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  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GenomicAlignments.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/bioconductor/genomicalignments",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "alphabetFrequencyFromBam",
    "as.data.frame",
    "as.data.frame.OverlapEncodings",
    "bindROWS",
    "cigar",
    "CIGAR_OPS",
    "cigarNarrow",
    "cigarOpTable",
    "cigarQNarrow",
    "cigarRangesAlongPairwiseSpace",
    "cigarRangesAlongQuerySpace",
    "cigarRangesAlongReferenceSpace",
    "cigarToRleList",
    "cigarWidthAlongPairwiseSpace",
    "cigarWidthAlongQuerySpace",
    "cigarWidthAlongReferenceSpace",
    "coerce",
    "countCompatibleOverlaps",
    "countDumpedAlignments",
    "coverage",
    "elementMetadata<-",
    "encodeOverlaps",
    "encodeOverlaps1",
    "encoding",
    "encodingHalves",
    "end",
    "explodeCigarOpLengths",
    "explodeCigarOps",
    "extractAlignmentRangesOnReference",
    "extractQueryStartInTranscript",
    "extractSkippedExonRanks",
    "extractSpannedExonRanks",
    "extractSteppedExonRanks",
    "findCompatibleOverlaps",
    "findMateAlignment",
    "findOverlaps",
    "findSpliceOverlaps",
    "first",
    "flippedQuery",
    "flipQuery",
    "flushDumpedAlignments",
    "GAlignmentPairs",
    "GAlignments",
    "GAlignmentsList",
    "GappedReads",
    "getDumpedAlignments",
    "getListElement",
    "granges",
    "grglist",
    "IntersectionNotEmpty",
    "IntersectionStrict",
    "invertStrand",
    "is.unsorted",
    "isCompatibleWithSkippedExons",
    "isCompatibleWithSplicing",
    "isProperPair",
    "junctions",
    "last",
    "Lencoding",
    "levels",
    "levels.OverlapEncodings",
    "Lnjunc",
    "Loffset",
    "makeGAlignmentPairs",
    "mapFromAlignments",
    "mapToAlignments",
    "narrow",
    "NATURAL_INTRON_MOTIFS",
    "njunc",
    "order",
    "parallel_slot_names",
    "pcompare",
    "pileLettersAt",
    "pintersect",
    "pmapFromAlignments",
    "pmapToAlignments",
    "qnarrow",
    "qseq",
    "qwidth",
    "ranges",
    "rank",
    "readGAlignmentPairs",
    "readGAlignments",
    "readGAlignmentsList",
    "readGappedReads",
    "readSTARJunctions",
    "readTopHatJunctions",
    "relistToClass",
    "Rencoding",
    "rglist",
    "rname",
    "rname<-",
    "Rnjunc",
    "Roffset",
    "second",
    "selectEncodingWithCompatibleStrand",
    "seqinfo",
    "seqinfo<-",
    "seqlevelsInUse",
    "seqnames",
    "seqnames<-",
    "sequenceLayer",
    "show",
    "sort",
    "stackStringsFromBam",
    "stackStringsFromGAlignments",
    "start",
    "strand",
    "strand<-",
    "strandMode",
    "strandMode<-",
    "summarizeJunctions",
    "summarizeOverlaps",
    "Union",
    "update",
    "updateObject",
    "validCigar",
    "width",
    "windows"
  ],
  "_help": [
    {
      "page": "cigar-utils",
      "title": "CIGAR utility functions",
      "topics": [
        "cigar-utils",
        "cigarNarrow",
        "cigarOpTable",
        "cigarQNarrow",
        "cigarRangesAlongPairwiseSpace",
        "cigarRangesAlongQuerySpace",
        "cigarRangesAlongReferenceSpace",
        "cigarToRleList",
        "cigarWidthAlongPairwiseSpace",
        "cigarWidthAlongQuerySpace",
        "cigarWidthAlongReferenceSpace",
        "CIGAR_OPS",
        "explodeCigarOpLengths",
        "explodeCigarOps",
        "extractAlignmentRangesOnReference",
        "validCigar"
      ]
    },
    {
      "page": "coverage-methods",
      "title": "Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList object",
      "topics": [
        "coverage",
        "coverage,BamFile-method",
        "coverage,character-method",
        "coverage,GAlignmentPairs-method",
        "coverage,GAlignments-method",
        "coverage,GAlignmentsList-method",
        "coverage-methods"
      ]
    },
    {
      "page": "encodeOverlaps-methods",
      "title": "Encode the overlaps between RNA-seq reads and the transcripts of a gene model",
      "topics": [
        "encodeOverlaps",
