loom-browser 0.0.15 → 0.0.16

package/dist/loom.js

@@ -23004,60 +23004,62 @@
     /**
      * Resolve a sequence provider from config.
      *
-     * Exactly one sequence source must be set. Throws if multiple are provided.
-     * Sources: sequenceProvider, twoBitURL, fastaURL, ucscGenome.
-     * When none is set, falls back to UCSC API via `id` if available.
+     * If a custom `sequenceProvider` is set, it is used directly. Otherwise,
+     * all available sources (twoBitURL, fastaURL, ucscGenome/id) are chained
+     * as a prioritized fallback list:
      *
-     * When twoBitURL is used and a genome ID is available, the UCSC REST API is
-     * automatically added as a fallback — if the 2-bit server is unreachable,
-     * the API is tried instead.
+     *   1. twoBitURL  — most efficient (binary range requests)
+     *   2. fastaURL   — reliable CDN fallback (igv.org hosts FASTA for common genomes)
+     *   3. UCSC API   — last resort (api.genome.ucsc.edu REST endpoint)
+     *
+     * This mirrors igv.js genomes3.json which provides both twoBitURL and fastaURL
+     * for common genomes. On networks where one server is unreachable (e.g.,
+     * hgdownload.soe.ucsc.edu blocked but igv.org reachable), the chain
+     * automatically falls through to the next available source.
      */
     function resolveSequenceProvider(config) {
-        var _a, _b;
-        const sources = [
-            config.sequenceProvider && 'sequenceProvider',
-            config.twoBitURL && 'twoBitURL',
-            config.fastaURL && 'fastaURL',
-            config.ucscGenome && 'ucscGenome',
-        ].filter(Boolean);
-        if (sources.length > 1) {
-            throw new Error(`GenomeConfig has multiple sequence sources: ${sources.join(', ')}. ` +
-                'Set exactly one of: sequenceProvider, twoBitURL, fastaURL, or ucscGenome.');
-        }
+        var _a;
+        // Custom provider — use directly, no chaining
         if (config.sequenceProvider) {
             return config.sequenceProvider;
         }
+        // Build prioritized provider list from available config fields
+        const providers = [];
         if (config.twoBitURL) {
-            const primary = createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl);
-            // Add UCSC REST API fallback when a genome ID is known
-            const genomeId = (_a = config.ucscGenome) !== null && _a !== void 0 ? _a : config.id;
-            if (genomeId) {
-                const fallback = (locus, signal) => fetchSequence(locus, { genome: genomeId }, signal);
-                return createCachedSequence(createFallbackProvider(primary, fallback));
-            }
-            return createCachedSequence(primary);
+            providers.push(createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl));
         }
         if (config.fastaURL) {
-            return createCachedSequence(createFastaSequenceProvider(config.fastaURL, config.indexURL, config.compressedIndexURL, config.fetchImpl));
+            providers.push(createFastaSequenceProvider(config.fastaURL, config.indexURL, config.compressedIndexURL, config.fetchImpl));
         }
-        // UCSC API — explicit ucscGenome, or implicit via id
-        const ucscGenome = (_b = config.ucscGenome) !== null && _b !== void 0 ? _b : config.id;
+        const ucscGenome = (_a = config.ucscGenome) !== null && _a !== void 0 ? _a : config.id;
         if (ucscGenome) {
-            return createCachedSequence((locus, signal) => fetchSequence(locus, { genome: ucscGenome }, signal));
+            providers.push((locus, signal) => fetchSequence(locus, { genome: ucscGenome }, signal));
         }
-        return undefined;
+        if (providers.length === 0)
+            return undefined;
+        if (providers.length === 1)
+            return createCachedSequence(providers[0]);
+        // Chain all providers: try each in order, fall back on failure
+        const chained = providers.reduceRight((fallback, primary) => createFallbackProvider(primary, fallback));
+        return createCachedSequence(chained);
     }
     // ─── Pre-built singletons ��─────────��─────────────────────────────────────────
     /**
-     * Pre-built hg38 genome with 2-bit sequence (UCSC API fallback).
+     * Pre-built hg38 genome with triple-fallback sequence chain.
      *
      * This is the default genome used by HeadlessGenomeBrowser when no genome
-     * is specified. Matches igv.js's default behavior: 2-bit file as primary
-     * sequence source, with UCSC REST API as automatic fallback for resilience.
+     * is specified. Sequence sources are tried in order:
+     *   1. 2-bit from hgdownload.soe.ucsc.edu (most efficient, binary range requests)
+     *   2. Indexed FASTA from igv.org (reliable CDN, reachable on restricted networks)
+     *   3. UCSC REST API from api.genome.ucsc.edu (last resort)
+     *
+     * URLs match igv.js genomes3.json configuration for hg38.
      */
     const hg38Genome = createGenomeSync({
         id: 'hg38',
         twoBitURL: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit',
+        fastaURL: 'https://igv.org/genomes/data/hg38/hg38.fa',
+        indexURL: 'https://igv.org/genomes/data/hg38/hg38.fa.fai',
         chromSizes: hg38ChromSizes,
     });