loom-browser 0.0.13 → 0.0.14

package/dist/loom.esm.js

@@ -3551,14 +3551,14 @@ class BinaryParser {
 // ─── Internal helpers ─────────────────────────────────────────────────────────
 // Cache BigWig instances by URL to reuse parsed headers and trees.
 // Auth-aware readers share the cache key (URL) — the fetchImpl is bound at creation.
-const readerCache$4 = new Map();
+const readerCache$5 = new Map();
 function getGmodReader(url, fetchImpl) {
     const resolvedUrl = normalizeGoogleURL(url);
-    let reader = readerCache$4.get(resolvedUrl);
+    let reader = readerCache$5.get(resolvedUrl);
     if (!reader) {
         const fileOpts = fetchImpl ? { fetch: fetchImpl } : undefined;
         reader = new BigWig({ filehandle: new RemoteFile(resolvedUrl, fileOpts) });
-        readerCache$4.set(resolvedUrl, reader);
+        readerCache$5.set(resolvedUrl, reader);
     }
     return reader;
 }
@@ -3679,7 +3679,7 @@ async function fetchBigWigFeatures(url, locus, options = {}) {
         // Evict the cached reader so the next fetch gets a fresh one.
         // @gmod/bbi caches the header promise; an aborted parse poisons it permanently.
         if (err instanceof Error && (err.name === 'AbortError' || ((_b = err.message) === null || _b === void 0 ? void 0 : _b.includes('aborted')))) {
-            readerCache$4.delete(url);
+            readerCache$5.delete(url);
         }
         throw err;
     }
@@ -3695,7 +3695,7 @@ async function fetchBigWigWGFeatures(url, chromNames, bpPerPixel, options = {})
 }
 /** Clear the BigWig reader cache (useful for testing or memory management). */
 function clearBigWigCache() {
-    readerCache$4.clear();
+    readerCache$5.clear();
 }
 
 /**
@@ -5040,12 +5040,12 @@ class GtxFetchCoordinator {
  * Layer 1 (Data + Layout): no DOM, no canvas.
  */
 // Cache readers by URL to reuse parsed headers, dictionaries, and indexes
-const readerCache$3 = new Map();
-function getReader$3(url, fetchImpl) {
-    let reader = readerCache$3.get(url);
+const readerCache$4 = new Map();
+function getReader$4(url, fetchImpl) {
+    let reader = readerCache$4.get(url);
     if (!reader) {
         reader = new GtxReader(url, fetchImpl);
-        readerCache$3.set(url, reader);
+        readerCache$4.set(url, reader);
     }
     return reader;
 }
@@ -5054,7 +5054,7 @@ function getReader$3(url, fetchImpl) {
  */
 async function fetchGtxFeatures(url, experimentId, locus, options = {}) {
     var _a;
-    const reader = getReader$3(url, options.fetchImpl);
+    const reader = getReader$4(url, options.fetchImpl);
     await reader.init(options.signal);
     const expIdx = reader.resolveExperimentIndex(experimentId);
     if (expIdx === undefined) {
@@ -5068,7 +5068,7 @@ async function fetchGtxFeatures(url, experimentId, locus, options = {}) {
  * Returns features with per-chromosome coordinates (caller transforms to genome-wide).
  */
 async function fetchGtxWGFeatures(url, experimentId, chromNames, bpPerPixel, options = {}) {
-    const reader = getReader$3(url, options.fetchImpl);
+    const reader = getReader$4(url, options.fetchImpl);
     await reader.init(options.signal);
     const expIdx = reader.resolveExperimentIndex(experimentId);
     if (expIdx === undefined) {
@@ -5097,7 +5097,7 @@ async function fetchGtxWGFeatures(url, experimentId, chromNames, bpPerPixel, opt
  */
 async function fetchGtxMultiFeatures(url, experimentIds, locus, options = {}) {
     var _a;
-    const reader = getReader$3(url, options.fetchImpl);
+    const reader = getReader$4(url, options.fetchImpl);
     await reader.init(options.signal);
     const idToIdx = new Map();
     const indexes = [];
@@ -5119,10 +5119,10 @@ async function fetchGtxMultiFeatures(url, experimentIds, locus, options = {}) {
 }
 /** Clear the GTX reader cache (useful for testing or memory management). */
 function clearGtxCache() {
-    for (const reader of readerCache$3.values()) {
+    for (const reader of readerCache$4.values()) {
         reader.dispose();
     }
-    readerCache$3.clear();
+    readerCache$4.clear();
     clearCoordinators();
 }
 
@@ -5144,12 +5144,12 @@ function clearGtxCache() {
  * Layer 1 (Data + Layout): no DOM, no canvas.
