igv 3.7.0 → 3.7.2

package/dist/igv.esm.js

@@ -10632,7 +10632,7 @@ function createMenuElements$1(itemList, popover) {
     return list;
 }
 
-/*! @license DOMPurify 3.3.0 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.0/LICENSE */
+/*! @license DOMPurify 3.3.1 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.1/LICENSE */
 
 const {
   entries,
@@ -10939,7 +10939,7 @@ const _createHooksMap = function _createHooksMap() {
 function createDOMPurify() {
   let window = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : getGlobal();
   const DOMPurify = root => createDOMPurify(root);
-  DOMPurify.version = '3.3.0';
+  DOMPurify.version = '3.3.1';
   DOMPurify.removed = [];
   if (!window || !window.document || window.document.nodeType !== NODE_TYPE.document || !window.Element) {
     // Not running in a browser, provide a factory function
@@ -11285,6 +11285,12 @@ function createDOMPurify() {
       }
       addToSet(FORBID_CONTENTS, cfg.FORBID_CONTENTS, transformCaseFunc);
     }
+    if (cfg.ADD_FORBID_CONTENTS) {
+      if (FORBID_CONTENTS === DEFAULT_FORBID_CONTENTS) {
+        FORBID_CONTENTS = clone(FORBID_CONTENTS);
+      }
+      addToSet(FORBID_CONTENTS, cfg.ADD_FORBID_CONTENTS, transformCaseFunc);
+    }
     /* Add #text in case KEEP_CONTENT is set to true */
     if (KEEP_CONTENT) {
       ALLOWED_TAGS['#text'] = true;
@@ -31912,7 +31918,7 @@ class RemoteFile$1 {
         headers['Range'] = rangeString;
 
         let url = this.url.slice();    // slice => copy
-        // headers['User-Agent'] = 'straw'
+        headers['User-Agent'] = 'IGV';
         if (this.config.oauthToken) {
             const token = resolveToken(this.config.oauthToken);
             headers['Authorization'] = `Bearer ${token}`;
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 };
 
 const isNode = typeof process !== 'undefined' && process.versions != null && process.versions.node != null;
@@ -34004,6 +34169,8 @@ class HicFile {
         this.normalizationTypes = ['NONE'];
         this.matrixCache = new LRU$1(10);
         this.blockCache = new BlockCache();
+        this.normVectorIndexPosition = -1;
+        this.normVectorIndexSize = -1;
 
         // args may specify an io.File object, a local path (Node only), or a url
         if (args.file) {
@@ -34023,9 +34190,9 @@ class HicFile {
             }
         } else if (args.path) {
             // path argument, assumed local file
-            throw Error(`path property is deprecated, use NodeLocalFile`)
+            throw Error(`path property is deprecated, use NodeLocalFile`);
         } else {
-            throw Error("Arguments must include file, blob, url, or path")
+            throw Error("Arguments must include file, blob, url, or path");
         }
     }
 
@@ -34050,15 +34217,15 @@ class HicFile {
             const binaryParser = new BinaryParser(new DataView(data));
             this.magic = binaryParser.getString();
             this.version = binaryParser.getInt();
-            return this.version
+            return this.version;
         } else {
-            return this.version
+            return this.version;
         }
     }
 
     async getMetaData() {
         await this.init();
-        return this.meta
+        return this.meta;
     }
 
     async readHeaderAndFooter() {
@@ -34066,13 +34233,13 @@ class HicFile {
         // Read initial fields magic, version, and footer position
         let data = await this.file.read(0, 16);
         if (!data || data.byteLength === 0) {
-            throw Error("File content is empty")
+            throw Error("File content is empty");
         }
         let binaryParser = new BinaryParser(new DataView(data));
         this.magic = binaryParser.getString();
         this.version = binaryParser.getInt();
         if (this.version < 5) {
-            throw Error("Unsupported hic version: " + this.version)
+            throw Error("Unsupported hic version: " + this.version);
         }
         this.footerPosition = binaryParser.getLong();
 
