LinearAlignmentsDisplay

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

Example usage#

Minimal BAM track — no display override needed for defaults. See the alignments track guide for all adapter and display options:

{
  type: 'AlignmentsTrack',
  trackId: 'ngs_reads',
  name: 'NGS reads',
  assemblyNames: ['hg38'],
  adapter: { type: 'BamAdapter', uri: 'https://example.com/sample.bam' },
}

CRAM colored by CpG methylation (modBAM MM/ML tags). The displayDefaults object shorthand applies settings without spelling out the display type or displayId — equivalent to displays: [{ type: 'LinearAlignmentsDisplay', displayId: '...', color: ... }]. See configuring displays:

{
  type: 'AlignmentsTrack',
  trackId: 'methylation',
  name: 'Methylation',
  assemblyNames: ['hg38'],
  adapter: { type: 'CramAdapter', uri: 'https://example.com/sample.cram' },
  displayDefaults: {
    baseColor: { field: 'modifications' },
    modifications: { unmodified: 'all' },
  },
}

Long reads — taller track, soft-clipping shown, split/chimeric reads connected by arcs, each segment colored by its strand against its molecule's:

{
  type: 'AlignmentsTrack',
  trackId: 'long_reads',
  name: 'Long reads',
  assemblyNames: ['hg38'],
  adapter: { type: 'BamAdapter', uri: 'https://example.com/longreads.bam' },
  displayDefaults: {
    height: 400,
    showSoftClipping: true,
    unit: 'chain',
    color: { field: 'pairOrientation' },
    readConnections: 'arc',
  },
}

Draws the reads of an AlignmentsTrack as a pileup under a coverage histogram.

Related links#

• Adapter: BamAdapter
• Adapter: CramAdapter
• Adapter: HtsgetBamAdapter
• Adapter: SamAdapter
• Extended by: LGVSyntenyDisplay
• State model: runtime API
• Base config: BaseLinearDisplay
• Tutorial: Display settings
• Tutorial: Methylation (bisulfite)
• User guide: Alignments track
• Config guide: Alignments track
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

These slots go on a display entry: "displays": [{ "type": "LinearAlignmentsDisplay", ... }], or in the track's displayDefaults when this is its default display. 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.

Retired keys#

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