  */
 // Cache readers by URL (shared with gtx/index.ts reader cache)
-const readerCache$2 = new Map();
-function getReader$2(url, fetchImpl) {
-    let reader = readerCache$2.get(url);
+const readerCache$3 = new Map();
+function getReader$3(url, fetchImpl) {
+    let reader = readerCache$3.get(url);
     if (!reader) {
         reader = new GtxReader(url, fetchImpl);
-        readerCache$2.set(url, reader);
+        readerCache$3.set(url, reader);
     }
     return reader;
 }
@@ -5159,7 +5159,7 @@ class GtxDataSource {
         this.experimentId = experimentId;
         this._windowFunction = windowFunction;
         this.fetchImpl = fetchImpl;
-        this.reader = getReader$2(url, fetchImpl);
+        this.reader = getReader$3(url, fetchImpl);
     }
     get windowFunction() { return this._windowFunction; }
     /** Update the window function for future fetches. */
@@ -15393,6 +15393,12 @@ function isBinaryFormat(format) {
 }
 /** BigWig/BigBed format set — these use BWSource in igv.js. */
 const bbFormats = new Set(['bigwig', 'bw', 'bigbed', 'bb', 'biginteract', 'biggenepred', 'bignarrowpeak']);
+/** BigBed-specific formats (annotation data, not quantitative). */
+const bigBedFormats = new Set(['bigbed', 'bb', 'biginteract', 'biggenepred', 'bignarrowpeak']);
+/** Check if a format string represents a BigBed (annotation) format vs BigWig (quantitative). */
+function isBigBedFormat(format) {
+    return bigBedFormats.has(format.toLowerCase());
+}
 /**
  * Check if a URL is likely tabix-indexed.
  *
@@ -22075,15 +22081,15 @@ class TwoBitFile {
  */
 // ─── Internal helpers ─────────────────────────────────────────────────────────
 // Cache TwoBitFile instances by URL to reuse parsed headers and indices.
-const readerCache$1 = new Map();
+const readerCache$2 = new Map();
 // Parallel filehandle cache for direct batched reads (bypasses @gmod/twobit).
 const filehandleCache = new Map();
-function getReader$1(url, fetchImpl) {
-    let reader = readerCache$1.get(url);
+function getReader$2(url, fetchImpl) {
+    let reader = readerCache$2.get(url);
     if (!reader) {
         const filehandle = getFilehandle(url, fetchImpl);
         reader = new TwoBitFile({ filehandle });
-        readerCache$1.set(url, reader);
+        readerCache$2.set(url, reader);
     }
     return reader;
 }
@@ -22147,7 +22153,7 @@ function mergeOffsetsToRanges(sortedOffsets) {
  * instead of 100K+.
  */
 async function fetchChromSizesBatched(url, fetchImpl) {
-    const reader = getReader$1(url, fetchImpl);
+    const reader = getReader$2(url, fetchImpl);
     const fh = getFilehandle(url, fetchImpl);
     // Step 1: get the index (name → file offset). Cached after first call.
     const index = await reader.getIndex();
@@ -22215,14 +22221,14 @@ async function fetchChromSizesBatched(url, fetchImpl) {
 function createTwoBitSequenceProvider(url, fetchImpl) {
     return async (locus) => {
         var _a;
-        const reader = getReader$1(url, fetchImpl);
+        const reader = getReader$2(url, fetchImpl);
         try {
             const sequence = await reader.getSequence(locus.chr, locus.start, locus.end);
             return sequence !== null && sequence !== void 0 ? sequence : '';
         }
         catch (err) {
             if (err instanceof Error && (err.name === 'AbortError' || ((_a = err.message) === null || _a === void 0 ? void 0 : _a.includes('aborted')))) {
-                readerCache$1.delete(url);
+                readerCache$2.delete(url);
                 filehandleCache.delete(url);
             }
             throw err;
@@ -22250,12 +22256,12 @@ async function fetchTwoBitChromSizes(url, fetchImpl) {
  * individual sequence records.
  */
 async function fetchTwoBitSequenceNames(url, fetchImpl) {
-    const reader = getReader$1(url, fetchImpl);
+    const reader = getReader$2(url, fetchImpl);
     return reader.getSequenceNames();
 }
 /** Clear the TwoBit reader cache (useful for testing or memory management). */
 function clearTwoBitCache() {
-    readerCache$1.clear();
+    readerCache$2.clear();
     filehandleCache.clear();
 }
 
@@ -22459,10 +22465,10 @@ class FetchableSmallFasta {
  */
 // ─── Internal helpers ─────────────────────────────────────────────────────────
 // Cache reader instances by URL to reuse parsed indices.
