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HicAdapter

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

Reads Hi-C contact matrices from a .hic file.

Example usage

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

JBrowse infers HicAdapter and HicTrack from map.hic, 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'],
}

Config slots

Adapter 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.

SlotDescription
hicLocation
fileLocation = { uri: '/path/to/my.hic', locationType: 'UriLocation' }		location of the .hic contact matrix (Juicer / Juicebox format). The file holds every resolution and an index, so there is nothing else to configure — the display picks a bin size from the current zoom.
controlAdapter
maybeFrozen		a second HicAdapter, the control condition the display's observed/control field divides by: both are scaled to one library depth, so two libraries sequenced to different depths compare. The two must be on one assembly; chromosome names may differ by a chr prefix. Leave it unset for a single map.

Retired keys

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

KeyOn load
resolutionMultiplierignored