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BedAdapter

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

Reads plain-text BED files. The adapter loads the whole file into memory, so use BedTabixAdapter for large files.

Example usage

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

JBrowse infers BedAdapter and FeatureTrack from features.bed, 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',
  assemblyNames: ['hg38'],
}
Gotcha

Named BED columns past name/score/strand (itemRgb, thickStart, ...) are only guaranteed for BED12 or a track with an autoSql/columnNames. For a BED7-BED11 file JBrowse cannot know what the extra columns mean, so it exposes them generically as field6, field7, ... and feature.itemRgb reads as undefined in a jexl callback. Set columnNames to refer to them by name.

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "BedAdapter", ... }. It also accepts the shorthand keys uri, baseUri 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
bedLocation
fileLocation = { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' }		path to bed file, also allows gzipped bed
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
colRef
number = 0		The column to use as a "refName" attribute
colStart
number = 1		The column to use as a "start" attribute
colEnd
number = 2		The column to use as a "end" attribute
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)