-const readerCache = new Map();
-function getReader(fastaURL, indexURL, compressedIndexURL, fetchImpl) {
+const readerCache$1 = new Map();
+function getReader$1(fastaURL, indexURL, compressedIndexURL, fetchImpl) {
     const cacheKey = fastaURL;
-    let reader = readerCache.get(cacheKey);
+    let reader = readerCache$1.get(cacheKey);
     if (!reader) {
         const fileOpts = fetchImpl ? { fetch: fetchImpl } : undefined;
         if (compressedIndexURL) {
@@ -22478,7 +22484,7 @@ function getReader(fastaURL, indexURL, compressedIndexURL, fetchImpl) {
                 fai: new RemoteFile(indexURL, fileOpts),
             });
         }
-        readerCache.set(cacheKey, reader);
+        readerCache$1.set(cacheKey, reader);
     }
     return reader;
 }
@@ -22498,14 +22504,14 @@ function createFastaSequenceProvider(fastaURL, indexURL, compressedIndexURL, fet
     const faiURL = indexURL !== null && indexURL !== void 0 ? indexURL : fastaURL + '.fai';
     return async (locus, signal) => {
         var _a;
-        const reader = getReader(fastaURL, faiURL, compressedIndexURL, fetchImpl);
+        const reader = getReader$1(fastaURL, faiURL, compressedIndexURL, fetchImpl);
         try {
             const sequence = await reader.getSequence(locus.chr, locus.start, locus.end, { signal });
             return sequence !== null && sequence !== void 0 ? sequence : '';
         }
         catch (err) {
             if (err instanceof Error && (err.name === 'AbortError' || ((_a = err.message) === null || _a === void 0 ? void 0 : _a.includes('aborted')))) {
-                readerCache.delete(fastaURL);
+                readerCache$1.delete(fastaURL);
             }
             throw err;
         }
@@ -22519,7 +22525,7 @@ function createFastaSequenceProvider(fastaURL, indexURL, compressedIndexURL, fet
  */
 async function fetchFastaChromSizes(fastaURL, indexURL, fetchImpl) {
     const faiURL = indexURL !== null && indexURL !== void 0 ? indexURL : fastaURL + '.fai';
-    const reader = getReader(fastaURL, faiURL, undefined, fetchImpl);
+    const reader = getReader$1(fastaURL, faiURL, undefined, fetchImpl);
     return reader.getSequenceSizes();
 }
 /**
@@ -22527,12 +22533,12 @@ async function fetchFastaChromSizes(fastaURL, indexURL, fetchImpl) {
  */
 async function fetchFastaSequenceNames(fastaURL, indexURL, fetchImpl) {
     const faiURL = indexURL !== null && indexURL !== void 0 ? indexURL : fastaURL + '.fai';
-    const reader = getReader(fastaURL, faiURL, undefined, fetchImpl);
+    const reader = getReader$1(fastaURL, faiURL, undefined, fetchImpl);
     return reader.getSequenceNames();
 }
 /** Clear the FASTA reader cache (useful for testing or memory management). */
 function clearFastaCache() {
-    readerCache.clear();
+    readerCache$1.clear();
 }
 
 /**
@@ -23056,7 +23062,7 @@ function indexGenomes(genomes, table) {
  * Layer 1 (Data): no DOM, no canvas.
  */
 /** Known data source config types. */
-const KNOWN_DS_TYPES = new Set(['bigwig', 'gtx', 'ucsc', 'text', 'memory']);
+const KNOWN_DS_TYPES = new Set(['bigwig', 'bigbed', 'gtx', 'ucsc', 'text', 'memory']);
 /** Check whether a data source config type is one of the known concrete types. */
 function isKnownDataSourceType(type) {
     return KNOWN_DS_TYPES.has(type);
@@ -23090,7 +23096,16 @@ function resolveDataSourceConfig(config) {
         auth.headers = config.headers;
     if (config.withCredentials)
         auth.withCredentials = config.withCredentials;
-    // BigWig / BigBed binary formats
+    // BigBed binary formats (annotation data)
+    if (format && isBigBedFormat(format)) {
+        log.warn(`Unknown data source type "${type}", inferred "bigbed" from URL: ${url}`);
+        return {
+            type: 'bigbed',
+            url,
+            ...auth,
+        };
+    }
+    // BigWig / other binary formats (quantitative data)
     if (format && (format === 'bigwig' || format === 'bw' || isBinaryFormat(format))) {
         log.warn(`Unknown data source type "${type}", inferred "bigwig" from URL: ${url}`);
         return {
@@ -23528,6 +23543,106 @@ class SequenceTrackCanvas extends BaseTrackCanvas {
     }
 }
 
+/**
+ * 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.
+ */
+// Cache BigBed instances by URL to reuse parsed headers and index trees.
+const readerCache = new Map();
+function getReader(url, fetchImpl) {
+    const resolvedUrl = normalizeGoogleURL(url);
+    let reader = readerCache.get(resolvedUrl);
+    if (!reader) {
+        const fileOpts = fetchImpl ? { fetch: fetchImpl } : undefined;
+        reader = new BigBed({ filehandle: new RemoteFile(resolvedUrl, fileOpts) });
+        readerCache.set(resolvedUrl, reader);
+    }
+    return reader;
+}
+class BigBedDataSource {
+    constructor(url, fetchImpl) {
+        this.url = url;
+        this.fetchImpl = fetchImpl;
+        this.bb = getReader(url, fetchImpl);
+    }
+    /** Set a chromosome name resolver for alias resolution (e.g., "1" → "chr1"). */
+    setChromNameResolver(resolver) {
+        this._resolveChromName = resolver;
+    }
+    async fetch(locus, _bpPerPixel, signal) {
+        var _a;
+        const chr = this._resolveChromName
+            ? this._resolveChromName(locus.chr)
+            : locus.chr;
+        try {
+            const rawFeatures = await this.bb.getFeatures(chr, locus.start, locus.end, { signal });
+            const result = [];
+            for (const f of rawFeatures) {
+                const parsed = parseBigBedFeature(chr, f.start, f.end, f.rest);
+                if (parsed)
+                    result.push(parsed);
+            }
+            return result;
+        }
+        catch (err) {
+            // Evict poisoned reader on abort (same pattern as BigWig)
+            if (err instanceof Error && (err.name === 'AbortError' || ((_a = err.message) === null || _a === void 0 ? void 0 : _a.includes('aborted')))) {
+                readerCache.delete(normalizeGoogleURL(this.url));
+            }
+            throw err;
+        }
+    }
+    /**
+     * Search for a feature by name via BigBed extra index.
