loom-browser 0.0.13 → 0.0.15

package/dist/types/browser/headless/headlessGenomeBrowser.d.ts

@@ -308,7 +308,7 @@ export declare class HeadlessGenomeBrowser {
      */
     setViewportWidth(width: number): void;
     /** Add a track with an optional data source for automatic data management. */
-    addTrack<F>(track: Track, dataSource?: DataSource<F>, dataSourceConfig?: DataSourceConfig, maxTrackHeight?: number, order?: number): string;
+    addTrack<F>(track: Track, dataSource?: DataSource<F>, dataSourceConfig?: DataSourceConfig, maxTrackHeight?: number, order?: number, id?: string): string;
     /** Remove a track by reference or by stable string ID. */
     removeTrack(trackOrId: Track | string): void;
     /**
@@ -507,6 +507,8 @@ export declare class HeadlessGenomeBrowser {
     addGeneTrack(options?: import('./trackFactories').AddAnnotationTrackOptions): AnnotationTrackCanvas;
     /** Add a BED/peak annotation track from a URL. */
     addBedTrack(url: string, options?: import('./trackFactories').AddBedTrackOptions): AnnotationTrackCanvas;
+    /** Add a BigBed annotation track from a URL. */
+    addBigBedTrack(url: string, options?: import('./trackFactories').AddBigBedTrackOptions): AnnotationTrackCanvas;
     /** Add an interaction (arc/BEDPE) track from a URL. */
     addInteractionTrack(url: string, options?: import('./trackFactories').AddInteractionTrackOptions): InteractionTrackCanvas;
     /** Add a BigWig-style signal track backed by in-memory features (no URL required). */

package/dist/types/browser/headless/trackFactories.d.ts

@@ -74,6 +74,20 @@ export interface AddBedTrackOptions {
     /** Static auth config (serializable, worker-safe, session-safe). */
     auth?: StaticAuthConfig;
 }
+export interface AddBigBedTrackOptions {
+    config?: Partial<AnnotationRenderConfig>;
+    maxTrackHeight?: number;
+    name?: string;
+    metadata?: Record<string, string>;
+    /** Enable feature name indexing for search. Default: true. */
+    searchable?: boolean;
+    /** Fields to index for search. Default: DEFAULT_SEARCHABLE_FIELDS. */
+    searchableFields?: string[];
+    /** Full auth provider for this track (main thread, supports token refresh). */
+    authProvider?: AuthProvider;
+    /** Static auth config (serializable, worker-safe, session-safe). */
+    auth?: StaticAuthConfig;
+}
 export interface AddInteractionTrackOptions {
     config?: Partial<InteractionRenderConfig>;
     format?: TextFileFormat;
@@ -176,6 +190,7 @@ export declare function createWigTrack(ctx: TrackFactoryContext, url: string, op
 export declare function createGtxTrack(ctx: TrackFactoryContext, url: string, options: AddGtxTrackOptions): FactoryResult<WigTrackCanvas>;
 export declare function createGeneTrack(ctx: TrackFactoryContext, options?: AddAnnotationTrackOptions): FactoryResult<AnnotationTrackCanvas>;
 export declare function createBedTrack(ctx: TrackFactoryContext, url: string, options?: AddBedTrackOptions): FactoryResult<AnnotationTrackCanvas>;
+export declare function createBigBedTrack(ctx: TrackFactoryContext, url: string, options?: AddBigBedTrackOptions): FactoryResult<AnnotationTrackCanvas>;
 export declare function createInteractionTrack(ctx: TrackFactoryContext, url: string, options?: AddInteractionTrackOptions): FactoryResult<InteractionTrackCanvas>;
 export declare function createWigTrackWithFeatures(ctx: TrackFactoryContext, features: WigFeature[], options?: AddWigTrackWithFeaturesOptions): FactoryResult<WigTrackCanvas>;
 export declare function createBedTrackWithFeatures(ctx: TrackFactoryContext, features: BedFeature[], options?: AddBedTrackWithFeaturesOptions): FactoryResult<AnnotationTrackCanvas>;

