igv 2.13.8 → 2.13.10

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/2.13.8/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.13.10/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.13.8/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.13.10/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.13.8/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.13.10/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.13.8/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.13.10/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.13.8/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.13.10/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.13.8/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.13.10/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.13.8/examples/)***
+***[More](https://igv.org/web/release/2.13.10/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@2.13.8/dist/](https://cdn.jsdelivr.net/npm/igv@2.13.8/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/](https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.13.8/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.13.8/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.13.10/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -18596,11 +18596,7 @@ RandomColorGenerator.prototype.get = function (saturation, value) {
 
 };
 
-const randomColorGenerator = new RandomColorGenerator();
-
-function randomColor() {
-    return randomColorGenerator.get()
-}
+new RandomColorGenerator();
 
 function randomRGB$1(min, max) {
 
@@ -24215,7 +24211,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.13.8";
+const _version = "2.13.10";
 function version() {
     return _version
 }
@@ -30104,13 +30100,17 @@ class BGZBlockLoader {
     /**
      * 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) {
+    async getData(minv, maxv) {
+
+        const startBlock = minv.block;
+        const endBlock = maxv.block;
+        const skipEnd = maxv.offset === 0;
 
-        const blocks = await this.getInflatedBlocks(startBlock, endBlock);
+        const blocks = await this.getInflatedBlocks(startBlock, endBlock, skipEnd);
         if (blocks.length === 1) {
             return blocks[0]
         }
@@ -30135,16 +30135,18 @@ class BGZBlockLoader {
      * @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)
@@ -30154,7 +30156,7 @@ class BGZBlockLoader {
                 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")
@@ -30193,14 +30195,21 @@ class BGZBlockLoader {
 
                     // Load end blocks, if any
                     if (endBlock > c.endBlock) {
-                        const endBuffer = await this.loadBLockData(c.endBlock, endBlock, {skipStart: true});
+                        const endBuffer = await this.loadBLockData(c.endBlock, endBlock, {skipStart: true, skipEnd});
                         arrayBuffers.push(endBuffer);
                     }
 
                     buffer = concatenateArrayBuffers(arrayBuffers);
                 }
 
-                this.cache = {startBlock, endBlock, buffer};
+                // 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)
             }
         }
@@ -30518,7 +30527,7 @@ class FeatureFileReader {
 
                 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: {
@@ -36655,7 +36664,7 @@ class BamReader {
             }
 
             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
@@ -42970,7 +42979,14 @@ class TrackView {
                         const max = visibleViewport.featureCache.features.getMax(start, end);
                         allFeatures = [{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);
+                            }
+                        }
                     }
                 }
             }
@@ -47304,21 +47320,16 @@ class EqtlTrack extends TrackBase {
  * 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)",
@@ -47366,9 +47377,28 @@ const Colors = {
 };
 
 //  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;
 }
 
 /*
@@ -47423,14 +47453,19 @@ class GWASTrack extends TrackBase {
         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 || {
-                    thresholds: [5e-8, 5e-4, 0.5],
-                    colors: ["rgb(255,50,50)", "rgb(251,100,100)", "rgb(251,170,170)", "rgb(227,238,249)"],
-                })
-            };
+        // 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);
     }
@@ -47439,7 +47474,7 @@ class GWASTrack extends TrackBase {
 
         if (typeof this.featureSource.getHeader === "function") {
             this.header = await this.featureSource.getHeader();
-            if(this.disposed) return;   // This track was removed during async load
+            if (this.disposed) return   // This track was removed during async load
         }
 
         // Set properties from track line
@@ -47497,20 +47532,20 @@ class GWASTrack extends TrackBase {
                 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));
@@ -47525,21 +47560,6 @@ class GWASTrack extends TrackBase {
         }
     }
 
-    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)"});
@@ -47576,7 +47596,7 @@ class GWASTrack extends TrackBase {
 
     popupData(clickState, features) {
 
-        if(features === undefined) features =  clickState.viewport.cachedFeatures;
+        if (features === undefined) features = clickState.viewport.cachedFeatures;
 
         let data = [];
         const track = clickState.viewport.trackView.track;
@@ -47637,13 +47657,10 @@ class GWASTrack extends TrackBase {
         } 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