+     * Returns matching features, or empty array if not found or not indexed.
+     */
+    async search(name) {
+        const header = await this.bb.getHeader();
+        const results = await this.bb.searchExtraIndex(name);
+        if (results.length === 0)
+            return [];
+        const refsByNumber = header.refsByNumber;
+        const features = [];
+        for (const r of results) {
+            const chromId = r.chromId;
+            if (chromId == null || !(refsByNumber === null || refsByNumber === void 0 ? void 0 : refsByNumber[chromId]))
+                continue;
+            const chr = refsByNumber[chromId].name;
+            const parsed = parseBigBedFeature(chr, r.start, r.end, r.rest);
+            if (parsed)
+                features.push(parsed);
+        }
+        return features;
+    }
+    dispose() {
+        readerCache.delete(normalizeGoogleURL(this.url));
+    }
+}
+/**
+ * Parse a BigBed feature's rest field into a BedFeature.
+ * Reconstructs BED tokens from chr/start/end + tab-delimited rest, then uses decodeBed().
+ */
+function parseBigBedFeature(chr, start, end, rest) {
+    const tokens = [chr, String(start), String(end)];
+    if (rest) {
+        tokens.push(...rest.split('\t'));
+    }
+    return decodeBed(tokens);
+}
+/** Clear the BigBed reader cache (useful for testing or memory management). */
+function clearBigBedCache() {
+    readerCache.clear();
+}
+
 /**
  * DataSource backed by an in-memory feature array.
  *
@@ -26672,6 +26787,8 @@ function createDataSource(config) {
     switch (config.type) {
         case 'bigwig':
             return new BigWigDataSource(config.url, config.windowFunction);
+        case 'bigbed':
+            return new BigBedDataSource(config.url);
         case 'gtx':
             return new GtxDataSource(config.url, config.experimentId, config.windowFunction);
         case 'ucsc':
@@ -26953,6 +27070,11 @@ registerTypeAlias('broadpeak', 'annotation');
 registerTypeAlias('genepred', 'annotation');
 registerTypeAlias('genepredext', 'annotation');
 registerTypeAlias('refflat', 'annotation');
+// BigBed format → annotation track type aliases
+registerTypeAlias('bigbed', 'annotation');
+registerTypeAlias('bedtype', 'annotation');
+registerTypeAlias('biggenepred', 'annotation');
+registerTypeAlias('bignarrowpeak', 'annotation');
 // Merged/overlay aliases
 registerTypeAlias('overlay', 'merged');
 // Interaction format aliases
@@ -27043,6 +27165,10 @@ const IGV_TRACK_TYPE_MAP = {
     'gtf': 'annotation',
     'narrowpeak': 'annotation',
     'broadpeak': 'annotation',
+    'bigbed': 'annotation',
+    'biggenepred': 'annotation',
+    'bignarrowpeak': 'annotation',
+    'biginteract': 'interact',
     'sequence': 'sequence',
     'interact': 'interact',
     'bedpe': 'interact',
@@ -27160,23 +27286,35 @@ function convertIgvWigTrack(igvTrack) {
     return result;
 }
 function convertIgvAnnotationTrack(igvTrack) {
+    var _a, _b;
     const result = { type: 'annotation' };
     if (igvTrack.name)
         result.name = igvTrack.name;
     if (igvTrack.order != null)
         result.order = igvTrack.order;
-    // Data source — gene tracks in igv.js can come from URLs (text files) or UCSC
+    // Data source — gene tracks in igv.js can come from BigBed, text files, or UCSC
     if (igvTrack.url) {
-        const ds = {
-            type: 'text',
-            url: igvTrack.url,
-            ...extractAuthFromIgv(igvTrack),
-        };
-        if (igvTrack.indexURL)
-            ds.indexURL = igvTrack.indexURL;
-        if (igvTrack.format)
-            ds.format = igvTrack.format;
-        result.dataSource = ds;
+        const format = (_b = (_a = igvTrack.format) === null || _a === void 0 ? void 0 : _a.toLowerCase()) !== null && _b !== void 0 ? _b : '';
+        if (isBigBedFormat(format) || /\.bb$/i.test(igvTrack.url) || /\.bigbed$/i.test(igvTrack.url)) {
+            const ds = {
+                type: 'bigbed',
+                url: igvTrack.url,
+                ...extractAuthFromIgv(igvTrack),
+            };
+            result.dataSource = ds;
+        }
+        else {
+            const ds = {
+                type: 'text',
+                url: igvTrack.url,
+                ...extractAuthFromIgv(igvTrack),
+            };
