igv 3.0.4 → 3.0.6

package/README.md

@@ -18,19 +18,19 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/3.0.3/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.0.6/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.0.3/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.0.6/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.0.3/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.0.6/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.0.3/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.0.6/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.3/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.6/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.0.3/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.0.6/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.0.3/examples/)***
+***[More](https://igv.org/web/release/3.0.6/examples/)***
 
  
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.0.3/dist/](https://cdn.jsdelivr.net/npm/igv@3.0.3/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.0.6/dist/](https://cdn.jsdelivr.net/npm/igv@3.0.6/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@3.0.3/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.0.6/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@3.0.3/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@3.0.6/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  
@@ -91,7 +91,9 @@ a browser on a single alignment track opened at a specific locus:
                 })
 ```
 
-For more details see the [Wiki](https://github.com/igvteam/igv.js/wiki) for full documentation of the API.
+## Documentation
+
+Full documentation of the igv.js API is available at [https://igv.org/doc/igvjs/](https://igv.org/doc/igvjs/).
 
 ## Development
 

package/dist/igv.esm.js

@@ -22874,6 +22874,20 @@ class BinaryParser$1 {
         this.length = dataView.byteLength;
     }
 
+    /**
+     * Print the first "n" bytes to the console.  Used for debugging.
+     * @param n
+     */
+    dumpBytes (n = 100) {
+        const pos = this.position;
+        const bytes = [];
+        for(let i=0; i<= n; i++) {
+            bytes.push(this.getByte());
+        }
+        console.log(bytes.join(" "));
+        this.setPosition(pos);
+    }
+
     setPosition(position) {
         this.position = position;
     }
@@ -31437,7 +31451,6 @@ class ChromTree {
             const idToName = [];
             let sumLengths = 0;
             const readTreeNode = (offset) => {
-
                 if (offset >= 0) binaryParser.position = offset;
                 const type = binaryParser.getByte();
                 binaryParser.getByte();
@@ -31474,7 +31487,7 @@ class ChromTree {
             };
 
             // Recursively walk tree to populate dictionary
-            readTreeNode(binaryParser);
+            readTreeNode( -1);
 
             return new ChromTree(header, nameToId, idToName, sumLengths)
         }
@@ -32165,6 +32178,16 @@ class BWReader {
         }
     }
 
+    /**
+     * The BB header consists of
+     *  (1) the common header
+     *  (2) the zoom headers
+     *  (3) autosql
+     *  (4) total summary block (version 2 and later)
+     *
+     *  In addition, we read the chromomsome B+ tree
+     * @returns {Promise<*>}
+     */
     async loadHeader() {
 
         if (this.header) {
@@ -32182,7 +32205,7 @@ class BWReader {
             // Assume low-to-high unless proven otherwise
             this.littleEndian = true;
 
-            let binaryParser = new BinaryParser$1(new DataView(data), this.littleEndian);
+            const binaryParser = new BinaryParser$1(new DataView(data), this.littleEndian);
             let magic = binaryParser.getUInt();
             if (magic === BIGWIG_MAGIC_LTH$1) {
                 this.type = "bigwig";
@@ -32217,30 +32240,33 @@ class BWReader {
                 extensionOffset: binaryParser.getLong()
             };
 
+            // Read the next chunk containing zoom headers, autosql, and total summary if present.  TotalSummary size = 40 bytes
             const startOffset = BBFILE_HEADER_SIZE;
+            const size = header.totalSummaryOffset > 0 ?
