igv 2.12.3 → 2.12.4

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/2.12.3/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.12.4/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.12.3/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.12.4/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.12.3/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.12.4/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.12.3/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.12.4/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.12.3/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.12.4/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.12.3/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.12.4/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.12.3/examples/)***
+***[More](https://igv.org/web/release/2.12.4/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@2.12.3/dist/](https://cdn.jsdelivr.net/npm/igv@2.12.3/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.12.4/dist/](https://cdn.jsdelivr.net/npm/igv@2.12.4/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.12.3/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.12.4/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.12.3/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.12.4/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -20506,10 +20506,15 @@ class SequenceTrack {
      * @returns {*|{}}
      */
     getState() {
-
-        const config = typeof super.getState === 'function' ? super.getState() : {};
-        if (this.reversed) config.revealed = true;
-        if (this.frameTranslate) config.frameTranslate = true;
+        const config = {
+            type: "sequence"
+        };
+        if (this.order !== defaultSequenceTrackOrder) {
+            config.order = this.order;
+        }
+        if (this.reversed) {
+            config.revealed = true;
+        }
         return config
     }
 
@@ -22809,7 +22814,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.12.3";
+const _version = "2.12.4";
 function version() {
     return _version
 }
@@ -29203,7 +29208,7 @@ class TrackBase {
     }
 
     get supportsWholeGenome() {
-        return false
+        return this.config.supportsWholeGenome === true
     }
 
     /**
@@ -39459,7 +39464,7 @@ function pack(featureList, maxRows) {
         let r = 0;
         const len = Math.min(rows.length, maxRows);
         for (r = 0; r < len; r++) {
-            if (feature.start > rows[r]) {
+            if (feature.start >= rows[r]) {
                 feature.row = r;
                 rows[r] = feature.end;
                 break
@@ -40976,7 +40981,7 @@ class BWSource {
     }
 
     supportsWholeGenome() {
-        return this.reader.type === "bigwig" || this.defaultVisibilityWindow() <= 0
+        return this.reader.type === "bigwig"
     }
 
     async trackType() {
@@ -42211,7 +42216,15 @@ class FeatureTrack extends TrackBase {
     }
 
     get supportsWholeGenome() {
-        return (this.config.indexed === false || !this.config.indexURL) && this.config.supportsWholeGenome !== false
+        if (this.config.supportsWholeGenome !== undefined) {
+            return this.config.supportsWholeGenome
+        } else if (this.featureSource && typeof this.featureSource.supportsWholeGenome === 'function') {
+            return this.featureSource.supportsWholeGenome()
+        } else {
+            if (this.visibilityWindow === undefined && (this.config.indexed === false || !this.config.indexURL)) {
+                return true
+            }
+        }
     }
 
     async getFeatures(chr, start, end, bpPerPixel) {
@@ -42268,7 +42281,7 @@ class FeatureTrack extends TrackBase {
             options.rowLastX = [];
             options.rowLastLabelX = [];
             for (let feature of featureList) {
-                if(feature.start > bpStart && feature.end < bpEnd) {
+                if (feature.start > bpStart && feature.end < bpEnd) {
                     const row = this.displayMode === "COLLAPSED" ? 0 : feature.row || 0;
                     if (rowFeatureCount[row] === undefined) {
                         rowFeatureCount[row] = 1;
@@ -44682,9 +44695,9 @@ class VariantTrack extends TrackBase {
         IGVGraphics.fillRect(context, 0, pixelTop, pixelWidth, pixelHeight, {'fillStyle': "rgb(255, 255, 255)"});
 
         const vGap = ("SQUISHED" === this.displayMode) ? this.squishedVGap : this.expandedVGap;
-        const rc = ("COLLAPSED" === this.displayMode) ? 1 : this.nVariantRows;
+        const rowCount = ("COLLAPSED" === this.displayMode) ? 1 : this.nVariantRows;
         const variantHeight = ("SQUISHED" === this.displayMode) ? this.squishedVariantHeight : this.expandedVariantHeight;
-        this.variantBandHeight = TOP_MARGIN + rc * (variantHeight + vGap);
+        this.variantBandHeight = TOP_MARGIN + rowCount * (variantHeight + vGap);
 
         const callSets = this.callSets;
         const nCalls = this.getCallsetsLength();
@@ -44817,15 +44830,17 @@ class VariantTrack extends TrackBase {
         if (yOffset <= this.variantBandHeight) {
             // Variant
             const variantHeight = ("SQUISHED" === this.displayMode) ? this.squishedVariantHeight : this.expandedVariantHeight;
-            const variantRow = (Math.floor)((yOffset - TOP_MARGIN) / (variantHeight + vGap));
-            featureList = featureList.filter(f => f.row === variantRow);
+            const variantRow = Math.floor((yOffset - TOP_MARGIN) / (variantHeight + vGap));
+            if("COLLAPSED" !== this.displayMode) {
+                featureList = featureList.filter(f => f.row === variantRow);
+            }
         } else if (this.callSets) {
             const callSets = this.callSets;
             const sampleY = yOffset - this.variantBandHeight;
             const sampleRow = Math.floor(sampleY / this.sampleHeight);
             if (sampleRow >= 0 && sampleRow < callSets.length) {
                 const variantRow = Math.floor((sampleY - sampleRow * this.sampleHeight) / callHeight);
-                const variants = featureList.filter(f => f.row === variantRow);
+                const variants = "COLLAPSED" === this.displayMode ? featureList : featureList.filter(f => f.row === variantRow);
                 const cs = callSets[sampleRow];
                 featureList = variants.map(v => {
                     const call = v.calls[cs.id];