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  "Title": "An R interface to the GMAP/GSNAP/GSTRUCT suite",
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  "Author": "Cory Barr, Thomas Wu, Michael Lawrence",
  "Description": "GSNAP and GMAP are a pair of tools to align short-read\ndata written by Tom Wu.  This package provides convenience\nmethods to work with GMAP and GSNAP from within R. In addition,\nit provides methods to tally alignment results on a\nper-nucleotide basis using the bam_tally tool.",
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        "bam_tally,BamFile-method",
        "bam_tally,character-method",
        "bam_tally,GmapBamReader-method",
        "bam_tally-methods",
        "genome,TallyIIT-method",
        "variantSummary"
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      "title": "Class '\"BamTallyParam\"'",
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        "BamTallyParam",
        "BamTallyParam-class",
        "coerce,BamTallyParam,list-method"
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    {
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    },
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    {
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      "title": "Build Gmap/Gsnap Genome",
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        "gmap_build,character,GmapGenome-method",
        "gmap_build,DNAStringSet,GmapGenome-method",
        "gmap_build-methods"
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      "title": "Class '\"GmapGenome\"'",
      "topics": [
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        "genome,GmapGenome-method",
        "getSeq,GmapGenome-method",
        "GmapGenome",
        "GmapGenome-class",
        "path,GmapGenome-method",
        "seqinfo,GmapGenome-method",
        "snps<-",
        "snps<-,GmapGenome,ANY,ANY-method",
        "spliceSites<-",
        "spliceSites<-,GmapGenome,GRangesList-method",
        "spliceSites<-,GmapGenome,TxDb-method"
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      "title": "Class '\"GmapGenomeDirectory\"'",
      "topics": [
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        "GmapGenomeDirectory",
        "GmapGenomeDirectory-class",
        "path,GmapGenomeDirectory-method",
        "path,NULL-method"
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      "title": "Class '\"GmapSnpDirectory\"'",
      "topics": [
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        "GmapSnpDirectory-class",
        "length,GmapSnpDirectory-method",
        "names,GmapSnpDirectory-method",
        "path,GmapSnpDirectory-method",
        "snps<-,GmapSnpDirectory,character,character-method",
        "snps<-,GmapSnpDirectory,character,VCF-method",
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      "topics": [
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        "GmapSnps",
        "GmapSnps-class"
      ]
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    {
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      "title": "Align a Set of Reads Using the GSNAP Aligner",
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        "gsnap,character,character_OR_NULL,GsnapParam-method",
        "gsnap-methods"
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        "GsnapOutput",
        "GsnapOutput-class",
        "path,GsnapOutput-method"
      ]
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      "title": "Class '\"GsnapParam\"'",
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