igv 2.13.10 → 2.13.11

package/README.md

@@ -12,19 +12,19 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/2.13.10/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.13.11/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.13.10/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.13.11/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.13.10/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.13.11/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.13.10/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.13.11/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.13.10/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.13.11/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.13.10/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.13.11/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.13.10/examples/)***
+***[More](https://igv.org/web/release/2.13.11/examples/)***
 
  
 # Quickstart
@@ -33,18 +33,18 @@ 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 ES5 (igv.min.js) and ES6 (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/](https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.13.11/dist/](https://cdn.jsdelivr.net/npm/igv@2.13.11/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.13.11/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.13.11/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -24211,7 +24211,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.13.10";
+const _version = "2.13.11";
 function version() {
     return _version
 }
@@ -42968,7 +42968,7 @@ class TrackView {
         }
 
         if (this.track.autoscale) {
-            let allFeatures;
+            let allFeatures = [];
             for (let visibleViewport of visibleViewports) {
                 const referenceFrame = visibleViewport.referenceFrame;
                 const start = referenceFrame.start;
@@ -42977,15 +42977,11 @@ class TrackView {
                     // If the "features" object has a getMax function use it.  Currently only alignmentContainer implements this, for coverage.
                     if (typeof visibleViewport.featureCache.features.getMax === 'function') {
                         const max = visibleViewport.featureCache.features.getMax(start, end);
-                        allFeatures = [{value: max}];
+                        allFeatures.push({value: max});
                     } else {
                         const viewFeatures = FeatureUtils.findOverlapping(visibleViewport.featureCache.features, start, end);
-                        if(!allFeatures) {
-                            allFeatures = viewFeatures;
-                        } else {
-                            for(let f of viewFeatures) {
-                                allFeatures.push(f);
-                            }
+                        for (let f of viewFeatures) {
+                            allFeatures.push(f);
                         }
                     }
                 }
@@ -44394,7 +44390,7 @@ class WigTrack extends TrackBase {
 
     async postInit() {
         const header = await this.getHeader();
-        if(this.disposed) return;   // This track was removed during async load
+        if (this.disposed) return   // This track was removed during async load
         if (header) this.setTrackProperties(header);
     }
 
@@ -44479,9 +44475,6 @@ class WigTrack extends TrackBase {
         const pixelWidth = options.pixelWidth;
         options.pixelHeight;
         const bpEnd = bpStart + pixelWidth * bpPerPixel + 1;
-        let lastPixelEnd = -1;
-        let lastValue = -1;
-        let lastNegValue = 1;
         const posColor = this.color || DEFAULT_COLOR;
 
         let baselineColor;
@@ -44502,6 +44495,9 @@ class WigTrack extends TrackBase {
             // nothing to paint.
             if (this.dataRange.max > this.dataRange.min) {
 
+                let lastPixelEnd = -1;
+                let lastY;
+                let lastValue = -1;
                 const y0 = yScale(0);
                 for (let f of features) {
 
@@ -44524,15 +44520,22 @@ class WigTrack extends TrackBase {
                         const px = x + width / 2;
                         IGVGraphics.fillCircle(ctx, px, y, pointSize / 2, {"fillStyle": color, "strokeStyle": color});
 
+                    } else if (this.graphType === "line") {
+                        if(lastY != undefined) {
+                            IGVGraphics.strokeLine(ctx, lastPixelEnd, lastY, x, y, {"fillStyle": color, "strokeStyle": color});
+                        }
+                        IGVGraphics.strokeLine(ctx, x, y, x + width, y, {"fillStyle": color, "strokeStyle": color});
                     } else {
                         let height = y - y0;
                         const pixelEnd = x + width;
                         if (pixelEnd > lastPixelEnd || (f.value >= 0 && f.value > lastValue) || (f.value < 0 && f.value < lastNegValue)) {
                             IGVGraphics.fillRect(ctx, x, y0, width, height, {fillStyle: color});
                         }
-                        lastValue = f.value;
-                        lastPixelEnd = pixelEnd;
                     }
+                    lastPixelEnd = x + width;
+                    lastValue = f.value;
+                    lastY = y;
+
                 }
 
                 // If the track includes negative values draw a baseline
@@ -44561,7 +44564,7 @@ class WigTrack extends TrackBase {
 
     popupData(clickState, features) {
 
-        if(features === undefined) features = this.clickedFeatures(clickState);
+        if (features === undefined) features = this.clickedFeatures(clickState);
 
         if (features && features.length > 0) {