.packJunctionAttributes
                        Pack junction attributes into a bed name column
.sanitizeAndMergeOptions
                        Sanitize and merge track configuration options
.sanitizeChromosomeColorMap
                        Check a chromosome color map before it reaches
                        igv.js
.sanitizeTrack          Sanitize one startup track specification
.sanitizeTracks         Sanitize a list of startup track specifications
display,GWASTrack-method
                        display the already constructed and configured
                        track
get_basic_genomes       get_basic_genomes
get_cas_genomes         get_cas_genomes
get_css_genomes         get_css_genomes
get_tracks_dir          get_tracks_dir Get the directory where tracks
                        are stored. The directory can be defined with
                        environmental variable. If not defined the
                        default is a directory called "tracks" in the
                        temp directory. We need a local directory to
                        write files - for instance, a vcf file
                        representing a genomic region of interest. We
                        then tell shiny about that directory, so that
                        shiny's built-in http server can serve up files
                        we write there, ultimately consumed by igv.js
getUrl,GWASTrack-method
                        the url of the gwas table
GWASTrack-class         Constructor for GWASTrack
igvShiny                Create an igvShiny instance
igvShinyOutput          create the UI for the widget
loadBamTrackFromLocalData
                        load GenomicAlignments data as an igv.js
                        alignment track
loadBamTrackFromURL     load a bam track which, with index, is served
                        up by http
loadBedGraphTrack       load a scored genome annotation track provided
                        as a data.frame
loadBedGraphTrackFromURL
                        load a bedgraph track from a URL
loadBedTrack            load a bed track provided as a data.frame
loadCramTrackFromLocalData
                        load a cram file sitting on the same machine as
                        the shiny app
loadCramTrackFromURL    load a cram track which, with index, is served
                        up by http
loadGFF3TrackFromLocalData
                        load a GFF3 track defined by local data
loadGFF3TrackFromURL    load a GFF3 track which, with index, is served
                        up by http
loadGwasTrack           load a GWAS (genome-wide association study)
                        track provided as a data.frame
loadSegTrack            load a seg track provided as a data.frame
loadSpliceJunctionTrackFromLocalData
                        load a splice junction track from a data.frame
loadSpliceJunctionTrackFromURL
                        load a splice junction track served up by http
loadVcfTrack            load a VCF (variant) track provided as a
                        Bioconductor VariantAnnotation object
parseAndValidateGenomeSpec
                        parseAndValidateGenomeSpec
removeTracksByName      remove tracks from the browser
removeUserAddedTracks   remove only those tracks explicitly added by
                        your app
renderIgvShiny          draw the igv genome browser element
show,GWASTrack-method   Display a short summary of a GWASTrack object
showGenomicRegion       focus igv on a region