@@ -34081,7 +34248,7 @@ class HicFile {
         await this.readFooter();
 
         const bodyPostion = Object.values(this.masterIndex).reduce((min, currentValue) => {
-            return Math.min(min, currentValue.start)
+            return Math.min(min, currentValue.start);
         }, Number.MAX_VALUE);
 
         const remainingSize = bodyPostion - 16;
@@ -34166,7 +34333,7 @@ class HicFile {
             "version": this.version,
             "genome": this.genomeId,
             "chromosomes": this.chromosomes,
-            "resolutions": this.bpResolutions,
+            "resolutions": this.bpResolutions
         };
 
 
@@ -34274,14 +34441,14 @@ class HicFile {
             chrIdx2 = tmp;
         }
 
-        const key = Matrix$2.getKey(chrIdx1 , chrIdx2);
+        const key = Matrix$2.getKey(chrIdx1, chrIdx2);
         const idx = this.masterIndex[key];
         if (!idx) {
-            return undefined
+            return undefined;
         }
         const data = await this.file.read(idx.start, idx.size);
         if (!data) {
-            return undefined
+            return undefined;
         }
 
         return Matrix$2.parseMatrix(data, this.chromosomes);
@@ -34304,7 +34471,7 @@ class HicFile {
 
         const blocks = await this.getBlocks(region1, region2, units, binsize);
         if (!blocks || blocks.length === 0) {
-            return []
+            return [];
         }
 
         const contactRecords = [];
@@ -34370,23 +34537,23 @@ class HicFile {
 
         if (idx1 === undefined) {
             console.log("No chromosome named: " + region1.chr);
-            return []
+            return [];
         }
         if (idx2 === undefined) {
             console.log("No chromosome named: " + region2.chr);
-            return []
+            return [];
         }
 
         const matrix = await this.getMatrix(idx1, idx2);
         if (!matrix) {
             console.log("No matrix for " + region1.chr + "-" + region2.chr);
-            return []
+            return [];
         }
 
         const zd = matrix.getZoomData(binSize, unit);
         if (!zd) {
-            let msg = `No data avalailble for resolution: ${binSize}  for map ${region1.chr}-${region2.chr}`;
-            throw new Error(msg)
+            let msg = `No data available for resolution: ${binSize}  for map ${region1.chr}-${region2.chr}`;
+            throw new Error(msg);
         }
 
         const blockNumbers = zd.getBlockNumbers(region1, region2, this.version);
@@ -34417,7 +34584,7 @@ class HicFile {
         const idx = await zd.blockIndex.getBlockIndexEntry(blockNumber);
 
         if (!idx) {
-            return undefined
+            return undefined;
         } else {
             let data = await this.file.read(idx.filePosition, idx.size);
             if (!data) {
@@ -34530,7 +34697,7 @@ class HicFile {
 
         const index = normVectorIndex[key];
 
-        return undefined !== index
+        return undefined !== index;
 
     }
 
@@ -34556,20 +34723,20 @@ class HicFile {
 
         if (!normVectorIndex) {
             console.log("Normalization vectors not present in this file");
-            return undefined
+            return undefined;
         }
 
         const status = await this.isNormalizationValueAvailableAtResolution(type, chr, unit, binSize);
 
         if (false === status) {
 
-            const str = `Normalization option ${ type } not available at resolution ${ binSize }. Will use NONE.`;
+            const str = `Normalization option ${type} not available at resolution ${binSize}. Will use NONE.`;
             console.log(str);
 
             if (this.alert) {
                 this.alert(str);
-            } 
-            return undefined
+            }
+            return undefined;
         }
 
         const idx = normVectorIndex[key];
@@ -34596,37 +34763,44 @@ class HicFile {
             return undefined;
         }
 
-        if (!this.normVectorIndex) {
+        if (this.normVectorIndex) {
+            return this.normVectorIndex;
+        }
+
 
