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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Rsamtools.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/bioconductor/rsamtools",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "applyPileups",
    "ApplyPileupsParam",
    "asBam",
    "asBcf",
    "asMates",
    "asMates<-",
    "asSam",
    "bamDirname<-",
    "bamExperiment",
    "BamFile",
    "BamFileList",
    "bamFlag",
    "bamFlag<-",
    "bamFlagAND",
    "bamFlagAsBitMatrix",
    "bamFlagTest",
    "bamIndicies",
    "bamMapqFilter",
    "bamMapqFilter<-",
    "bamPaths",
    "bamRanges",
    "bamRanges<-",
    "bamReverseComplement",
    "bamReverseComplement<-",
    "BamSampler",
    "bamSamples",
    "bamSamples<-",
    "bamSimpleCigar",
    "bamSimpleCigar<-",
    "bamTag",
    "bamTag<-",
    "bamTagFilter",
    "bamTagFilter<-",
    "BamViews",
    "bamWhat",
    "bamWhat<-",
    "bamWhich",
    "bamWhich<-",
    "BcfFile",
    "BcfFileList",
    "bcfFixed",
    "bcfGeno",
    "bcfInfo",
    "bcfMode",
    "bcfSamples",
    "bcfTrimEmpty",
    "bcfWhich",
    "bgzip",
    "bgzipTabix",
    "close.BamFile",
    "close.BcfFile",
    "close.FaFile",
    "close.RsamtoolsFileList",
    "close.TabixFile",
    "countBam",
    "countFa",
    "countTabix",
    "FaFile",
    "FaFileList",
    "filterBam",
    "FLAG_BITNAMES",
    "getSeq",
    "gzindex",
    "gzindex<-",
    "headerTabix",
    "idxstatsBam",
    "index",
    "index<-",
    "indexBam",
    "indexBcf",
    "indexFa",
    "indexTabix",
    "isIncomplete",
    "isOpen",
    "mergeBam",
    "obeyQname",
    "obeyQname<-",
    "open.BamFile",
    "open.BcfFile",
    "open.FaFile",
    "open.RsamtoolsFileList",
    "open.TabixFile",
    "phred2ASCIIOffset",
    "pileup",
    "PileupFiles",
    "PileupParam",
    "plpFiles",
    "plpFlag",
    "plpFlag<-",
    "plpMaxDepth",
    "plpMaxDepth<-",
    "plpMinBaseQuality",
    "plpMinBaseQuality<-",
    "plpMinDepth",
    "plpMinDepth<-",
    "plpMinMapQuality",
    "plpMinMapQuality<-",
    "plpParam",
    "plpWhat",
    "plpWhat<-",
    "plpWhich",
    "plpWhich<-",
    "plpYieldAll",
    "plpYieldAll<-",
    "plpYieldBy",
    "plpYieldBy<-",
    "plpYieldSize",
    "plpYieldSize<-",
    "qnamePrefixEnd",
    "qnamePrefixEnd<-",
    "qnameSuffixStart",
    "qnameSuffixStart<-",
    "quickBamCounts",
    "quickBamFlagSummary",
    "quickCountBam",
    "razip",
    "readPileup",
    "scanBam",
    "scanBamFlag",
    "scanBamHeader",
    "ScanBamParam",
    "scanBamWhat",
    "scanBcf",
    "scanBcfHeader",
    "ScanBcfParam",
    "scanFa",
    "scanFaIndex",
    "scanTabix",
    "seqinfo",
    "seqnamesTabix",
    "show",
    "sortBam",
    "TabixFile",
    "TabixFileList",
    "testPairedEndBam",
    "yieldSize",
    "yieldSize<-",
    "yieldTabix"
  ],
  "_help": [
    {
      "page": "Rsamtools-package",
      "title": "'samtools' aligned sequence utilities interface",
      "topics": [
        "Rsamtools-package",
        "bzfile-class",
        "fifo-class",
        "gzfile-class",
        "pipe-class",
        "Rsamtools",
        "unz-class",
        "url-class"
      ]
    },
    {
      "page": "applyPileups",
      "title": "Apply a user-provided function to calculate pile-up statistics across multiple BAM files.",
      "topics": [
        "applyPileups"
      ]
    },
    {
      "page": "ApplyPileupsParam-class",
      "title": "Parameters for creating pileups from BAM files",
      "topics": [
        "ApplyPileupsParam",
        "ApplyPileupsParam-class",
        "plpFlag",
        "plpFlag<-",
        "plpMaxDepth",
        "plpMaxDepth<-",
        "plpMinBaseQuality",
        "plpMinBaseQuality<-",
        "plpMinDepth",
        "plpMinDepth<-",
        "plpMinMapQuality",
        "plpMinMapQuality<-",
        "plpWhat",
        "plpWhat<-",
        "plpWhich",
        "plpWhich<-",
        "plpYieldAll",
        "plpYieldAll<-",
        "plpYieldBy",