+                header.totalSummaryOffset - startOffset + 40 :
+                Math.min(header.fullDataOffset, header.chromTreeOffset) - startOffset;
             let range = {
                 start: startOffset,
-                size: (header.fullDataOffset - startOffset + 4)
+                size: size
             };
             data = await this.loader.loadArrayBuffer(this.path, buildOptions(this.config, {range: range}));
-
-            const nZooms = header.nZoomLevels;
-            binaryParser = new BinaryParser$1(new DataView(data), this.littleEndian);
+            const extHeaderParser = new BinaryParser$1(new DataView(data), this.littleEndian);
 
             // Load zoom headers, store in order of decreasing reduction level (increasing resolution)
+            const nZooms = header.nZoomLevels;
             this.zoomLevelHeaders = [];
             this.firstZoomDataOffset = Number.MAX_SAFE_INTEGER;
             for (let i = 1; i <= nZooms; i++) {
                 const zoomNumber = nZooms - i;
-                const zlh = new ZoomLevelHeader(zoomNumber, binaryParser);
+                const zlh = new ZoomLevelHeader(zoomNumber, extHeaderParser);
                 this.firstZoomDataOffset = Math.min(zlh.dataOffset, this.firstZoomDataOffset);
                 this.zoomLevelHeaders[zoomNumber] = zlh;
             }
 
             // Autosql
             if (header.autoSqlOffset > 0) {
-                binaryParser.position = header.autoSqlOffset - startOffset;
-                const autoSqlString = binaryParser.getString();
+                extHeaderParser.position = header.autoSqlOffset - startOffset;
+                const autoSqlString = extHeaderParser.getString();
                 if (autoSqlString) {
                     this.autoSql = parseAutoSQL(autoSqlString);
                 }
@@ -32248,37 +32274,75 @@ class BWReader {
 
             // Total summary
             if (header.totalSummaryOffset > 0) {
-                binaryParser.position = header.totalSummaryOffset - startOffset;
-                this.totalSummary = new BWTotalSummary(binaryParser);
-            }
-
-            // Chrom data index
-            if (header.chromTreeOffset > 0) {
-                binaryParser.position = header.chromTreeOffset - startOffset;
-                this.chromTree = await ChromTree.parseTree(binaryParser, startOffset, this.genome);
-                this.chrNames = new Set(this.chromTree.idToName);
-            } else {
-                // TODO -- this is an error, not expected
-                throw "BigWig chromosome tree offset <= 0"
+                extHeaderParser.position = header.totalSummaryOffset - startOffset;
+                this.totalSummary = new BWTotalSummary(extHeaderParser);
             }
 
-            //Finally total data count
-            binaryParser.position = header.fullDataOffset - startOffset;
-            header.dataCount = binaryParser.getInt();
+            // Chrom data index.  The start is known, size is not, but we can estimate it
+            const bufferSize = Math.min(200000, Math.max(10000, header.fullDataOffset - header.chromTreeOffset));
+            this.chromTree = await this.#readChromTree(header.chromTreeOffset, bufferSize);
+            this.chrNames = new Set(this.chromTree.idToName);
 
-            this.featureDensity = header.dataCount / this.chromTree.sumLengths;
+            // Estimate feature density from dataCount (bigbed only)
+            if("bigbed" === this.type) {
+                const dataCount = await this.#readDataCount(header.fullDataOffset);
+                this.featureDensity = dataCount / this.chromTree.sumLengths;
+            }
 
             this.header = header;
 
-
             //extension
             if (header.extensionOffset > 0) {
                 await this.loadExtendedHeader(header.extensionOffset);
             }
-          return this.header
+            return this.header
         }
     }
 
+    async #readDataCount(offset) {
+        const data = await this.loader.loadArrayBuffer(this.path, buildOptions(this.config, {
+            range: {
+                start: offset,
+                size: 4
+            }
+        }));
+        const binaryParser = new BinaryParser$1(new DataView(data), this.littleEndian);
+        return binaryParser.getInt()
+    }
+
+    /**
+     * Used when the chromTreeOffset is > fullDataOffset, that is when the chrom tree is not in the initial chunk
+     * read for parsing the header.  We know the start position, but not the total size of the chrom tree
+     *
+     * @returns {Promise<void>}
+     */
+    async #readChromTree(chromTreeOffset, bufferSize) {
+
+        let size = bufferSize;
+        const load = async () => {
+            const data = await this.loader.loadArrayBuffer(this.path, buildOptions(this.config, {
+                range: {
+                    start: chromTreeOffset,
+                    size: size
+                }
+            }));
+            const binaryParser = new BinaryParser$1(new DataView(data), this.littleEndian);
+            return ChromTree.parseTree(binaryParser, chromTreeOffset, this.genome)