+            if (igvTrack.indexURL)
+                ds.indexURL = igvTrack.indexURL;
+            if (igvTrack.format)
+                ds.format = igvTrack.format;
+            result.dataSource = ds;
+        }
     }
     // Config overrides
     const config = {};
@@ -27272,13 +27410,23 @@ function convertToIgvWigTrack(track) {
     return igv;
 }
 function convertToIgvAnnotationTrack(track) {
-    var _a;
+    var _a, _b;
     const igv = { type: 'annotation' };
     if (track.name)
         igv.name = track.name;
     if (track.order != null)
         igv.order = track.order;
     if (((_a = track.dataSource) === null || _a === void 0 ? void 0 : _a.type) === 'text') {
+        igv.url = track.dataSource.url;
+        if (track.dataSource.format)
+            igv.format = track.dataSource.format;
+        if (track.dataSource.indexURL)
+            igv.indexURL = track.dataSource.indexURL;
+        Object.assign(igv, extractAuthForIgv(track.dataSource));
+    }
+    else if (((_b = track.dataSource) === null || _b === void 0 ? void 0 : _b.type) === 'bigbed') {
+        igv.url = track.dataSource.url;
+        igv.format = 'bigbed';
         Object.assign(igv, extractAuthForIgv(track.dataSource));
     }
     if (track.config) {
@@ -28827,6 +28975,9 @@ function wireDataSource(ds, ctx) {
         if (ds instanceof BigWigDataSource || ds instanceof GtxDataSource) {
             ds.setChromNameResolver(alias => ctx.genome.getChromosomeName(alias));
         }
+        else if (ds instanceof BigBedDataSource) {
+            ds.setChromNameResolver(alias => ctx.genome.getChromosomeName(alias));
+        }
         else if (ds instanceof TextFeatureSource) {
             ds.setChromNameResolver(alias => ctx.genome.getChromosomeName(alias));
             if (ctx.cumulativeOffsets) {
@@ -29014,6 +29165,30 @@ function createBedTrack(ctx, url, options) {
         searchableFields: options === null || options === void 0 ? void 0 : options.searchableFields,
     };
 }
+function createBigBedTrack(ctx, url, options) {
+    var _a;
+    const { canvas } = ctx.canvasProvider.createCanvas(0, 0);
+    const track = new AnnotationTrackCanvas(canvas, {
+        locus: ctx.locus,
+        features: [],
+        config: options === null || options === void 0 ? void 0 : options.config,
+        theme: ctx.theme,
+        canvasProvider: ctx.canvasProvider,
+        name: options === null || options === void 0 ? void 0 : options.name,
+    });
+    const dataSourceConfig = { type: 'bigbed', url, ...options === null || options === void 0 ? void 0 : options.auth };
+    const fetchImpl = resolveTrackFetchImpl(ctx, options);
+    const { dataSource } = getOrCreateDataSource(dataSourceConfig, () => new BigBedDataSource(url, fetchImpl), ctx);
+    return {
+        track,
+        dataSource,
+        dataSourceConfig,
+        maxTrackHeight: options === null || options === void 0 ? void 0 : options.maxTrackHeight,
+        metadata: options === null || options === void 0 ? void 0 : options.metadata,
+        searchable: (_a = options === null || options === void 0 ? void 0 : options.searchable) !== null && _a !== void 0 ? _a : true,
+        searchableFields: options === null || options === void 0 ? void 0 : options.searchableFields,
+    };
+}
 function createInteractionTrack(ctx, url, options) {
     var _a;
     const { canvas } = ctx.canvasProvider.createCanvas(0, 0);
@@ -29363,10 +29538,10 @@ class HeadlessGenomeBrowser {
     }
     // ─── Track lifecycle ─────────────────────────────────────────────────────
     /** Add a track with an optional data source for automatic data management. */
-    addTrack(track, dataSource, dataSourceConfig, maxTrackHeight, order) {
+    addTrack(track, dataSource, dataSourceConfig, maxTrackHeight, order, id) {
         var _a;
         this._snapshotForUndo('track-add');
-        const id = generateTrackId(track.type);
+        id !== null && id !== void 0 ? id : (id = generateTrackId(track.type));
         const mt = {
             id,
             track,
@@ -30245,11 +30420,9 @@ class HeadlessGenomeBrowser {
                 if (!this.dataSourceWorkerProvider && dataSource) {
                     wireDataSource(dataSource, ctx);
                 }
