HtsgetBamAdapter

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

Example usage#

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

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

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

Related links#

• Track: AlignmentsTrack
• Display: LinearAlignmentsDisplay
• Guide: Supported file types

Config slots#

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