-            // If nvi is not supplied, try reading from remote lambda service
-            if (!this.config.nvi && this.remote && this.url) {
-                const url = new URL(this.url);
-                const key = encodeURIComponent(url.hostname + url.pathname);
-                if(nvi.hasOwnProperty(key)) {
-                    this.config.nvi = nvi[key];
-                }
+        // If we know the position of the norm vector index, read it directly.  This is the case for hic v9 files
+        if (this.normVectorIndexPosition > 0 && this.normVectorIndexSize > 0) {
+            const range = {start: this.normVectorIndexPosition, size: this.normVectorIndexSize};
+            return this.readNormVectorIndex(range);
+        }
+
+        // See if nvi (normVector position and size) is provided in config or can be inferred from url
+        if (!this.config.nvi && this.remote && this.url) {
+            const url = new URL(this.url);
+            const key = encodeURIComponent(url.hostname + url.pathname);
+            if (nvi.hasOwnProperty(key)) {
+                this.config.nvi = nvi[key];
             }
+        }
 
-            if (this.config.nvi) {
-                const nviArray = decodeURIComponent(this.config.nvi).split(",");
-                const range = {start: parseInt(nviArray[0]), size: parseInt(nviArray[1])};
-                return this.readNormVectorIndex(range)
-            } else {
-                try {
-                    await this.readNormExpectedValuesAndNormVectorIndex();
-                    return this.normVectorIndex
-                } catch (e) {
-                    if (e.code === "416" || e.code === 416) {
-                        // This is expected if file does not contain norm vectors
-                        this.normExpectedValueVectorsPosition = undefined;
-                    } else {
-                        console.error(e);
-                    }
+        if (this.config.nvi) {
+            const nviArray = decodeURIComponent(this.config.nvi).split(",");
+            const range = {start: parseInt(nviArray[0]), size: parseInt(nviArray[1])};
+            return this.readNormVectorIndex(range);
+        } else {
+            try {
+                await this.readNormExpectedValuesAndNormVectorIndex();
+                return this.normVectorIndex;
+            } catch (e) {
+                if (e.code === "416" || e.code === 416) {
+                    // This is expected if file does not contain norm vectors
+                    this.normExpectedValueVectorsPosition = undefined;
+                } else {
+                    console.error(e);
                 }
             }
         }
 
-        return this.normVectorIndex
     }
 
     async getNormalizationOptions() {
@@ -34816,9 +34990,9 @@ class HicFile {
 
     getFileChrName(chrAlias) {
         if (this.chrAliasTable.hasOwnProperty(chrAlias)) {
-            return this.chrAliasTable[chrAlias]
+            return this.chrAliasTable[chrAlias];
         } else {
-            return chrAlias
+            return chrAlias;
         }
     }
 
@@ -34847,7 +35021,7 @@ function getNormalizationVectorKey(type, chrIdx, unit, resolution) {
 }
 
 function isGoogleDrive(url) {
-    return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0
+    return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0;
 }
 
 class Block {
@@ -44251,7 +44425,7 @@ class MergedTrack extends TrackBase {
                     track.autoscaleGroup = name;
                 }
                 track.isMergedTrack = false;
-                browser.addTrack(track);
+                await browser.addTrack(track);
             }
             await browser.updateViews();
             browser.reorderTracks();
@@ -44337,7 +44511,7 @@ class OverlayTrackButton extends NavbarButton {
 
         const mouseClickHandler = () => {
             this.setVisibility(false);
-            trackOverlayClickHandler.call(this);
+            this.trackOverlayClickHandler();
         };
 
         this.boundMouseClickHandler = mouseClickHandler.bind(this);
@@ -44347,50 +44521,49 @@ class OverlayTrackButton extends NavbarButton {
         this.setVisibility(true);
 
     }
-}
 
-async function trackOverlayClickHandler(e) {
+    async trackOverlayClickHandler() {
 