        "encodeOverlaps,GRangesList,GRangesList-method",
        "encodeOverlaps,IntegerRanges,IntegerRangesList-method",
        "encodeOverlaps,IntegerRangesList,IntegerRanges-method",
        "encodeOverlaps,IntegerRangesList,IntegerRangesList-method",
        "encodeOverlaps-methods",
        "encodeOverlaps1",
        "extractQueryStartInTranscript",
        "extractSkippedExonRanks",
        "extractSkippedExonRanks,character-method",
        "extractSkippedExonRanks,factor-method",
        "extractSkippedExonRanks,OverlapEncodings-method",
        "extractSpannedExonRanks",
        "extractSpannedExonRanks,character-method",
        "extractSpannedExonRanks,factor-method",
        "extractSpannedExonRanks,OverlapEncodings-method",
        "extractSteppedExonRanks",
        "extractSteppedExonRanks,character-method",
        "extractSteppedExonRanks,factor-method",
        "extractSteppedExonRanks,OverlapEncodings-method",
        "flipQuery",
        "isCompatibleWithSkippedExons",
        "isCompatibleWithSkippedExons,character-method",
        "isCompatibleWithSkippedExons,factor-method",
        "isCompatibleWithSkippedExons,OverlapEncodings-method",
        "selectEncodingWithCompatibleStrand"
      ]
    },
    {
      "page": "findCompatibleOverlaps-methods",
      "title": "Finding hits between reads and transcripts that are _compatible_ with the splicing of the transcript",
      "topics": [
        "countCompatibleOverlaps",
        "findCompatibleOverlaps",
        "findCompatibleOverlaps,GAlignmentPairs,GRangesList-method",
        "findCompatibleOverlaps,GAlignments,GRangesList-method",
        "findCompatibleOverlaps-methods"
      ]
    },
    {
      "page": "findMateAlignment",
      "title": "Pairing the elements of a GAlignments object",
      "topics": [
        "countDumpedAlignments",
        "findMateAlignment",
        "flushDumpedAlignments",
        "getDumpedAlignments",
        "makeGAlignmentPairs"
      ]
    },
    {
      "page": "findOverlaps-methods",
      "title": "Finding overlapping genomic alignments",
      "topics": [
        "findOverlaps",
        "findOverlaps,GAlignmentPairs,GAlignmentPairs-method",
        "findOverlaps,GAlignmentPairs,Vector-method",
        "findOverlaps,GAlignments,GAlignments-method",
        "findOverlaps,GAlignments,Vector-method",
        "findOverlaps,GAlignmentsList,GAlignmentsList-method",
        "findOverlaps,GAlignmentsList,Vector-method",
        "findOverlaps,Vector,GAlignmentPairs-method",
        "findOverlaps,Vector,GAlignments-method",
        "findOverlaps,Vector,GAlignmentsList-method",
        "findOverlaps-methods"
      ]
    },
    {
      "page": "findSpliceOverlaps-methods",
      "title": "Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events",
      "topics": [
        "findSpliceOverlaps",
        "findSpliceOverlaps,BamFile,ANY-method",
        "findSpliceOverlaps,character,ANY-method",
        "findSpliceOverlaps,GAlignmentPairs,GRangesList-method",
        "findSpliceOverlaps,GAlignments,GRangesList-method",
        "findSpliceOverlaps,GRangesList,GRangesList-method",
        "findSpliceOverlaps-methods"
      ]
    },
    {
      "page": "GAlignmentPairs-class",
      "title": "GAlignmentPairs objects",
      "topics": [
        "as.data.frame,GAlignmentPairs-method",
        "bindROWS,GAlignmentPairs-method",
        "class:GAlignmentPairs",
        "coerce,GAlignmentPairs,DataFrame-method",
        "coerce,GAlignmentPairs,GAlignments-method",
        "coerce,GAlignmentPairs,GRanges-method",
        "coerce,GAlignmentPairs,GRangesList-method",
        "coerce,GAlignmentPairs,IntegerRanges-method",
        "first",
        "first,GAlignmentPairs-method",
        "GAlignmentPairs",
        "GAlignmentPairs-class",
        "getListElement,GAlignmentPairs-method",
        "granges,GAlignmentPairs-method",
        "grglist,GAlignmentPairs-method",
        "invertStrand,GAlignmentPairs-method",
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      "page": "sequenceLayer",
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