  "_created": "2026-07-13T11:47:46.000Z",
  "_published": "2026-07-13T12:04:29.743Z",
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  "_buildurl": "https://github.com/r-universe/abiomix/actions/runs/29247316002",
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    "author": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "committer": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "message": "Update bundled minibwa to upstream 0.4\n\nRefresh the pinned native sources to minibwa 0.4-r400 while retaining the reviewed portability and SIMD patch queue. Update the package version, installed provenance, CLI version assertion, and release documentation.\n",
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    "name": "Sounkou Mahamane Toure",
    "email": "sounkoutoure@gmail.com",
    "login": "sounkou-bioinfo",
    "mastodon": "@bioinfhotep@genomic.social",
    "description": "Sequences and Consequences.",
    "uuid": 56392505
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  "_registered": true,
  "_dependencies": [
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      "version": ">= 4.1.0",
      "role": "Depends"
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      "role": "Imports"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
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  "_owner": "abiomix",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "n": 20
    }
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  "_stars": 0,
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    "type": "organization",
    "name": "Litpeaks",
    "followers": 3,
    "description": "Litpeaks Github Organization"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RBCFTools"
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  "_devurl": "https://github.com/abiomix/abiomix-r-open",
  "_pkgdown": "https://rgenomicsetl.github.io/RBCFTools/",
  "_searchresults": 27,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RBCFTools.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_exports": [
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    "bcftools_bin_dir",
    "bcftools_path",
    "bcftools_plugins",
    "bcftools_plugins_dir",
    "bcftools_run",
    "bcftools_tools",
    "bcftools_version",
    "bgzip_path",
    "htsfile_path",
    "htslib_bin_dir",
    "htslib_plugins_dir",
    "htslib_tools",
    "htslib_version",
    "rbcftools_binary",
    "rbcftools_capabilities",
    "rbcftools_run",
    "rbcftools_versions",
    "ref_cache_path",
    "setup_hts_env",
    "tabix_path"
  ],
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    {
      "page": "bcftools_run",
      "title": "Run the packaged bcftools executable",
      "topics": [
        "bcftools_run"
      ]
    },
    {
      "page": "rbcftools_binary",
      "title": "Locate a packaged native executable",
      "topics": [
        "annot_tsv_path",
        "bcftools_path",
        "bgzip_path",
        "htsfile_path",
        "rbcftools_binary",
        "ref_cache_path",
        "tabix_path"
      ]
    },
    {
      "page": "rbcftools_capabilities",
      "title": "Report the installed binary surface",
      "topics": [
        "rbcftools_capabilities"
      ]
    },
    {
      "page": "rbcftools_directories",
      "title": "Locate packaged tool directories",
      "topics": [
        "bcftools_bin_dir",
        "bcftools_plugins_dir",
        "htslib_bin_dir",
        "htslib_plugins_dir",
        "rbcftools_directories"
      ]
    },
    {
      "page": "rbcftools_inventory",
      "title": "List packaged tools and plugins",
      "topics": [
        "bcftools_plugins",
        "bcftools_tools",
        "htslib_tools",
        "rbcftools_inventory"
      ]
    },
    {
      "page": "rbcftools_run",
      "title": "Run a packaged native tool",
      "topics": [
        "rbcftools_run"
      ]
    },
    {
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      "title": "Inspect packaged native-tool versions",
      "topics": [
        "bcftools_version",
        "htslib_version",
        "rbcftools_versions"
      ]
    },
    {
      "page": "setup_hts_env",
      "title": "Configure native-tool plugin lookup for the current R process",
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      ]
    }
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