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BigBedTextSearchAdapter

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

Example usage

{
  type: 'BigBedTextSearchAdapter',
  bigBedLocation: { uri: 'bbi/ncbiRefSeq.bb' },
  ixFilePath: { uri: 'ixIxx/ncbiRefSeq.ix' },
  ixxFilePath: { uri: 'ixIxx/ncbiRefSeq.ixx' },
}

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

Finds features by the names a BigBed was built to look up, its bedToBigBed -extraIndex columns, which a UCSC hub declares with searchIndex. The hub's searchTrix index, when given, adds prefix and case-insensitive matching. A UCSC track hub connection configures one for its first gene track declaring a searchIndex, GenArk's ncbiRefSeq.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BigBedTextSearchAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. 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
bigBedLocation
fileLocation = { uri: '/path/to/my.bb', locationType: 'UriLocation' }		the BigBed whose extra indexes resolve a name to its features
ixFilePath
fileLocation = { uri: '', locationType: 'UriLocation' }		a UCSC searchTrix .ix, whose records are the names the extra indexes hold. Unset, a search matches a name exactly as typed
ixxFilePath
fileLocation = { uri: '', locationType: 'UriLocation' }		the .ixx beside ixFilePath
assemblyNames
stringArray = []		List of assemblies covered by text search adapter