igv 2.13.8 → 2.13.10

package/dist/igv.js

@@ -16829,10 +16829,7 @@
       var rgb = this.hsvToRgb(this.hue, saturation, value);
       return "#" + this.padHex(rgb[0].toString(16)) + this.padHex(rgb[1].toString(16)) + this.padHex(rgb[2].toString(16));
     };
-    const randomColorGenerator = new RandomColorGenerator();
-    function randomColor() {
-      return randomColorGenerator.get();
-    }
+    new RandomColorGenerator();
     function randomRGB$1(min, max) {
       min = IGVMath.clamp(min, 0, 255);
       max = IGVMath.clamp(max, 0, 255);
@@ -21939,7 +21936,7 @@
       }
     };
 
-    const _version = "2.13.8";
+    const _version = "2.13.10";
     function version$1() {
       return _version;
     }
@@ -27263,12 +27260,15 @@
       /**
        * Return inflated data from startBlock through endBlock as an UInt8Array
        *
-       * @param startBlock
-       * @param endBlock
+       * @param minv minimum virtual pointer  {block, offset}
+       * @param maxv maximum virtual pointer  {block, offset}
        * @returns {Promise<Uint8Array>}
        */
-      async getData(startBlock, endBlock) {
-        const blocks = await this.getInflatedBlocks(startBlock, endBlock);
+      async getData(minv, maxv) {
+        const startBlock = minv.block;
+        const endBlock = maxv.block;
+        const skipEnd = maxv.offset === 0;
+        const blocks = await this.getInflatedBlocks(startBlock, endBlock, skipEnd);
         if (blocks.length === 1) {
           return blocks[0];
         }
@@ -27292,14 +27292,16 @@
        * @param endBlock
        * @returns {Promise<*[Uint8Array]>}
        */
-      async getInflatedBlocks(startBlock, endBlock) {
+      async getInflatedBlocks(startBlock, endBlock, skipEnd) {
         if (!this.cacheBlocks) {
-          const buffer = await this.loadBLockData(startBlock, endBlock);
+          const buffer = await this.loadBLockData(startBlock, endBlock, {
+            skipEnd
+          });
           return inflateBlocks(buffer);
         } else {
           const c = this.cache;
-          if (c && c.startBlock <= startBlock && c.endBlock >= endBlock) {
-            //console.log("Complete overlap")
+          if (c && c.startBlock <= startBlock && (c.endBlock >= endBlock || skipEnd && c.nextEndBlock === endBlock)) {
+            console.log("Complete overlap");
             const startOffset = startBlock - c.startBlock;
             const endOffset = endBlock - c.startBlock;
             return inflateBlocks(c.buffer, startOffset, endOffset);
@@ -27308,7 +27310,9 @@
             let buffer;
             if (!c || c.startBlock > endBlock || c.endBlock < startBlock) {
               // no overlap with cache
-              buffer = await this.loadBLockData(startBlock, endBlock);
+              buffer = await this.loadBLockData(startBlock, endBlock, {
+                skipEnd
+              });
             } else {
               //console.log("Some overlap")
               const arrayBuffers = [];
@@ -27350,15 +27354,24 @@
               // Load end blocks, if any
               if (endBlock > c.endBlock) {
                 const endBuffer = await this.loadBLockData(c.endBlock, endBlock, {
-                  skipStart: true
+                  skipStart: true,
+                  skipEnd
                 });
                 arrayBuffers.push(endBuffer);
               }
               buffer = concatenateArrayBuffers(arrayBuffers);
             }
+
+            // If skipEnd === true we need to find boundary of last block in cache
+            let nextEndBlock = endBlock;
+            if (skipEnd) {
+              const boundaries = findBlockBoundaries(buffer);
+              endBlock = boundaries[boundaries.length - 1];
+            }
             this.cache = {
               startBlock,
               endBlock,
+              nextEndBlock,
               buffer
             };
             return inflateBlocks(buffer);
@@ -27650,7 +27663,7 @@
           for (let chunk of chunks) {
             let inflated;
             if (tabix) {
-              inflated = await this._blockLoader.getData(chunk.minv.block, chunk.maxv.block);
+              inflated = await this._blockLoader.getData(chunk.minv, chunk.maxv);
             } else {
               const options = buildOptions(config, {
                 range: {
@@ -33598,7 +33611,7 @@
             return alignmentContainer;
           }
           for (let c of chunks) {
-            const ba = await this._blockLoader.getData(c.minv.block, c.maxv.block);
+            const ba = await this._blockLoader.getData(c.minv, c.maxv);
             const done = BamUtils.decodeBamRecords(ba, c.minv.offset, alignmentContainer, this.indexToChr, chrId, bpStart, bpEnd, this.filter);
             if (done) {
               break;
@@ -52976,7 +52989,14 @@
                   value: max
                 }];
               } else {
-                allFeatures = FeatureUtils.findOverlapping(visibleViewport.featureCache.features, start, end);
+                const viewFeatures = FeatureUtils.findOverlapping(visibleViewport.featureCache.features, start, end);
+                if (!allFeatures) {
+                  allFeatures = viewFeatures;
+                } else {
+                  for (let f of viewFeatures) {
+                    allFeatures.push(f);
+                  }
+                }
               }
             }
           }
@@ -56892,21 +56912,16 @@
      * Colors used for coding omosomes
      */
 
