alignments
Auto-generated from exported functions tagged #api in the source. See
imports and re-exports for how to
import these from a plugin.
alignmentTables
A region's reads 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 color object paints
it, with the key the display shows: legend, and ramps, its color bars
(rampKeyOf). Under a facet each section lays out
on its own, every row names its section, and sections lists them in
stacking order; ungrouped, there is one section, labelled ''. 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, region, display, refNames, byteLimit, }: AlignmentTablesArgs) => Promise<…>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>