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BedTabixAdapter

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the bed plugin. View source.

Reads bgzip-compressed, tabix-indexed BED files.

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',
  },
}

JBrowse infers BedTabixAdapter and FeatureTrack from features.bed.gz, 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'],
}

Config slots

Adapter 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.
index
TabixIndex		The tabix index location and its kind. The uri shorthand derives both, so a config using it states neither.
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)