package/dist/types/dataSources/bigBedDataSource.d.ts

@@ -0,0 +1,33 @@
+/**
+ * BigBed data source — fetches BED features from BigBed binary files.
+ *
+ * Uses @gmod/bbi's BigBed class for binary parsing and range queries.
+ * Returns BedFeature[] suitable for annotation track rendering.
+ *
+ * Mirrors igv.js BWSource behavior for bigbed format:
+ * - Features are decoded from BED rest fields via decodeBed()
+ * - No zoom-level summarization (unlike BigWig)
+ * - Feature density estimation from header dataCount
+ *
+ * Layer 1 (Data + Layout): no DOM.
+ */
+import type { DataSource, ConfigurableDataSource, Locus, BedFeature } from '../types';
+import type { FetchImpl } from '../io/rangeReader';
+export declare class BigBedDataSource implements DataSource<BedFeature>, ConfigurableDataSource {
+    private _resolveChromName?;
+    private readonly bb;
+    private readonly url;
+    private readonly fetchImpl?;
+    constructor(url: string, fetchImpl?: FetchImpl);
+    /** Set a chromosome name resolver for alias resolution (e.g., "1" → "chr1"). */
+    setChromNameResolver(resolver: (chr: string) => string): void;
+    fetch(locus: Locus, _bpPerPixel: number, signal: AbortSignal): Promise<BedFeature[]>;
+    /**
+     * Search for a feature by name via BigBed extra index.
+     * Returns matching features, or empty array if not found or not indexed.
+     */
+    search(name: string): Promise<BedFeature[]>;
+    dispose(): void;
+}
+/** Clear the BigBed reader cache (useful for testing or memory management). */
+export declare function clearBigBedCache(): void;

package/dist/types/dataSources/config.d.ts

@@ -30,12 +30,16 @@ export interface DataSourceAuthConfig {
 /** Alias for DataSourceAuthConfig — used on per-track options for clarity. */
 export type StaticAuthConfig = DataSourceAuthConfig;
 /** Discriminated union for data source reconstruction. */
-export type DataSourceConfig = BigWigDataSourceConfig | GtxDataSourceConfig | UCSCDataSourceConfig | TextDataSourceConfig | MemoryDataSourceConfig;
+export type DataSourceConfig = BigWigDataSourceConfig | BigBedDataSourceConfig | GtxDataSourceConfig | UCSCDataSourceConfig | TextDataSourceConfig | MemoryDataSourceConfig;
 export interface BigWigDataSourceConfig extends DataSourceAuthConfig {
     type: 'bigwig';
     url: string;
     windowFunction?: WindowFunction;
 }
+export interface BigBedDataSourceConfig extends DataSourceAuthConfig {
+    type: 'bigbed';
+    url: string;
+}
 export interface GtxDataSourceConfig extends DataSourceAuthConfig {
     type: 'gtx';
     url: string;

package/dist/types/formats/formatDetection.d.ts

@@ -21,6 +21,8 @@ export declare function inferFormatFromPath(path: string): string | undefined;
 export declare function isBinaryFormat(format: string): boolean;
 /** BigWig/BigBed format set — these use BWSource in igv.js. */
 export declare const bbFormats: Set<string>;
+/** Check if a format string represents a BigBed (annotation) format vs BigWig (quantitative). */
+export declare function isBigBedFormat(format: string): boolean;
 /**
  * Check if a URL is likely tabix-indexed.
  *

package/dist/types/genome/genome.d.ts

@@ -35,9 +35,10 @@ export declare function createGenomeSync(config: GenomeConfig & {
  */
 export declare function createGenome(config: GenomeConfig): Promise<Genome>;
 /**
- * Pre-built hg38 genome with UCSC sequence API.
+ * Pre-built hg38 genome with 2-bit sequence (UCSC API fallback).
  *
  * This is the default genome used by HeadlessGenomeBrowser when no genome
- * is specified. Equivalent to igv.js's default behavior of loading hg38.
+ * is specified. Matches igv.js's default behavior: 2-bit file as primary
+ * sequence source, with UCSC REST API as automatic fallback for resilience.
  */
 export declare const hg38Genome: Genome;

