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HtsgetBamAdapter

Auto-generated from the config schema in the source. See the config guide for concepts. Provided by the alignments plugin. View source.

Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library

Example usage

{
  type: 'AlignmentsTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'HtsgetBamAdapter',
    htsgetBase: 'https://htsget.example.com/reads',
    htsgetTrackId: 'NA12878',
  },
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "HtsgetBamAdapter", ... }. HtsgetBamAdapter 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.

Slot Description
htsgetBase
fileLocation = { uri: '', locationType: 'UriLocation' }		 The endpoint tickets are requested from. htsgetTrackId is appended to it, so a trailing slash produces a doubled one in the request path.
htsgetTrackId
string = ''		 the trackId, which is appended to the base URL

Retired keys

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

Key On load
sequenceAdapter ignored