igv 2.15.8 → 2.15.10

package/README.md

@@ -18,19 +18,19 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/2.15.8/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.15.10/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.15.8/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.15.10/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.15.8/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.15.10/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.15.8/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.15.10/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.8/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.10/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.15.8/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.15.10/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.15.8/examples/)***
+***[More](https://igv.org/web/release/2.15.10/examples/)***
 
  
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 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@2.15.8/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.8/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.15.10/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.10/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.8/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.10/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.15.8/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.15.10/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -18673,6 +18673,7 @@ class IGVXhr {
     async _loadURL(url, options) {
 
         const self = this;
+        const _url = url;   // The unmodified URL, needed in case of an oAuth retry
 
         url = mapUrl$1(url);
 
@@ -18834,10 +18835,10 @@ class IGVXhr {
 
             async function tryGoogleAuth() {
                 try {
-                    const accessToken = await fetchGoogleAccessToken(url);
+                    const accessToken = await fetchGoogleAccessToken(_url);
                     options.retries = 1;
                     options.oauthToken = accessToken;
-                    const response = await self.load(url, options);
+                    const response = await self.load(_url, options);
                     resolve(response);
                 } catch (e) {
                     if (e.error) {
@@ -23989,7 +23990,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.15.8";
+const _version = "2.15.10";
 function version() {
     return _version
 }
@@ -44030,7 +44031,7 @@ class TrackView {
             const {width} = viewport.$viewport.get(0).getBoundingClientRect();
             delta.deltaX += width;
         }
-
+        
         if (true === this.browser.showSampleNames) {
             this.sampleNameViewport.renderSVGContext(context, delta);
         }
@@ -59279,6 +59280,23 @@ class ROIManager {
         return regionElement
     }
 
+    renderSVGContext(context, {deltaX, deltaY}) {
+
+        for (const regionElement of document.querySelectorAll('.igv-roi-region')) {
+
+            // body
+            const { x, y, width, height } = regionElement.getBoundingClientRect();
+            context.fillStyle = regionElement.style.backgroundColor;
+            context.fillRect(x+deltaX, y+deltaY, width, height);
+
+            // header
+            const header = regionElement.querySelector('div');
+            const { x:xx, y:yy, width:ww, height:hh } = header.getBoundingClientRect();
+            context.fillStyle = header.style.backgroundColor;
+            context.fillRect(xx+deltaX, yy+deltaY, ww, hh);
+        }
+    }
+
     async getUserDefinedROISet() {
         return this.roiSets.find(roiSet => true === roiSet.isUserDefined)
     }
@@ -60101,9 +60119,13 @@ class Browser {
         const context = new ctx(config);
 
         // tracks -> SVG
+        const delta = {deltaX: 0, deltaY: -y};
         for (let trackView of this.trackViews) {
-            trackView.renderSVGContext(context, {deltaX: 0, deltaY: -y});
+            trackView.renderSVGContext(context, delta);
         }
+
+        this.roiManager.renderSVGContext(context, delta);
+
         // reset height to trim away unneeded svg canvas real estate. Yes, a bit of a hack.
         context.setHeight(height);