{
  "_id": "6a117513acfb0bcc41cf8a46",
  "Package": "vcfppR",
  "Title": "Rapid Manipulation of the Variant Call Format (VCF)",
  "Version": "0.8.3",
  "Authors@R": "c(\nperson(\"Zilong\", \"Li\", , \"zilong.dk@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5859-2078\")),\nperson(\"Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies, Robert M\",  role = \"cph\",\ncomment = \"Authors of included htslib library\")\n)",
  "Copyright": "See the file COPYRIGHTS for various htslib copyright details",
  "Description": "The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>)\nprovides an easy-to-use 'C++' 'API' of 'htslib', offering full\nfunctionality for manipulating Variant Call Format (VCF) files.\nThe 'vcfppR' package serves as the R bindings of the 'vcfpp.h'\nlibrary, enabling rapid processing of both compressed and\nuncompressed VCF files. Explore a range of powerful features\nfor efficient VCF data manipulation.",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "SystemRequirements": "libcurl: libcurl-devel (rpm) or\nlibcurl4-openssl-dev (deb), GNU make.",
  "URL": "https://github.com/Zilong-Li/vcfppR",
  "BugReports": "https://github.com/Zilong-Li/vcfppR/issues",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-23 09:30:56 UTC",
    "User": "root"
  },
  "Author": "Zilong Li [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5859-2078>), Bonfield, James K and\nMarshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu\nand Whitwham, Andrew and Keane, Thomas and Davies, Robert M\n[cph] (Authors of included htslib library)",
  "Maintainer": "Zilong Li <zilong.dk@gmail.com>",
  "Config/pak/sysreqs": "make libssl-dev",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-03-31 21:00:13 UTC",
  "RemoteUrl": "https://github.com/cran/vcfppR",
  "RemoteRef": "HEAD",
  "RemoteSha": "537c8c385ae984a17e13f6490c37117992ffd57f",
  "MD5sum": "d12c8ff94d91b794d78370929e086bf8",
  "_user": "cran",
  "_type": "src",
  "_file": "vcfppR_0.8.3.tar.gz",
  "_fileid": "b72eeeae7a5f539b2f4f3b79b741262fc8fbc8a6d6859e3a6b8911e9d0c8b23d",
  "_filesize": 2899549,
  "_sha256": "b72eeeae7a5f539b2f4f3b79b741262fc8fbc8a6d6859e3a6b8911e9d0c8b23d",
  "_created": "2026-05-23T09:30:56.000Z",
  "_published": "2026-05-23T09:36:19.713Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77512553950,
      "time": 174,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7175985636"
    },
    {
      "job": 77512553946,
      "time": 193,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7175987376"
    },
    {
      "job": 77512553953,
      "time": 227,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7175990623"
    },
    {
      "job": 77512553959,
      "time": 194,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7175987647"
    },
    {
      "job": 77512301064,
      "time": 305,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7175969875"
    },
    {
      "job": 77512553940,
      "time": 110,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26329231305",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/vcfppR",
  "_commit": {
    "id": "537c8c385ae984a17e13f6490c37117992ffd57f",
    "author": "Zilong Li <zilong.dk@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.8.3\n",
    "time": 1774990813
  },
  "_maintainer": {
    "name": "Zilong Li",
    "email": "zilong.dk@gmail.com",
    "login": "zilong-li",
    "orcid": "0000-0001-5859-2078",
    "twitter": "@zilongli21",
    "description": "MSCA postdoctoral fellow at Oxford",
    "uuid": 11785793
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "codetools",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-27",
      "n": 1
    },
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2026-14",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.8.0",
      "date": "2025-07-02"
    },
    {
      "name": "0.8.1",
      "date": "2025-08-25"
    },
    {
      "name": "0.8.2",
      "date": "2025-11-06"
    },
    {
      "name": "0.8.3",
      "date": "2026-03-31"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zilong-li",
      "count": 15,
      "uuid": 11785793
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 340,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/vcfppR"
  },
  "_devurl": "https://github.com/zilong-li/vcfppr",
  "_searchresults": 32,
  "_topics": [
    "zlib",
    "bzip2",
    "xz-utils",
    "curl",
    "libdeflate",
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/vcfppR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/zilong-li/vcfppr",
  "_realowner": "zilong-li",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.3.5",
      "date": "2023-12-14"
    },
    {
      "version": "0.3.8",
      "date": "2024-01-14"
    },
    {
      "version": "0.4.0",
      "date": "2024-02-26"
    },
    {
      "version": "0.4.3",
      "date": "2024-03-27"
    },
    {
      "version": "0.4.5",
      "date": "2024-04-08"
    },
    {
      "version": "0.4.6",
      "date": "2024-05-24"
    },
    {
      "version": "0.5.0",
      "date": "2024-09-22"
    },
    {
      "version": "0.6.0",
      "date": "2024-09-29"
    },
    {
      "version": "0.7.0",
      "date": "2024-12-21"
    },
    {
      "version": "0.7.1",
      "date": "2024-12-26"
    },
    {
      "version": "0.7.6",
      "date": "2025-03-31"
    },
    {
      "version": "0.8.0",
      "date": "2025-07-02"
    },
    {
      "version": "0.8.1",
      "date": "2025-08-25"
    },
    {
      "version": "0.8.2",
      "date": "2025-11-06"
    },
    {
      "version": "0.8.3",
      "date": "2026-03-31"
    }
  ],
  "_exports": [
    "plot_variants_per_haplotype",
    "vcfcomp",
    "vcfinfo",
    "vcfplot",
    "vcfpopgen",
    "vcfpp_calc_info_persite",
    "vcfreader",
    "vcfsummary",
    "vcftable",
    "vcfwriter"
  ],
  "_help": [
