HicAdapter

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

Example usage#

{
  type: 'HicTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'HicAdapter',
    uri: 'https://example.com/map.hic',
  },
}

map.hic infers HicAdapter and HicTrack 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/map.hic',
  assemblyNames: ['hg38'],
}

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

used to load Hi-C contact matrix data from a .hic file

Related links#

• Track: HicTrack
• Display: LinearHicDisplay
• Guide: Hi-C track
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "HicAdapter", ... }. 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.