{
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  "Package": "alabaster.files",
  "Title": "Wrappers to Save Common File Formats",
  "Version": "1.10.0",
  "Date": "2023-12-30",
  "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")",
  "License": "MIT + file LICENSE",
  "Description": "Save common bioinformatics file formats within the\nalabaster framework. This includes BAM, BED, VCF, bigWig,\nbigBed, FASTQ, FASTA and so on. We save and load additional\nmetadata for each file, and we support linkage between each\nfile and its corresponding index.",
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  "RoxygenNote": "7.2.3",
  "biocViews": "DataRepresentation, DataImport",
  "Config/pak/sysreqs": "libbz2-dev liblzma-dev libssl-dev libnode-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:07 UTC",
  "RemoteUrl": "https://github.com/bioc/alabaster.files",
  "RemoteRef": "RELEASE_3_23",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
  },
  "Author": "Aaron Lun [aut, cre]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "609586f2dedc520a531784e1baa8cde3",
  "_user": "bioc-release",
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  "_published": "2026-05-29T10:42:22.114Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
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    "email": "infinite.monkeys.with.keyboards@gmail.com",
    "login": "ltla",
    "twitter": "@realAaronLun",
    "description": "(ノಠ益ಠ)ノ彡┻━┻\n",
    "uuid": 8166669
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      "package": "alabaster.base",
      "role": "Depends"
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    {
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    },
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    },
    {
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    },
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    },
    {
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  "_selfowned": false,
  "_usedby": 0,
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    },
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      "version": "1.10.0",
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    "dataimport"
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
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    "BamFileReference",
    "BamIndexWrapper",
    "BamWrapper",
    "BcfFileReference",
    "BedFileReference",
    "BedWrapper",
    "BgzipIndexWrapper",
    "BigBedFileReference",
    "BigBedWrapper",
    "BigWigFileReference",
    "BigWigWrapper",
    "compression",
    "FaIndexWrapper",
    "FastaFileReference",
    "FastaWrapper",
    "FastqFileReference",
    "FastqWrapper",
    "GffFileReference",
    "GffWrapper",
    "GmtFileReference",
    "GmtWrapper",
    "index",
    "loadBamIndexWrapper",
    "loadBamWrapper",
    "loadBedWrapper",
    "loadBgzipIndexWrapper",
    "loadBigBedWrapper",
    "loadBigWigWrapper",
    "loadFaIndexWrapper",
    "loadFastaWrapper",
    "loadFastqWrapper",
    "loadGffWrapper",
    "loadGmtWrapper",
    "loadTabixIndexWrapper",
    "loadVcfWrapper",
    "path",
    "readBamFileReference",
    "readBcfFileReference",
    "readBedFileReference",
    "readBigBedFileReference",
    "readBigWigFileReference",
    "readFastaFileReference",
    "readFastqFileReference",
    "readGffFileReference",
    "readGmtFileReference",
    "saveObject",
    "show",
    "stageObject",
    "TabixIndexWrapper",
    "VcfWrapper"
  ],
  "_help": [
    {
      "page": "BamFileReference",
      "title": "Reference to a BAM file",
      "topics": [
        "BamFileReference",
        "BamFileReference-class",
        "BamIndexWrapper",
        "BamIndexWrapper-class",
        "BamWrapper",
        "BamWrapper-class",
        "loadBamIndexWrapper",
        "loadBamWrapper",
        "readBamFileReference",
        "saveObject,BamFileReference-method",
        "stageObject,BamIndexWrapper-method",
        "stageObject,BamWrapper-method"
      ]
    },
    {
      "page": "BcfFileReference",
      "title": "Reference to a BCF file",
      "topics": [
        "BcfFileReference",
        "BcfFileReference-class",
        "loadVcfWrapper",
        "readBcfFileReference",
        "saveObject,BcfFileReference-method",
        "stageObject,VcfWrapper-method",
        "VcfWrapper",
        "VcfWrapper-class"
      ]
    },
    {
      "page": "BedFileReference",
      "title": "Reference to a BED file",
      "topics": [
