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@jbrowse/plugin-variants

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

variantDensityAlpha

Each record's alpha factor where records too short to see share pixels at bpPerPx, as the multi-sample variant display fades a zoomed-out row (recordDensityAlpha) at the power of two bpPerPx rounds to: 1 where a record covers its pixels alone. For a host that draws the cells at its own scale.

// type signature
({ start, end, bpPerPx, }: { start: readonly number[]; end: readonly number[]; bpPerPx: number; }) => number[]

Source code

variantRecordTables

The VCF columns of the records a feature table lists, by its features.id, for a host drawing a VCF as the plain variant display does, which draws every record, a record calling no genotype included:

  • records: each one's ref, alt (its alleles joined by ,) and filter, aligned to ids.
  • info and infoFields: its INFO, as variantTables gives them.
  • samples: a row per record and sample in header order, feature (an index into ids) and sample; format, a column per FORMAT key aligned to it, typed as INFO is; and formatFields, each key's declaration.
  • annotations and annotationFields: its ANN or CSQ consequences, as variantTables gives them, feature an index into ids.
// type signature
(pluginManager: PluginManager, { adapterConfig, sequenceAdapter, regions, ids, }: {…}) => Promise<{ samples: {…}; format: Record<string, unknown[]>; formatFields: { key: string[]; number: string[]; type: string[]; description: string[]; }; annotations: { [x: string]: number[] | string[] | (string | null)[]; key: string[]; }; annotationFields: { key: string[]; field: string[]; }; info: Record<string, unknown[]>; infoFields: { key: string[]; number: string[]; type: string[]; description: string[]; }; records: { ref: string[]; alt: string[]; filter: (string | null)[]; }; }>

Source code

variantTables

A region of a multi-sample VCF as the multi-sample variant display fetches, filters and paints it, as tables: variants, each record the display keeps, with its lane color and its filter; info, each INFO key's values aligned to variants, and infoFields, the header's declaration of each key; annotations, each record's SnpEff ANN or VEP CSQ consequences, a row per record and consequence, which then leave info (consequenceTables); cells, each sample's (or under unit: 'haplotype' each haplotype's) cell at each record, with its genotype, its dosage and the fill the display paints it; rows, the rows the cells name, top to bottom as the display arranges them by rows and stacks them in facet's bands, each with its label and band; bands, each band's value, label and the rows it spans; and legend and ramps, the key the display shows. Under referenceDrawingMode: 'skip', the default, a reference call draws no cell. Several regions share the rows and the key, as the display's regions do: a record crossing regions is listed in each, under one key, every variants and cells row names its region's index, and cells.variant indexes the joined variants. For a host that draws them itself, such as R through V8. The adapters must be registered on pluginManager (registerVariantAdapters).

// type signature
(pluginManager: PluginManager, { adapterConfig, sequenceAdapter, region, regions, display, byteLimit, }: VariantTablesArgs) => Promise<{ cells: {…}; rows: {…}; legend: {…}; ramps: {…}[]; rowLegend: {…}; rowLegendTitle: string; bands: {…}; config: Record<…>; warnings: string[]; annotations: {…}; annotationFields: {…}; info: Record<…>; infoFields: {…}; variants: { start: number[]; end: number[]; id: string[]; name: string[]; ref: string[]; alt: string[]; type: string[]; color: string[]; filter: (string | null)[]; region: number[]; key: number[]; }; }>

Source code