        "plpYieldBy<-",
        "plpYieldSize",
        "plpYieldSize<-",
        "show,ApplyPileupsParam-method"
      ]
    },
    {
      "page": "BamFile-class",
      "title": "Maintain and use BAM files",
      "topics": [
        "asMates",
        "asMates,BamFile-method",
        "asMates,BamFileList-method",
        "asMates<-",
        "asMates<-,BamFile-method",
        "asMates<-,BamFileList-method",
        "BamFile",
        "BamFile-class",
        "BamFileList",
        "BamFileList-class",
        "close.BamFile",
        "countBam,BamFile-method",
        "countBam,BamFileList-method",
        "filterBam,BamFile-method",
        "idxstatsBam,BamFile-method",
        "indexBam,BamFile-method",
        "isIncomplete,BamFile-method",
        "isOpen,BamFile-method",
        "mergeBam,BamFileList-method",
        "obeyQname",
        "obeyQname,BamFile-method",
        "obeyQname,BamFileList-method",
        "obeyQname<-",
        "obeyQname<-,BamFile-method",
        "obeyQname<-,BamFileList-method",
        "open.BamFile",
        "qnamePrefixEnd",
        "qnamePrefixEnd,BamFile-method",
        "qnamePrefixEnd,BamFileList-method",
        "qnamePrefixEnd<-",
        "qnamePrefixEnd<-,BamFile-method",
        "qnamePrefixEnd<-,BamFileList-method",
        "qnameSuffixStart",
        "qnameSuffixStart,BamFile-method",
        "qnameSuffixStart,BamFileList-method",
        "qnameSuffixStart<-",
        "qnameSuffixStart<-,BamFile-method",
        "qnameSuffixStart<-,BamFileList-method",
        "quickBamFlagSummary,BamFile-method",
        "scanBam,BamFile-method",
        "scanBamHeader,BamFile-method",
        "seqinfo,BamFile-method",
        "seqinfo,BamFileList-method",
        "show,BamFile-method",
        "show,BamFileList-method",
        "sortBam,BamFile-method"
      ]
    },
    {
      "page": "scanBam",
      "title": "Import, count, index, filter, sort, and merge `BAM' (binary alignment) files.",
      "topics": [
        "asBam",
        "asBam,character-method",
        "asSam",
        "asSam,character-method",
        "countBam",
        "countBam,character-method",
        "filterBam",
        "filterBam,character-method",
        "idxstatsBam",
        "idxstatsBam,character-method",
        "indexBam",
        "indexBam,character-method",
        "mergeBam",
        "mergeBam,character-method",
        "scanBam",
        "scanBam,character-method",
        "scanBamHeader",
        "scanBamHeader,character-method",
        "sortBam",
        "sortBam,character-method"
      ]
    },
    {
      "page": "BamViews-class",
      "title": "Views into a set of BAM files",
      "topics": [
        "bamDirname<-",
        "bamExperiment",
        "bamIndicies",
        "bamPaths",
        "bamRanges",
        "bamRanges<-",
        "bamSamples",
        "bamSamples<-",
        "BamViews",
        "BamViews,GRanges-method",
        "BamViews,missing-method",
        "BamViews-class",
        "countBam,BamViews-method",
        "dim,BamViews-method",
        "dimnames,BamViews-method",
        "dimnames<-,BamViews,ANY-method",
        "dimnames<-,BamViews-method",
        "names,BamViews-method",
        "names<-,BamViews-method",
        "scanBam,BamViews-method",
        "show,BamViews-method",
        "[,BamViews,ANY,ANY-method",
        "[,BamViews,ANY,missing-method",
        "[,BamViews,missing,ANY-method"
      ]
    },
    {
      "page": "BcfFile-class",
      "title": "Manipulate BCF files.",
      "topics": [
        "BcfFile",
        "BcfFile-class",
        "BcfFileList",
        "BcfFileList-class",
        "bcfMode",
        "close.BcfFile",
        "indexBcf,BcfFile-method",
        "isOpen,BcfFile-method",
        "open.BcfFile",
        "scanBcf,BcfFile-method",
        "scanBcfHeader,BcfFile-method"
      ]
    },
    {
      "page": "scanBcf",
      "title": "Operations on `BCF' files.",
      "topics": [
        "asBcf",
        "asBcf,character-method",
        "indexBcf",
