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@jbrowse/plugin-alignments

Auto-generated from exported functions tagged #api in the source. See imports and re-exports for how to import these from a plugin.

alignmentMarkAlpha

Each insertion's width in px and each insertion's, deletion's, mismatch's and clip's alpha as the pileup draws them at pxPerBp, through the shaders' generated twins, for a host that draws the marks at its figure's scale. fade is a mark's fade column, length its length in bp (a deletion's end - start) and quality a mismatch's, 255 where the read has none. A column may be a number, for one mark. featureHeight is readPitch.featureHeight, fadeLowFrequency the display's pileup.fadeLowFrequency, and mismatchOpacity its pileup.mismatches.encoding.opacity as a config writes it; each of the three takes the pileup config's default when left out.

  • An insertion's widthPx is insertionBarWidthPx, and its alpha insertionSizeAlpha times, under LONG_INSERTION_MIN_LENGTH, frequencyFadeGate over pxPerBp squared.
  • A deletion's alpha is sizeAlpha of its width in px times frequencyFadeGate over that width squared.
  • A mismatch's alpha is qualityFade times frequencyFadeGate over pxPerBp, and a clip's that gate alone. quality may be left out while mismatchOpacity names no field.
// type signature
({ pxPerBp, featureHeight, fadeLowFrequency, mismatchOpacity, insertions, deletions, mismatches, clips, }: { pxPerBp: number; featureHeight?: number | undefined; fadeLowFrequency?: boolean | undefined; mismatchOpacity?: PileupMismatchesOpacitySnapshot | undefined; insertions?: {…} | undefined; deletions?: {…} | undefined; mismatches?: {…} | undefined; clips?: { fade: MarkColumn; } | undefined; }) => { insertions: { widthPx: number[]; alpha: number[]; }; deletions: { alpha: number[]; }; mismatches: { alpha: number[]; }; clips: { alpha: number[]; }; }

Source code

alignmentTables

A region's reads, or several regions', as the alignments display fetches, filters, lays out and colors them, as tables: the worker's reads, mismatches, gaps, insertions, clips, modifications, per-base qualities, coverage and splice junctions, each read on the row the display's pileup layout gives it and in the color the display's encoding.color paints it, with the key the display shows: legend, and ramps, its color bars (rampKeyOf). Under a facet each section lays out separately, every row has a section, and sections lists them in stacking order; ungrouped, there is one section, labelled ''. Several regions lay out as the display lays out a view's regions, on one set of rows: a read crossing regions is listed in each, under one key and on one row, and every row names its region's index. warnings names what the config asked for that the tables dropped. For a host that draws them itself, such as R through V8. The adapters must be registered on pluginManager (registerAlignmentsAdapters).

// type signature
(pluginManager: PluginManager, { adapterConfig, sequenceAdapter, regions, display, refNames, byteLimit, spanLimit, }: AlignmentTablesArgs) => Promise<{…}>

Source code

isLinearAlignmentsDisplay

Whether a track's display is the reads display, for a host that reaches it through view.getTrack(id)?.activeDisplay to drive its own controls.

// type signature
(display: unknown) => display is LinearAlignmentsDisplayModel

Source code

referenceSequence

A region of the reference, as the sequence adapter a track's assembly names reads it: the bases as one string, for a host drawing them under a pileup.

// type signature
(pluginManager: PluginManager, { sequenceAdapter, region, }: { sequenceAdapter: Record<string, unknown>; region: { refName: string; start: number; end: number; }; }) => Promise<string>

Source code