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BedTabixAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the bed plugin. View source.

Example usage

The uri shorthand auto-resolves the .tbi index; add csi: true for a .csi index instead:

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BedTabixAdapter',
    uri: 'https://example.com/features.bed.gz',
  },
}

features.bed.gz infers BedTabixAdapter and FeatureTrack on its own, and name defaults to the file name. In a config declaring one assembly, assemblyNames comes from there too — see the shortest track.

{
  trackId: 'my_track',
  uri: 'https://example.com/features.bed.gz',
  assemblyNames: ['hg38'],
}

See the Config slots section below for all available configuration fields.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BedTabixAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi in place of writing a location slot out. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
bedGzLocation
fileLocation = { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' }		location of the bgzip-compressed BED, sorted by position. Must be bgzip rather than plain gzip, which tabix cannot index.
columnNames
stringArray = []		List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text
scoreColumn
string = ''		The column to use as a "score" attribute
autoSql
string = ''		The autoSql definition for the data fields in the file
disableGeneHeuristic
boolean = false		Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)
index.indexType
stringEnum (TBI, CSI) = 'TBI'		TBI is the usual tabix output. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
index.location
fileLocation = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' }		location of the tabix index. Only needed when it is not named <file>.tbi (or .csi), which is what the uri shorthand assumes.