LinearAlignmentsDisplay

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

Draws the reads of an AlignmentsTrack as a stack of bands: the coverage histogram with the sashimi arcs over it, the read connections, and the pileup. Each band is one object, coverage, sashimi, readConnections and pileup, holding whether it draws and its height; the settings every band shares sit beside them: filter, one list of the read, junction and connection tests, unit, facet, sort, encoding and legend.

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: '...', pileup: ... }]. See configuring displays:

{
  type: 'AlignmentsTrack',
  trackId: 'methylation',
  name: 'Methylation',
  assemblyNames: ['hg38'],
  adapter: { type: 'CramAdapter', uri: 'https://example.com/sample.cram' },
  displayDefaults: {
    pileup: {
      bases: {
        show: true,
        encoding: { color: 'modifications' },
        unmodified: { show: true },
      },
    },
  },
}

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,
    unit: 'chain',
    encoding: { color: 'insertSizeAndOrientation' },
    pileup: { softClips: { show: true } },
    readConnections: { show: true },
  },
}

RNA-seq — sashimi arcs placed to avoid crossings, labelled with their read counts, dropping junctions under five reads, the non-canonical ones and the split-read joins:

{
  type: 'AlignmentsTrack',
  trackId: 'rnaseq',
  name: 'RNA-seq',
  assemblyNames: ['hg38'],
  adapter: { type: 'BamAdapter', uri: 'https://example.com/rnaseq.bam' },
  displayDefaults: {
    coverage: { height: 80 },
    sashimi: { placement: 'auto', labels: { show: true } },
    filter: [
      { field: 'junction.reads', gte: 5 },
      { field: 'junction.canonical', equal: true },
      { field: 'junction.source', equal: 'gap' },
    ],
  },
}

Related links#

• Adapter: BamAdapter
• Adapter: CramAdapter
• Adapter: HtsgetBamAdapter
• Adapter: SamAdapter
• State model: runtime API
• Base config: BaseLinearAlignmentsDisplay
• Tutorial: Display settings
• User guide: Alignments track
• Config guide: Alignments track
• Config guide: Tracks
• Developer guide: Custom track and display types

Color channels#

Config slots#

Display 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.