-                this.addTrack(created.track, dataSource !== null && dataSource !== void 0 ? dataSource : undefined, (_a = created.dataSourceConfig) !== null && _a !== void 0 ? _a : undefined, undefined, (_b = created.order) !== null && _b !== void 0 ? _b : undefined);
+                this.addTrack(created.track, dataSource !== null && dataSource !== void 0 ? dataSource : undefined, (_a = created.dataSourceConfig) !== null && _a !== void 0 ? _a : undefined, undefined, (_b = created.order) !== null && _b !== void 0 ? _b : undefined, trackConfig.id);
                 // Restore bookkeeping fields for round-trip serialization
                 const mt = this.findMT(created.track);
-                if (trackConfig.id)
-                    mt.id = trackConfig.id;
                 if (created.name)
                     mt.name = created.name;
                 if (trackConfig.metadata)
@@ -30335,10 +30508,8 @@ class HeadlessGenomeBrowser {
                 wireDataSource(dataSource, ctx);
             }
         }
-        this.addTrack(created.track, dataSource !== null && dataSource !== void 0 ? dataSource : undefined, dataSourceConfig !== null && dataSourceConfig !== void 0 ? dataSourceConfig : undefined, undefined, (_a = created.order) !== null && _a !== void 0 ? _a : undefined);
+        this.addTrack(created.track, dataSource !== null && dataSource !== void 0 ? dataSource : undefined, dataSourceConfig !== null && dataSourceConfig !== void 0 ? dataSourceConfig : undefined, undefined, (_a = created.order) !== null && _a !== void 0 ? _a : undefined, trackConfig.id);
         const mt = this.findMT(created.track);
-        if (trackConfig.id)
-            mt.id = trackConfig.id;
         if (created.name)
             mt.name = created.name;
         if (trackConfig.metadata)
@@ -30397,6 +30568,10 @@ class HeadlessGenomeBrowser {
     addBedTrack(url, options) {
         return this.registerFactory(createBedTrack(this.factoryContext(), url, options));
     }
+    /** Add a BigBed annotation track from a URL. */
+    addBigBedTrack(url, options) {
+        return this.registerFactory(createBigBedTrack(this.factoryContext(), url, options));
+    }
     /** Add an interaction (arc/BEDPE) track from a URL. */
     addInteractionTrack(url, options) {
         return this.registerFactory(createInteractionTrack(this.factoryContext(), url, options));
@@ -35876,8 +36051,12 @@ function createFeatureSource(config) {
         const windowFunction = (_d = config.windowFunction) !== null && _d !== void 0 ? _d : 'mean';
         dataSource = new GtxDataSource(config.url, (_e = config.experimentId) !== null && _e !== void 0 ? _e : '', windowFunction);
     }
+    else if (isBigBedFormat(format)) {
+        // BigBed → BigBedDataSource (annotation features)
+        dataSource = new BigBedDataSource(config.url);
+    }
     else if (isBinaryFormat(format)) {
-        // BigWig/BigBed → BigWigDataSource
+        // BigWig → BigWigDataSource (quantitative features)
         const windowFunction = (_f = config.windowFunction) !== null && _f !== void 0 ? _f : 'mean';
         dataSource = new BigWigDataSource(config.url, windowFunction);
     }
@@ -35895,4 +36074,4 @@ function createFeatureSource(config) {
     return { dataSource, trackType, format };
 }
 
-export { AnnotationTrackCanvas, AuthProviderChain, BaseCompositeTrack, BaseTrackCanvas, BigBedAnnotationSource, BigWigDataSource, BigWigReader, BrowserEvent, C2S, CSS_VAR_NAMES, ChromAliasBB, ChromAliasDefaults, ChromAliasFile, CommandDispatcher, CommandError, CredentialStore, DEFAULT_BPP_SEQUENCE_THRESHOLD, DEFAULT_SEARCHABLE_FIELDS, DOMCanvasProvider, DefaultContextMenuProvider, DefaultPopupProvider, EventEmitter, FeatureCache, FeatureNameIndex, GeneDataSource, GenomeBrowser, GoogleAuthManager, GoogleAuthProvider, GtxDataSource, GtxReader, HeadlessGenomeBrowser, IdeogramTrackCanvas, InteractionTrackCanvas, IntervalTree, LoomBrowserShell, LoomChromosomeSelect, LoomContextMenu, LoomExportControls, LoomInputDialog, LoomLocusInput, LoomNavbar, LoomPopup, LoomWindowSize, LoomZoomControls, MainThreadProvider, MemoryDataSource, MergedDataSource, MergedFeatureCollection, MergedTrackCanvas, NodeWorkerProvider, PeakOverlayTrackCanvas, READY_STATE_OPEN, ROISet, ROI_DEFAULT_COLOR, ROI_USER_DEFINED_COLOR, RemoteConnection, RulerTrackCanvas, SESSION