+        };
+
+        let error;
+        while (size < 1000000) {
+            try {
+                const chromTree = await load();
+                return chromTree
+            } catch (e) {
+                error = e;
+                size *= 2;
+            }
+        }
+        throw (error)
+    }
+
     async loadExtendedHeader(offset) {
 
         let data = await this.loader.loadArrayBuffer(this.path, buildOptions(this.config, {
@@ -33453,7 +33517,10 @@ class TextFeatureSource extends BaseFeatureSource {
         for (let feature of featureList) {
             for (let field of searchableFields) {
                 let key;
-                if (typeof feature.getAttributeValue === 'function') {
+                if(feature.hasOwnProperty(field)) {
+                    key = feature[field];
+                }
+                else if (typeof feature.getAttributeValue === 'function') {
                     key = feature.getAttributeValue(field);
                 }
                 if (key) {
@@ -39605,6 +39672,10 @@ class DynamicFeatureSource {
         if (this.featureMap[chr]) {
             const match = `${chr}-${start}-${end}`;
             this.featureMap[chr] = this.featureMap[chr].filter(feature => match !== `${feature.chr}-${feature.start}-${feature.end}`);
+            // Check if featureMap for a specific chromosome is empty now and delete it if yes
+            if (this.featureMap[chr].length === 0) {
+                delete this.featureMap[chr];
+            }
         }
     }
 }
@@ -43052,7 +43123,7 @@ class TrackView {
         const viewportsToRepaint = visibleViewports.filter(vp => vp.needsRepaint()).filter(viewport => viewport.checkZoomIn());
 
         // Get viewports that require a data load
-        const viewportsToReload = visibleViewports.filter(viewport => viewport.needsReload());
+        const viewportsToReload = visibleViewports.filter(viewport => viewport.checkZoomIn()).filter(viewport => viewport.needsReload());
 
         // Trigger viewport to load features needed to cover current genomic range
         // NOTE: these must be loaded synchronously, do not user Promise.all,  not all file readers are thread safe
@@ -70517,7 +70588,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.0.4";
+const _version = "3.0.6";
 function version() {
     return _version
 }
@@ -72067,9 +72138,16 @@ class ROIMenu {
                 '<hr/>',
                 {
                     label: 'Delete',
-                    click: () => {
-                        this.browser.roiManager.deleteRegionWithKey(regionElement.dataset.region, this.browser.columnContainer);
-                        this.browser.roiManager.repaintTable();
+                    click: async () => {
+                        roiSet.removeFeature(feature);
+                        const userDefinedFeatures = await roiSet.getAllFeatures();
+                        
+                        // Delete user defined ROI Set if it is empty
+                        if (Object.keys(userDefinedFeatures).length === 0) {
+                            roiManager.deleteUserDefinedROISet();
+                        }
+                        roiManager.deleteRegionWithKey(regionElement.dataset.region, columnContainer);
+                        roiManager.repaintTable();
                     }
                 }
             );
@@ -72597,6 +72675,10 @@ class ROIManager {
         return this.roiSets.find(roiSet => true === roiSet.isUserDefined)
     }
 
+    deleteUserDefinedROISet(){
+        this.roiSets = this.roiSets.filter(roiSet => roiSet.isUserDefined !== true);
+    }
+    
     initializeUserDefinedROISet() {
 
         const config =
@@ -72612,15 +72694,8 @@ class ROIManager {
     }
 
     async deleteRegionWithKey(regionKey, columnContainer) {
-
         columnContainer.querySelectorAll(createSelector(regionKey)).forEach(node => node.remove());
 
-        const {feature, set} = await this.findRegionWithKey(regionKey);
-
-        if (set) {
-            set.removeFeature(feature);
-        }
-
         const records = await this.getTableRecords();
 
         if (0 === records.length) {
@@ -72630,23 +72705,6 @@ class ROIManager {
 
     }
 
-    async findRegionWithKey(regionKey) {
-
-        const {chr, start, end} = parseRegionKey(regionKey);
-
-        for (let set of this.roiSets) {
-            const features = await set.getFeatures(chr, start, end);
-
-            for (let feature of features) {
-                if (feature.chr === chr && feature.start >= start && feature.end <= end) {
-                    return {feature, set}
-                }
-            }
-        }
-
-        return {feature: undefined, set: undefined}
-    }
-
     toJSON() {
         return this.roiSets.map(roiSet => roiSet.toJSON())
     }
@@ -76265,7 +76323,7 @@ function mouseUpOrLeave(e) {
 async function keyUpHandler(event) {
 
     // Feature jumping disabled in multi-locus view
-    if (this.referenceFrameList.length > 1) return
+    if (!this.referenceFrameList || this.referenceFrameList.length > 1) return
 
     if (event.code === 'KeyF' || event.code === 'KeyB') {