        "BedFileReference",
        "BedFileReference-class",
        "BedWrapper",
        "BedWrapper-class",
        "loadBedWrapper",
        "readBedFileReference",
        "saveObject,BedFileReference-method",
        "stageObject,BedWrapper-method"
      ]
    },
    {
      "page": "BgzipIndexWrapper",
      "title": "Wrapper for a Bgzip index file",
      "topics": [
        "BgzipIndexWrapper",
        "BgzipIndexWrapper-class",
        "loadBgzipIndexWrapper",
        "stageObject,BgzipIndexWrapper-method"
      ]
    },
    {
      "page": "BigBedFileReference",
      "title": "Reference to a bigBed file",
      "topics": [
        "BigBedFileReference",
        "BigBedFileReference-class",
        "BigBedWrapper",
        "BigBedWrapper-class",
        "loadBigBedWrapper",
        "readBigBedFileReference",
        "saveObject,BigBedFileReference-method",
        "stageObject,BigBedWrapper-method"
      ]
    },
    {
      "page": "BigWigFileReference",
      "title": "Reference to a bigWig file",
      "topics": [
        "BigWigFileReference",
        "BigWigFileReference-class",
        "BigWigWrapper",
        "BigWigWrapper-class",
        "loadBigWigWrapper",
        "readBigWigFileReference",
        "saveObject,BigWigFileReference-method",
        "stageObject,BigWigWrapper-method"
      ]
    },
    {
      "page": "FastaFileReference",
      "title": "Reference to a FASTA file",
      "topics": [
        "FaIndexWrapper",
        "FaIndexWrapper-class",
        "FastaFileReference",
        "FastaFileReference-class",
        "FastaWrapper",
        "FastaWrapper-class",
        "loadFaIndexWrapper",
        "loadFastaWrapper",
        "readFastaFileReference",
        "saveObject,FastaFileReference-method",
        "show,FastaWrapper-method",
        "stageObject,FaIndexWrapper-method",
        "stageObject,FastaWrapper-method"
      ]
    },
    {
      "page": "FastqFileReference",
      "title": "Reference to a FASTQ file",
      "topics": [
        "FastqFileReference",
        "FastqFileReference-class",
        "FastqWrapper",
        "FastqWrapper-class",
        "loadFastqWrapper",
        "readFastqFileReference",
        "saveObject,FastqFileReference-method",
        "show,FastqWrapper-method",
        "stageObject,FastqWrapper-method"
      ]
    },
    {
      "page": "FileReference",
      "title": "Virtual file reference class",
      "topics": [
        "$,FileReference-method",
        "$<-,FileReference-method",
        "FileReference",
        "FileReference-class",
        "path,FileReference-method",
        "show,FileReference-method",
        "[[,FileReference-method",
        "[[<-,FileReference-method"
      ]
    },
    {
      "page": "GffFileReference",
      "title": "Reference to a GFF file",
      "topics": [
        "GffFileReference",
        "GffFileReference-class",
        "GffWrapper",
        "GffWrapper-class",
        "loadGffWrapper",
        "readGffFileReference",
        "saveObject,GffFileReference-method",
        "stageObject,GffWrapper-method"
      ]
    },
    {
      "page": "GmtFileReference",
      "title": "Reference to a GMT file",
      "topics": [
        "GmtFileReference",
        "GmtFileReference-class",
        "GmtWrapper",
        "GmtWrapper-class",
        "loadGmtWrapper",
        "readGmtFileReference",
        "saveObject,GmtFileReference-method",
        "stageObject,GmtWrapper-method"
      ]
    },
    {
      "page": "TabixIndexWrapper",
      "title": "Wrapper for a Tabix file",
      "topics": [
        "loadTabixIndexWrapper",
        "stageObject,TabixIndexWrapper-method",
        "TabixIndexWrapper",
        "TabixIndexWrapper-class"
      ]
    },
    {
      "page": "virtual-wrapper",
      "title": "Virtual wrapper classes",
      "topics": [
        "CompressedIndexedWrapper-class",
        "CompressedWrapper-class",
        "compression",
        "index",
        "index,IndexedWrapper-method",
        "IndexedWrapper-class",
        "path",
        "path,Wrapper-method",
        "show,CompressedIndexedWrapper-method",
        "show,CompressedWrapper-method",
        "show,IndexedWrapper-method",
        "show,Wrapper-method",
        "virtual-wrapper",
        "Wrapper-class"
      ]
    }
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      "engine": "knitr::rmarkdown",
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      "modified": "2023-12-31 09:22:03",
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