_VERSION, SequenceDataSource, SequenceTrackCanvas, StateProjection, TabixReader, TextFeatureSource, TrackFeatureLRU, UndoManager, WebWorkerPool, WebWorkerProvider, WigGroupDataSource, WigGroupFeatureCollection, WigGroupTrackCanvas, WigTrackCanvas, WorkerDataSource, addCaseAliases, addGoogleApiKey, aggregateWigFeatures, assembleGFFTranscripts, autoThemeCSS, bufferLocus, buildFetchFromCredentials, cacheCoversViewport, clampLocus, classicThemeCSS, classicThemeValues, clearBigWigCache, clearFastaCache, clearGenomeRegistry, clearGtxCache, clearTwoBitCache, commonContextMenuItems, complementBase, complementSequence, computeCumulativeOffsets, computeWigDataRange, createAuthenticatedFetch, createBrowser, createCachedSequence, createDefaultContextMenuProvider, createDefaultPopupProvider, createFastaSequenceProvider, createFeatureSource, createGenome, createGenomeSync, createReferenceFrame, createShell, createTrackFromConfig, createTrackFromSession, createTwoBitSequenceProvider, createWorkerAuthFetch, darkRenderTheme, darkThemeValues, dataSourceCacheKey, decodeBed, decodeBedGraph, decodeBedpe, decodeBroadPeak, decodeGFF3, decodeGFFAttribute, decodeGTF, decodeGappedPeak, decodeGenePred, decodeGenePredExt, decodeInteract, decodeNarrowPeak, decodeRefGeneJson, decodeRefflat, defaultCanvasProvider, defaultNucleotideColors, defaultRenderTheme, drawLetterGlyph, encodeGCSObject, fetchBigWigFeatures, fetchBigWigWGFeatures, fetchCytobands, fetchFastaChromSizes, fetchFastaSequenceNames, fetchGeneFeatures, fetchGtxFeatures, fetchGtxMultiFeatures, fetchGtxWGFeatures, fetchSequence, fetchTwoBitChromSizes, fetchTwoBitSequenceNames, findUTRs, fixBedPE, formatBpLength, formatLocus, fromIgvSession, generateCSSVariableBlock, generateFrameId, generateROIId, genomeToChromCoord, getChromLength, getCodingEnd, getCodingLength, getCodingStart, getDecoder, getDriveDownloadURL, getGoogleDriveFileID, getKnownGenome, getKnownGenomes, getLogLevel, getThemeCSS, getTrackCreator, hg38ChromSizes, hg38Genome, inferFormatFromPath, inferIndexURL, inferTrackType, initializeGenomeRegistry, isBinaryFormat, isCoding, isExon, isGoogleDriveURL, isGoogleStorageSigned, isGoogleStorageURL, isGoogleURL, isHiccups, isIntron, isKnownDataSourceType, isLikelyIndexed, isMainChromosome, isTranscript, isTranscriptPart, isUTR, isValidHGVS, isWholeGenomeView, isZoomAware, knownFileExtensions, knownTrackTypes, lineWigConfig, mainChromosomeNames, mainThreadProvider, matchesSelector, mergeThemeFromCSS, modernRenderTheme, modernThemeCSS, modernThemeValues, normalizeWigGroupRawArrays, numericDataMenuItems, packFeatures, parseBucketName, parseChromSizes, parseColorString, parseCytobandLine, parseCytobands, parseFeatures, parseGFFAttributes, parseHeader, parseLocus, parseSearchResults, parseStrand, peakPopupData, positionString, prettyPrintNumber, recalcBpPerPixel, registerTrackCreator, registerTypeAlias, renderAnnotationTrack, renderDOMBrowserSVG, renderDynSeqFeature, renderIdeogram, renderInteractionTrack, renderPeakOverlay, renderQuantitativeAxis, renderROIOverlays, renderRulerTrack, renderSequenceTrack, renderTrackNameLabel, renderViewportIndicator, renderWholeGenomeRuler, renderWigTrack, resolveAnnotationConfig, resolveDataSourceConfig, resolveGenomeConfig, resolveIdeogramConfig, resolveInteractionConfig, resolvePeakOverlayConfig, resolveRulerConfig, resolveSequenceConfig, resolveTheme, resolveThemeFromCSSVariables, resolveToken, resolveWigConfig, resolveWigGroupConfig, reverseComplementSequence, roiContextMenuItems, searchHGVS, searchWebService, selectTracks, setLogLevel, summarizeWigData, svgToPNG, toIgvSession, toTrackSelector, translateGoogleCloudURL, translateSequence, translationDict, triggerDownload, warmWigConfig, wildcardMatch, wildcardToRegExp };