    {
      "page": "vcfppR-package",
      "title": "vcfppR: Rapid Manipulation of the Variant Call Format (VCF)",
      "topics": [
        "vcfppR-package",
        "vcfppR"
      ]
    },
    {
      "page": "plot_variants_per_haplotype",
      "title": "Plot variants on haplotypes across multiple samples",
      "topics": [
        "plot_variants_per_haplotype"
      ]
    },
    {
      "page": "subset.vcftable",
      "title": "Subset a vcftable object",
      "topics": [
        "subset.vcftable"
      ]
    },
    {
      "page": "vcfcomp",
      "title": "Compare two VCF/BCF files reporting various statistics",
      "topics": [
        "vcfcomp"
      ]
    },
    {
      "page": "vcfinfo",
      "title": "read a INFO tag in the VCF/BCF into R data structure",
      "topics": [
        "vcfinfo"
      ]
    },
    {
      "page": "vcfplot",
      "title": "Make sensible and beautiful plots based on various objects in vcfppR",
      "topics": [
        "vcfplot"
      ]
    },
    {
      "page": "vcfpopgen",
      "title": "count the heterozygous sites per sample in the VCF/BCF",
      "topics": [
        "vcfpopgen"
      ]
    },
    {
      "page": "vcfpp_calc_info_persite",
      "title": "Calculate INFO score from GP after genotype imputation",
      "topics": [
        "vcfpp_calc_info_persite"
      ]
    },
    {
      "page": "vcfreader",
      "title": "API for manipulating the VCF/BCF.",
      "topics": [
        "vcfreader"
      ]
    },
    {
      "page": "vcfsummary",
      "title": "summarize the various variant types at both variant level and sample level.",
      "topics": [
        "vcfsummary"
      ]
    },
    {
      "page": "vcftable",
      "title": "read VCF/BCF contents into R data structure",
      "topics": [
        "vcftable"
      ]
    },
    {
      "page": "vcfwriter",
      "title": "API for writing the VCF/BCF.",
      "topics": [
        "vcfwriter"
      ]
    }
  ],
  "_readme": "https://github.com/cran/vcfppR/raw/HEAD/README.md",
  "_rundeps": [
    "Rcpp"
  ],
  "_sysdeps": [
    {
      "shlib": "libz",
      "package": "zlib1g",
      "headers": "zlib1g-dev",
      "source": "zlib",
      "version": "1:1.3.dfsg-3.1ubuntu2.1",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    },
    {
      "shlib": "libbz2",
      "package": "libbz2-1.0",
      "headers": "libbz2-dev",
      "source": "bzip2",
      "version": "1.0.8-5.1build0.1",
      "name": "bzip2",
      "homepage": "https://sourceware.org/bzip2/",
      "description": "high-quality block-sorting file compressor library - runtime"
    },
    {
      "shlib": "liblzma",
      "package": "liblzma5",
      "headers": "liblzma-dev",
      "source": "xz-utils",
      "version": "5.6.1+really5.4.5-1ubuntu0.2",
      "name": "xz-utils",
      "homepage": "https://tukaani.org/xz/",
      "description": "XZ-format compression library"
    },
    {
      "shlib": "libcurl",
      "package": "libcurl4t64",
      "headers": "libcurl4-openssl-dev",
      "source": "curl",
      "version": "8.5.0-2ubuntu10.9",
      "name": "curl",
      "homepage": "https://curl.se/",
      "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)"
    },
    {
      "shlib": "libdeflate",
      "package": "libdeflate0",
      "headers": "libdeflate-dev",
      "source": "libdeflate",
      "version": "1.19-1build1.1",
      "name": "libdeflate",
      "homepage": "https://github.com/ebiggers/libdeflate",
      "description": "fast, whole-buffer DEFLATE-based compression and decompression"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "concordance-of-two-vcf-files.Rmd",
      "filename": "concordance-of-two-vcf-files.html",
      "title": "Assess the concordance between VCFs",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background",
        "Case 1: Genotype imputation accuracy",
        "Case 2: Genotype concordance",
        "Case 3: Phasing switch error",
        "Case 4: Multiple testing repetitively",
        "Q&A",
        "Where is the allele frequency from and can I use customized one?",
        "How to fix the error \"inconsistent samples name\"",
        "NA values returned"
      ],
      "created": "2024-05-25 03:05:19",
      "modified": "2025-07-02 13:50:02",
      "commits": 2
    }
  ],
  "_score": 3.8061799739838875,
  "_indexed": false,
  "_nocasepkg": "vcfppr",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://zilong-li.r-universe.dev/vcfppR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.8.3",
      "date": "2026-05-23T09:34:29.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "537c8c385ae984a17e13f6490c37117992ffd57f",
      "fileid": "10cd99e545bc8db30869e45403998c12170177251833e66c666454081af2f31c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26329231305"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.8.3",
      "date": "2026-05-23T09:34:38.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "537c8c385ae984a17e13f6490c37117992ffd57f",
      "fileid": "e80b59d009af345a9bb0a216bc52e73fd73bacc27849a5425be7bccef4d4b465",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26329231305"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.8.3",
      "date": "2026-05-23T09:35:20.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "537c8c385ae984a17e13f6490c37117992ffd57f",
      "fileid": "dd6783fa0d60aec6b0b19723f8345522fef994ca85d93b75af56257326c8fba7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26329231305"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.8.3",
      "date": "2026-05-23T09:34:46.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "537c8c385ae984a17e13f6490c37117992ffd57f",
      "fileid": "1ac86db1fb93ade6157dba57e02866cbf01c8dd7ef83d24976ff643d26868812",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26329231305"
    }
  ]
}