package/dist/types/index.d.ts

@@ -40,7 +40,7 @@ export type { CytobandFeature, IdeogramRenderConfig, IdeogramTrackSessionConfig,
 export type { DataSource, ConfigurableDataSource, DataSourceConfigMethod, FeatureCacheEntry, DataDrivenTrack, ZoomAwareTrack } from './types';
 export { isZoomAware } from './types';
 export type { PopupDataItem, HitTestResult, TrackInteractionEvent, ContextMenuItem, TrackContextMenuEvent, NumericState, ROI, ROISetConfig, ROIInteractionEvent, FeatureRect } from './types';
-export type { LocusChangeEvent, ReferenceFrameSession, SessionConfig, TrackSessionConfig, WigTrackSessionConfig, AnnotationTrackSessionConfig, RulerTrackSessionConfig, MergedTrackSessionConfig, MergedSessionOverrides, PeakOverlayTrackSessionConfig, PeakOverlaySessionOverrides, WigAnnotationConfig, WigSessionOverrides, AnnotationSessionOverrides, RulerSessionOverrides, DataSourceConfig, DataSourceAuthConfig, BigWigDataSourceConfig, GtxDataSourceConfig, UCSCDataSourceConfig, TextDataSourceConfig, MemoryDataSourceConfig, SequenceProvider, Chromosome, Genome, GenomeConfig, ChromAliasRecord, Strand, TextFileFormat, BedFeature, PeakFeature, BedGraphFeature, GFFRecord, GFFFeature, TextFeature, } from './types';
+export type { LocusChangeEvent, ReferenceFrameSession, SessionConfig, TrackSessionConfig, WigTrackSessionConfig, AnnotationTrackSessionConfig, RulerTrackSessionConfig, MergedTrackSessionConfig, MergedSessionOverrides, PeakOverlayTrackSessionConfig, PeakOverlaySessionOverrides, WigAnnotationConfig, WigSessionOverrides, AnnotationSessionOverrides, RulerSessionOverrides, DataSourceConfig, DataSourceAuthConfig, BigWigDataSourceConfig, BigBedDataSourceConfig, GtxDataSourceConfig, UCSCDataSourceConfig, TextDataSourceConfig, MemoryDataSourceConfig, SequenceProvider, Chromosome, Genome, GenomeConfig, ChromAliasRecord, Strand, TextFileFormat, BedFeature, PeakFeature, BedGraphFeature, GFFRecord, GFFFeature, TextFeature, } from './types';
 export type { IgvSessionObject, IgvReferenceConfig, IgvTrackConfig } from './types/igvCompat';
 export type { Packable } from './pack';
 export { packFeatures } from './pack';
@@ -147,6 +147,7 @@ export type { FetchGtxOptions, GtxHeader, ChromEntry, ExperimentEntry } from './
 export { TabixReader } from './tabix';
 export type { TabixReaderOptions, TabixHeader } from './tabix';
 export { BigWigDataSource } from './dataSources/bigWigDataSource';
+export { BigBedDataSource } from './dataSources/bigBedDataSource';
 export { GtxDataSource } from './dataSources/gtxDataSource';
 export { GeneDataSource } from './dataSources/geneDataSource';
 export { TextFeatureSource } from './dataSources/textFeatureSource';

package/dist/types/types.d.ts

@@ -7,7 +7,7 @@ export type { SequenceType, SequenceRenderConfig } from './tracks/sequence/confi
 export type { ArcOrientation, ArcDisplayMode, InteractionRenderConfig } from './tracks/interaction/config';
 export type { MergedRenderConfig } from './tracks/merged/config';
 export type { IdeogramRenderConfig } from './tracks/ideogram/config';
-export type { DataSourceConfig, DataSourceAuthConfig, BigWigDataSourceConfig, GtxDataSourceConfig, UCSCDataSourceConfig, TextDataSourceConfig, MemoryDataSourceConfig, } from './dataSources/config';
+export type { DataSourceConfig, DataSourceAuthConfig, BigWigDataSourceConfig, BigBedDataSourceConfig, GtxDataSourceConfig, UCSCDataSourceConfig, TextDataSourceConfig, MemoryDataSourceConfig, } from './dataSources/config';
 /** Genomic locus — a chromosome region. */
 export interface Locus {
     chr: string;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "loom-browser",
-  "version": "0.0.13",
+  "version": "0.0.15",
   "main": "dist/loom.esm.js",
   "module": "dist/loom.esm.js",
   "types": "dist/types/index.d.ts",