-    if (true === isOverlayTrackCriteriaMet(this.browser)) {
+        if (true === isOverlayTrackCriteriaMet(this.browser)) {
 
-        const tracks = this.browser.getSelectedTrackViews().map(({track}) => track);
-        for (const track of tracks) {
-            track.selected = false;
-        }
+            const tracks = this.browser.getSelectedTrackViews().map(({track}) => track);
+            for (const track of tracks) {
+                track.selected = false;
+            }
 
-        // Flatten any merged tracks.  Must do this before their removal
-        const flattenedTracks = [];
-        for (let t of tracks) {
-            if ("merged" === t.type) {
-                flattenedTracks.push(...t.tracks);
-            } else {
-                flattenedTracks.push(t);
+            // Flatten any merged tracks.  Must do this before their removal
+            const flattenedTracks = [];
+            for (let t of tracks) {
+                if ("merged" === t.type) {
+                    flattenedTracks.push(...t.tracks);
+                } else {
+                    flattenedTracks.push(t);
+                }
             }
-        }
 
-        const config =
-            {
-                name: 'Overlay',
-                type: 'merged',
-                autoscale: false,
-                alpha: 0.5, //fudge * (1.0/tracks.length),
-                height: Math.max(...tracks.map(({height}) => height)),
-                order: Math.min(...tracks.map(({order}) => order)),
-            };
+            const config =
+                {
+                    name: 'Overlay',
+                    type: 'merged',
+                    autoscale: false,
+                    alpha: 0.5, //fudge * (1.0/tracks.length),
+                    height: Math.max(...tracks.map(({height}) => height)),
+                    order: Math.min(...tracks.map(({order}) => order))
+                };
 
-        const mergedTrack = new MergedTrack(config, this.browser, flattenedTracks);
+            const mergedTrack = new MergedTrack(config, this.browser, flattenedTracks);
 
-        for (const track of tracks) {
-            const idx = this.browser.trackViews.indexOf(track.trackView);
-            this.browser.trackViews.splice(idx, 1);
-            track.trackView.dispose();
-        }
+            for (const track of tracks) {
+                const idx = this.browser.trackViews.indexOf(track.trackView);
+                this.browser.trackViews.splice(idx, 1);
+                track.trackView.dispose();
+            }
 
-        this.browser.addTrack(mergedTrack);
-        await mergedTrack.trackView.updateViews();
-        this.browser.reorderTracks();
+            await this.browser.addTrack(mergedTrack);
+            await mergedTrack.trackView.updateViews();
+            this.browser.reorderTracks();
+        }
     }
-
 }
 
 function isOverlayTrackCriteriaMet(browser) {
@@ -76477,7 +76650,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.7.0";
+const _version = "3.7.2";
 function version() {
     return _version
 }
@@ -76541,10 +76714,13 @@ class ChromosomeSelectWidget {
             genome.wgChromosomeNames.map(nm => genome.getChromosomeDisplayName(nm)) :
             [];
 
+        const alreadyAdded = genome.wgChromosomeNames ? new Set(genome.wgChromosomeNames) : new Set();
+
         if (this.showAllChromosomes && genome.chromosomeNames.length > 1) {
             const exclude = new Set(list);
-            let count = 0;
+            let count = alreadyAdded.size;
             for (let nm of genome.chromosomeNames) {
+                if(alreadyAdded.has(nm)) continue
                 if (++count === 1000) {
                     list.push(maximumSequenceCountExceeded);
                     break
@@ -79130,6 +79306,15 @@ class ChromAliasFile {
         }
     }
 
