igv 3.8.3 → 3.8.4

package/dist/igv.js

@@ -8826,6 +8826,8 @@
            if (isFile(url)) {
                return this._loadFileSlice(url, options)
            } else if (isString$3(url)) {
+               // Convert "virtual" URLs (keys that don't exist) to real URLs before any other action
+               url = await convert(url);
                if (url.startsWith("data:")) {
                    const buffer = decodeDataURI$1(url).buffer;
                    if (options.range) {
@@ -9332,6 +9334,34 @@
        }
    }
 
+   let mappings;
+
+   const mappingURL = "https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/data/url_mappings.tsv";
+
+   async function convert(url) {
+
+       if (!mappings) {
+           mappings = new Map();
+
+           try {
+               const data = await igvxhr.loadString(mappingURL);
+               const lines = data.split("\n");
+               for (const line of lines) {
+                   if (line.startsWith("#")) continue
+
+                   const tokens = line.split('\t');
+                   if (tokens.length === 2) {
+                       mappings.set(tokens[0], tokens[1]);
+                   }
+               }
+           } catch (e) {
+               console.error(`Error loading url mappings`, e);
+           }
+       }
+
+       return mappings.has(url) ? mappings.get(url) : url
+   }
+
 
    const igvxhr = new IGVXhr();
 
@@ -51150,7 +51180,9 @@
            nameValues.push('<hr/>');
            nameValues.push({name: 'Genomic Location: ', value: numberFormatter$1(1 + genomicLocation)});
            nameValues.push({name: 'Read Base:', value: readBase});
-           nameValues.push({name: 'Base Quality:', value: this.readBaseQualityAt(genomicLocation)});
+
+           let quality = this.readBaseQualityAt(genomicLocation);
+           nameValues.push({name: 'Base Quality:', value: 255 === quality ? "unknown" : quality});
 
            const bmSets = this.getBaseModificationSets();
            if (bmSets) {
@@ -51201,13 +51233,13 @@
            const block = this.blockAtGenomicLocation(genomicLocation);
            if (block) {
                if ("*" === this.qual) {
-                   return 30
+                   return undefined
                } else {
                    const idx = block.seqIndexAt(genomicLocation);
                    if (idx >= 0 && this.qual && idx < this.qual.length) {
                        return this.qual[idx]
                    } else {
-                       return 30
+                       return undefined
                    }
                }
            } else {
@@ -77572,7 +77604,7 @@ ${indent}columns: ${matrix.columns}
        })
    }
 
-   const _version = "3.8.3";
+   const _version = "3.8.4";
    function version() {
        return _version
    }