igv 2.13.9 → 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/2.13.9/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.13.11/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.13.9/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.13.11/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.13.9/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.13.11/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.13.9/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/2.13.9/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/2.13.9/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/2.13.9/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@2.13.9/dist/](https://cdn.jsdelivr.net/npm/igv@2.13.9/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@2.13.9/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@2.13.9/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 = "2.13.9";
+const _version = "2.13.11";
 function version() {
     return _version
 }
@@ -30100,13 +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 blocks = await this.getInflatedBlocks(startBlock, endBlock);
+        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]
         }
@@ -30131,16 +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)
@@ -30150,7 +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")
@@ -30189,14 +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)
             }
         }
@@ -30514,7 +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: {
@@ -36651,7 +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
@@ -42955,7 +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;
@@ -42964,15 +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);
                         }
                     }
                 }
@@ -44381,7 +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);
     }
 
@@ -44466,9 +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;
@@ -44489,6 +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) {
 
@@ -44511,15 +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
@@ -44548,7 +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) {