+    /**
+     * Search for chromosome alias record.  If found, cache results in the alias -> chr map
+     *
+     * An alias record is an object with keys corresponding to the chromosome name set (e.g. "ucsc", "refseq", etc) and
+     * value the corresponding chromosome alias for that name set.
+     *
+     * @param alias - the sequence name or alias
+     * @returns {Promise<any>} promise to resolve to the alias record.
+     */
     async search(alias) {
         if(this.aliasRecordCache.size === 0) {
             await this.loadAliases();
@@ -79477,7 +79662,7 @@ class Genome {
         this.ucscID = config.ucscID || ucsdIDMap.get(this.id) || this.id;
         this.blatDB = config.blatDB || this.ucscID;
         this.name = config.name;
-        this.nameSet = config.nameSet || 'ucsc';
+        this.nameSet = config.nameSet;
     }
 
 
@@ -80779,7 +80964,7 @@ class Browser {
             }
         }
 
-        const genomeOrReference = session.reference || session.genome;
+        const genomeOrReference = session.reference || session.genome || session.genarkAccession;
         if (!genomeOrReference) {
             console.warn("No genome or reference object specified");
             return
@@ -80996,6 +81181,15 @@ class Browser {
         return genome
     }
 
+    async expandGenarkAccession(genarkAccession) {
+
+        const url = convertToHubURL(genarkAccession);
+        const hub = await loadHub(url);
+        const genomeConfig = hub.getGenomeConfig();
+        genomeConfig.nameSet = "ucsc";
+        return genomeConfig
+    }
+
     /**
      * Load a genome, defined by a string ID or a json-like configuration object. This includes a fasta reference
      * as well as optional cytoband and annotation tracks.
@@ -81005,31 +81199,33 @@ class Browser {
      */
     async loadGenome(idOrConfig) {
 
-        if (idOrConfig.genarkAccession) {
-            idOrConfig.url = convertToHubURL(idOrConfig.genarkAccession);
-        }
+        let genomeConfig;
 
-        // Translate the generic "url" field, used by clients such as igv-webapp
-        if (idOrConfig.url) {
-            if (isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
-                idOrConfig.hubURL = idOrConfig.url;
-                delete idOrConfig.url;
-            } else if ("gbk" === getFileExtension(idOrConfig.url)) {
-                idOrConfig.gbkURL = idOrConfig.url;
-                delete idOrConfig.url;
+        if (idOrConfig.genarkAccession) {
+            genomeConfig = await this.expandGenarkAccession(idOrConfig.genarkAccession);
+        } else {
+            // Translate the generic "url" field, used by clients such as igv-webapp
+            if (idOrConfig.url) {
+                if (isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
+                    idOrConfig.hubURL = idOrConfig.url;
+                    delete idOrConfig.url;
+                } else if ("gbk" === getFileExtension(idOrConfig.url)) {
+                    idOrConfig.gbkURL = idOrConfig.url;
+                    delete idOrConfig.url;
+                }
             }
-        }
 
-        let genomeConfig;
-        const isHubGenome = idOrConfig.hubURL || (idOrConfig.url && isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt"));
-        if (isHubGenome) {
-            const hub = await loadHub(idOrConfig.hubURL || idOrConfig.url);
-            genomeConfig = hub.getGenomeConfig();
-        } else if (isString$3(idOrConfig) || !(idOrConfig.url || idOrConfig.fastaURL || idOrConfig.twoBitURL || idOrConfig.gbkURL)) {
-            // Either an ID, a json string, or an object missing required properties.
-            genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig);
-        } else {
-            genomeConfig = idOrConfig;
+
+            const isHubGenome = idOrConfig.hubURL || (idOrConfig.url && isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt"));
+            if (isHubGenome) {
+                const hub = await loadHub(idOrConfig.hubURL || idOrConfig.url);
+                genomeConfig = hub.getGenomeConfig();
+            } else if (isString$3(idOrConfig) || !(idOrConfig.url || idOrConfig.fastaURL || idOrConfig.twoBitURL || idOrConfig.gbkURL)) {
+                // Either an ID, a json string, or an object missing required properties.
+                genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig);
+            } else {
+                genomeConfig = idOrConfig;
+            }
         }
 
         await this.loadReference(genomeConfig);