        "indexBcf,character-method",
        "scanBcf",
        "scanBcf,character-method",
        "scanBcfHeader",
        "scanBcfHeader,character-method"
      ]
    },
    {
      "page": "zip",
      "title": "File compression for tabix (bgzip) and fasta (razip) files. IMPORTANT NOTE: Starting with Rsamtools 1.99.0 (Bioconductor 3.9), 'razip()' is defunct. Please use 'bgzip()' instead.",
      "topics": [
        "bgzip",
        "razip"
      ]
    },
    {
      "page": "deprecated",
      "title": "Deprecated functions",
      "topics": [
        "BamSampler",
        "BamSampler-class",
        "scanBam,BamSampler-method",
        "show,BamSampler-method",
        "yieldTabix",
        "yieldTabix,TabixFile-method"
      ]
    },
    {
      "page": "FaFile-class",
      "title": "Manipulate indexed fasta files.",
      "topics": [
        "close.FaFile",
        "countFa,FaFile-method",
        "FaFile",
        "FaFile-class",
        "FaFileList",
        "FaFileList-class",
        "getSeq,FaFile-method",
        "getSeq,FaFileList-method",
        "gzindex",
        "gzindex,FaFile-method",
        "gzindex,FaFileList-method",
        "gzindex<-",
        "gzindex<-,FaFile-method",
        "gzindex<-,FaFileList-method",
        "indexFa,FaFile-method",
        "isOpen,FaFile-method",
        "open.FaFile",
        "scanFa,FaFile,GRanges-method",
        "scanFa,FaFile,IntegerRangesList-method",
        "scanFa,FaFile,missing-method",
        "scanFaIndex,FaFile-method",
        "scanFaIndex,FaFileList-method",
        "seqinfo,FaFile-method",
        "show,FaFile-method"
      ]
    },
    {
      "page": "scanFa",
      "title": "Operations on indexed 'fasta' files.",
      "topics": [
        "countFa",
        "countFa,character-method",
        "indexFa",
        "indexFa,character-method",
        "scanFa",
        "scanFa,character,GRanges-method",
        "scanFa,character,IntegerRangesList-method",
        "scanFa,character,missing-method",
        "scanFaIndex",
        "scanFaIndex,character-method"
      ]
    },
    {
      "page": "headerTabix",
      "title": "Retrieve sequence names defined in a tabix file.",
      "topics": [
        "headerTabix",
        "headerTabix,character-method"
      ]
    },
    {
      "page": "indexTabix",
      "title": "Compress and index tabix-compatible files.",
      "topics": [
        "indexTabix"
      ]
    },
    {
      "page": "pileup",
      "title": "Use filters and output formats to calculate pile-up statistics for a BAM file.",
      "topics": [
        "cycle_bins",
        "distinguish_nucleotides",
        "distinguish_strands",
        "ignore_query_Ns",
        "include_deletions",
        "include_insertions",
        "left_bins",
        "max_depth",
        "min_base_quality",
        "min_mapq",
        "min_minor_allele_depth",
        "min_nucleotide_depth",
        "phred2ASCIIOffset",
        "pileup",
        "pileup,BamFile-method",
        "pileup,character-method",
        "PileupParam",
        "PileupParam-class",
        "query_bins",
        "show,PileupParam-method"
      ]
    },
    {
      "page": "PileupFiles-class",
      "title": "Represent BAM files for pileup summaries.",
      "topics": [
        "applyPileups,PileupFiles,ApplyPileupsParam-method",
        "applyPileups,PileupFiles,missing-method",
        "isOpen,PileupFiles-method",
        "PileupFiles",
        "PileupFiles,character-method",
        "PileupFiles,list-method",
        "PileupFiles-class",
        "plpFiles",
        "plpParam",
        "show,PileupFiles-method"
      ]
    },
    {
      "page": "quickBamFlagSummary",
      "title": "Group the records of a BAM file based on their flag bits and count the number of records in each group",
      "topics": [
        "quickBamFlagSummary",
        "quickBamFlagSummary,character-method",
        "quickBamFlagSummary,list-method"
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