+export { AnnotationTrackCanvas, AuthProviderChain, BaseCompositeTrack, BaseTrackCanvas, BigBedAnnotationSource, BigBedDataSource, BigWigDataSource, BigWigReader, BrowserEvent, C2S, CSS_VAR_NAMES, ChromAliasBB, ChromAliasDefaults, ChromAliasFile, CommandDispatcher, CommandError, CredentialStore, DEFAULT_BPP_SEQUENCE_THRESHOLD, DEFAULT_SEARCHABLE_FIELDS, DOMCanvasProvider, DefaultContextMenuProvider, DefaultPopupProvider, EventEmitter, FeatureCache, FeatureNameIndex, GeneDataSource, GenomeBrowser, GoogleAuthManager, GoogleAuthProvider, GtxDataSource, GtxReader, HeadlessGenomeBrowser, IdeogramTrackCanvas, InteractionTrackCanvas, IntervalTree, LoomBrowserShell, LoomChromosomeSelect, LoomContextMenu, LoomExportControls, LoomInputDialog, LoomLocusInput, LoomNavbar, LoomPopup, LoomWindowSize, LoomZoomControls, MainThreadProvider, MemoryDataSource, MergedDataSource, MergedFeatureCollection, MergedTrackCanvas, NodeWorkerProvider, PeakOverlayTrackCanvas, READY_STATE_OPEN, ROISet, ROI_DEFAULT_COLOR, ROI_USER_DEFINED_COLOR, RemoteConnection, RulerTrackCanvas, SESSION_VERSION, SequenceDataSource, SequenceTrackCanvas, StateProjection, TabixReader, TextFeatureSource, TrackFeatureLRU, UndoManager, WebWorkerPool, WebWorkerProvider, WigGroupDataSource, WigGroupFeatureCollection, WigGroupTrackCanvas, WigTrackCanvas, WorkerDataSource, addCaseAliases, addGoogleApiKey, aggregateWigFeatures, assembleGFFTranscripts, autoThemeCSS, bufferLocus, buildFetchFromCredentials, cacheCoversViewport, clampLocus, classicThemeCSS, classicThemeValues, clearBigWigCache, clearFastaCache, clearGenomeRegistry, clearGtxCache, clearTwoBitCache, commonContextMenuItems, complementBase, complementSequence, computeCumulativeOffsets, computeWigDataRange, createAuthenticatedFetch, createBrowser, createCachedSequence, createDefaultContextMenuProvider, createDefaultPopupProvider, createFastaSequenceProvider, createFeatureSource, createGenome, createGenomeSync, createReferenceFrame, createShell, createTrackFromConfig, createTrackFromSession, createTwoBitSequenceProvider, createWorkerAuthFetch, darkRenderTheme, darkThemeValues, dataSourceCacheKey, decodeBed, decodeBedGraph, decodeBedpe, decodeBroadPeak, decodeGFF3, decodeGFFAttribute, decodeGTF, decodeGappedPeak, decodeGenePred, decodeGenePredExt, decodeInteract, decodeNarrowPeak, decodeRefGeneJson, decodeRefflat, defaultCanvasProvider, defaultNucleotideColors, defaultRenderTheme, drawLetterGlyph, encodeGCSObject, fetchBigWigFeatures, fetchBigWigWGFeatures, fetchCytobands, fetchFastaChromSizes, fetchFastaSequenceNames, fetchGeneFeatures, fetchGtxFeatures, fetchGtxMultiFeatures, fetchGtxWGFeatures, fetchSequence, fetchTwoBitChromSizes, fetchTwoBitSequenceNames, findUTRs, fixBedPE, formatBpLength, formatLocus, fromIgvSession, generateCSSVariableBlock, generateFrameId, generateROIId, genomeToChromCoord, getChromLength, getCodingEnd, getCodingLength, getCodingStart, getDecoder, getDriveDownloadURL, getGoogleDriveFileID, getKnownGenome, getKnownGenomes, getLogLevel, getThemeCSS, getTrackCreator, hg38ChromSizes, hg38Genome, inferFormatFromPath, inferIndexURL, inferTrackType, initializeGenomeRegistry, isBinaryFormat, isCoding, isExon, isGoogleDriveURL, isGoogleStorageSigned, isGoogleStorageURL, isGoogleURL, isHiccups, isIntron, isKnownDataSourceType, isLikelyIndexed, isMainChromosome, isTranscript, isTranscriptPart, isUTR, isValidHGVS, isWholeGenomeView, isZoomAware, knownFileExtensions, knownTrackTypes, lineWigConfig, mainChromosomeNames, mainThreadProvider, matchesSelector, mergeThemeFromCSS, modernRenderTheme, modernThemeCSS, modernThemeValues, normalizeWigGroupRawArrays, numericDataMenuItems, packFeatures, parseBucketName, parseChromSizes, parseColorString, parseCytobandLine, parseCytobands, parseFeatures, parseGFFAttributes, parseHeader, parseLocus, parseSearchResults, parseStrand, peakPopupData, positionString, prettyPrintNumber, recalcBpPerPixel, registerTrackCreator, registerTypeAlias, renderAnnotationTrack, renderDOMBrowserSVG, renderDynSeqFeature, renderIdeogram, renderInteractionTrack, renderPeakOverlay, renderQuantitativeAxis, renderROIOverlays, renderRulerTrack, renderSequenceTrack, renderTrackNameLabel, renderViewportIndicator, renderWholeGenomeRuler, renderWigTrack, resolveAnnotationConfig, resolveDataSourceConfig, resolveGenomeConfig, resolveIdeogramConfig, resolveInteractionConfig, resolvePeakOverlayConfig, resolveRulerConfig, resolveSequenceConfig, resolveTheme, resolveThemeFromCSSVariables, resolveToken, resolveWigConfig, resolveWigGroupConfig, reverseComplementSequence, roiContextMenuItems, searchHGVS, searchWebService, selectTracks, setLogLevel, summarizeWigData, svgToPNG, toIgvSession, toTrackSelector, translateGoogleCloudURL, translateSequence, translationDict, triggerDownload, warmWigConfig, wildcardMatch, wildcardToRegExp };