-    const Colors = {
+    const GWASColors = {
       "X": "rgb(204, 153, 0)",
       "Y": "rgb(153, 204, 0)",
       "Un": "darkGray)",
       "1": "rgb(80, 80, 255)",
-      //"1": Color.red);
-      "I": "rgb(139, 155, 187)",
       "2": "rgb(206, 61, 50)",
-      "II": "rgb(206, 61, 50)",
       "2a": "rgb(210, 65, 55)",
       "2b": "rgb(215, 70, 60)",
       "3": "rgb(116, 155, 88)",
-      "III": "rgb(116, 155, 88)",
       "4": "rgb(240, 230, 133)",
-      "IV": "rgb(240, 230, 133)",
       "5": "rgb(70, 105, 131)",
       "6": "rgb(186, 99, 56)",
       "7": "rgb(93, 177, 221)",
@@ -56954,9 +56969,25 @@
     };
 
     //  aliasing
-    for (let key of Object.keys(Colors)) {
+    for (let key of Object.keys(GWASColors)) {
       const altName = "chr" + key;
-      Colors[altName] = Colors[key];
+      GWASColors[altName] = GWASColors[key];
+    }
+
+    // romanizing
+    for (let a = 1; a <= 48; a++) {
+      if (a === 10) continue; // Don't overide "X"
+      const roman = romanize(a);
+      GWASColors[roman] = GWASColors[a.toString()];
+    }
+    function romanize(num) {
+      if (!+num) return false;
+      var digits = String(+num).split('');
+      var key = ['', 'C', 'CC', 'CCC', 'CD', 'D', 'DC', 'DCC', 'DCCC', 'CM', '', 'X', 'XX', 'XXX', 'XL', 'L', 'LX', 'LXX', 'LXXX', 'XC', '', 'I', 'II', 'III', 'IV', 'V', 'VI', 'VII', 'VIII', 'IX'];
+      var roman = '',
+        i = 3;
+      while (i--) roman = (key[+digits.pop() + i * 10] || '') + roman;
+      return Array(+digits.join('') + 1).join('M') + roman;
     }
 
     /*
@@ -57004,12 +57035,18 @@
         this.divider = config.divider || "rgb(225,225,225)";
         this.dotSize = config.dotSize || 3;
         this.popoverWindow = config.popoverWindow === undefined ? DEFAULT_POPOVER_WINDOW : config.popoverWindow;
-        this.colorScales = config.color ? new ConstantColorScale(config.color) : {
-          "*": new BinnedColorScale(config.colorScale || {
+
+        // Color settings
+        if (this.useChrColors) {
+          this.colorScale = new ColorTable(config.colorTable || GWASColors);
+        } else if (config.color) {
+          this.colorScale = new ConstantColorScale(config.color);
+        } else {
+          this.colorScale = new BinnedColorScale(config.colorScale || {
             thresholds: [5e-8, 5e-4, 0.5],
             colors: ["rgb(255,50,50)", "rgb(251,100,100)", "rgb(251,170,170)", "rgb(227,238,249)"]
-          })
-        };
+          });
+        }
         this.featureSource = FeatureSource(config, this.browser.genome);
       }
       async postInit() {
@@ -57072,18 +57109,16 @@
             const pos = variant.start;
             if (pos < bpStart) continue;
             if (pos > bpEnd) break;
-            const colorScale = this.getColorScale(variant._f ? variant._f.chr : variant.chr);
-            let color;
             let val;
             if (this.posteriorProbability) {
               val = variant[this.valueProperty];
-              color = colorScale.getColor(val);
             } else {
               const pvalue = variant[this.valueProperty];
               if (!pvalue) continue;
               val = -Math.log10(pvalue);
-              color = colorScale.getColor(val);
             }
+            const colorKey = this.useChrColors ? variant._f ? variant._f.chr : variant.chr : val;
+            const color = this.colorScale.getColor(colorKey);
             const yScale = (this.dataRange.max - this.dataRange.min) / pixelHeight;
             const px = Math.round((pos - bpStart) / bpPerPixel);
             const py = Math.max(this.dotSize, pixelHeight - Math.round((val - this.dataRange.min) / yScale));
@@ -57099,19 +57134,6 @@
           }
         }
       }
-      getColorScale(chr) {
-        if (this.useChrColors) {
-          let cs = this.colorScales[chr];
-          if (!cs) {
-            const color = Colors[chr] || randomColor();
-            cs = new ConstantColorScale(color);
-            this.colorScales[chr] = cs;
-          }
-          return cs;
-        } else {
-          return this.colorScales("*");
-        }
-      }
       paintAxis(ctx, pixelWidth, pixelHeight) {
         IGVGraphics.fillRect(ctx, 0, 0, pixelWidth, pixelHeight, {
           'fillStyle': "rgb(255, 255, 255)"
@@ -57224,11 +57246,15 @@
         } else {
           // No features -- pick something reasonable for PPAs and p-values
           if (this.posteriorProbability) {
-            this.dataRange.min = this.config.min || 0;
-            this.dataRange.max = this.config.max || 1;
+            this.dataRange = {
+              min: this.config.min || 0,
+              max: this.config.max || 1
+            };
           } else {
-            this.dataRange.max = this.config.max || 25;
-            this.dataRange.min = this.config.min || 0;
+            this.dataRange = {
+              min: this.config.max || 25,
+              max: this.config.min || 0
+            };
           }
         }
         return this.dataRange;