igv 3.8.3 → 3.8.4

package/README.md

@@ -18,19 +18,19 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/3.8.3/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.8.4/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.8.3/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.8.4/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.8.3/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.8.4/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.8.3/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.8.4/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.8.3/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.8.4/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.8.3/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.8.4/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.8.3/examples/)***
+***[More](https://igv.org/web/release/3.8.4/examples/)***
 
  
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.8.3/dist/](https://cdn.jsdelivr.net/npm/igv@3.8.3/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.8.4/dist/](https://cdn.jsdelivr.net/npm/igv@3.8.4/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@3.8.3/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.8.4/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@3.8.3/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@3.8.4/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -8820,6 +8820,8 @@ class IGVXhr {
         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) {
@@ -9326,6 +9328,34 @@ function getGlobalObject() {
     }
 }
 
+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();
 
@@ -51144,7 +51174,9 @@ class BamAlignment {
         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) {
@@ -51195,13 +51227,13 @@ class BamAlignment {
         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 {
@@ -77566,7 +77598,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.8.3";
+const _version = "3.8.4";
 function version() {
     return _version
 }