igv 2.12.3 → 2.12.4

package/dist/igv.js

@@ -20670,9 +20670,18 @@
 
 
       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;
       }
 
@@ -23113,7 +23122,7 @@
       }
     };
 
-    const _version = "2.12.3";
+    const _version = "2.12.4";
 
     function version$1() {
       return _version;
@@ -24646,10 +24655,10 @@
       (module.exports = function (key, value) {
         return sharedStore[key] || (sharedStore[key] = value !== undefined ? value : {});
       })('versions', []).push({
-        version: '3.22.0',
+        version: '3.22.2',
         mode: 'global',
         copyright: '© 2014-2022 Denis Pushkarev (zloirock.ru)',
-        license: 'https://github.com/zloirock/core-js/blob/v3.22.0/LICENSE',
+        license: 'https://github.com/zloirock/core-js/blob/v3.22.2/LICENSE',
         source: 'https://github.com/zloirock/core-js'
       });
     });
@@ -45645,7 +45654,7 @@
       }
 
       get supportsWholeGenome() {
-        return false;
+        return this.config.supportsWholeGenome === true;
       }
       /**
        * Does the track support sample names.  Current sample aware tracks include VCF (with genotypes), MUT, MAF, and SEG
@@ -56182,7 +56191,7 @@
         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;
@@ -57655,7 +57664,7 @@
       }
 
       supportsWholeGenome() {
-        return this.reader.type === "bigwig" || this.defaultVisibilityWindow() <= 0;
+        return this.reader.type === "bigwig";
       }
 
       async trackType() {
@@ -58913,7 +58922,15 @@
       }
 
       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) {
@@ -61480,9 +61497,9 @@
           '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();
 
@@ -61624,7 +61641,10 @@
           // 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);
+
+          if ("COLLAPSED" !== this.displayMode) {
+            featureList = featureList.filter(f => f.row === variantRow);
+          }
         } else if (this.callSets) {
           const callSets = this.callSets;
           const sampleY = yOffset - this.variantBandHeight;
@@ -61632,7 +61652,7 @@
 
           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];