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  "Description": "Provides efficient containers for storing and manipulating\nshort genomic alignments (typically obtained by aligning short\nreads to a reference genome). This includes read counting,\ncomputing the coverage, junction detection, and working with\nthe nucleotide content of the alignments.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:25 UTC",
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    "explodeCigarOpLengths",
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    "extractAlignmentRangesOnReference",
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    "start",
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      "title": "CIGAR utility functions",
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        "explodeCigarOps",
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        "coverage,character-method",
        "coverage,GAlignmentPairs-method",
        "coverage,GAlignments-method",
        "coverage,GAlignmentsList-method",
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        "encodeOverlaps,IntegerRanges,IntegerRangesList-method",
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        "encodeOverlaps-methods",
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        "extractSkippedExonRanks,factor-method",
        "extractSkippedExonRanks,OverlapEncodings-method",
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        "extractSpannedExonRanks,character-method",
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        "extractSpannedExonRanks,OverlapEncodings-method",
        "extractSteppedExonRanks",
        "extractSteppedExonRanks,character-method",
        "extractSteppedExonRanks,factor-method",
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        "flipQuery",
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        "isCompatibleWithSkippedExons,character-method",
        "isCompatibleWithSkippedExons,factor-method",
        "isCompatibleWithSkippedExons,OverlapEncodings-method",
        "selectEncodingWithCompatibleStrand"
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      "page": "findCompatibleOverlaps-methods",
      "title": "Finding hits between reads and transcripts that are _compatible_ with the splicing of the transcript",
      "topics": [
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        "findCompatibleOverlaps",
        "findCompatibleOverlaps,GAlignmentPairs,GRangesList-method",
        "findCompatibleOverlaps,GAlignments,GRangesList-method",
        "findCompatibleOverlaps-methods"
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      "page": "findMateAlignment",
      "title": "Pairing the elements of a GAlignments object",
      "topics": [
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        "findMateAlignment",
        "flushDumpedAlignments",
        "getDumpedAlignments",
        "makeGAlignmentPairs"
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      "page": "findOverlaps-methods",
      "title": "Finding overlapping genomic alignments",
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        "findOverlaps,GAlignmentPairs,GAlignmentPairs-method",
        "findOverlaps,GAlignmentPairs,Vector-method",
        "findOverlaps,GAlignments,GAlignments-method",
        "findOverlaps,GAlignments,Vector-method",
        "findOverlaps,GAlignmentsList,GAlignmentsList-method",
        "findOverlaps,GAlignmentsList,Vector-method",
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        "findOverlaps,Vector,GAlignments-method",
        "findOverlaps,Vector,GAlignmentsList-method",
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      "title": "Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events",
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        "findSpliceOverlaps,BamFile,ANY-method",
        "findSpliceOverlaps,character,ANY-method",
        "findSpliceOverlaps,GAlignmentPairs,GRangesList-method",
        "findSpliceOverlaps,GAlignments,GRangesList-method",
        "findSpliceOverlaps,GRangesList,GRangesList-method",
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        "bindROWS,GAlignmentPairs-method",
        "class:GAlignmentPairs",
        "coerce,GAlignmentPairs,DataFrame-method",
        "coerce,GAlignmentPairs,GAlignments-method",
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        "first",
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        "GAlignmentPairs",
        "GAlignmentPairs-class",
        "granges,GAlignmentPairs-method",
        "grglist,GAlignmentPairs-method",
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        "last",
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        "njunc,GAlignmentPairs-method",
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        "second",
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        "seqinfo,GAlignmentPairs-method",
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      "page": "sequenceLayer",
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      "page": "setops-methods",
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