igv 3.3.0 → 3.4.1

package/dist/igv.js

@@ -379,7 +379,7 @@
     * @param x
     * @returns {boolean}
     */
-   function isString$2(x) {
+   function isString$3(x) {
        return typeof x === "string" || x instanceof String
    }
 
@@ -479,7 +479,7 @@
 
        if (urlOrFile.name !== undefined) {
            return urlOrFile.name
-       } else if (isString$2(urlOrFile)) {
+       } else if (isString$3(urlOrFile)) {
 
            let index = urlOrFile.lastIndexOf("/");
            let filename = index < 0 ? urlOrFile : urlOrFile.substr(index + 1);
@@ -10684,7 +10684,7 @@
    };
 
    async function getFilename$1(url) {
-       if (isString$2(url) && url.startsWith("https://drive.google.com")) {
+       if (isString$3(url) && url.startsWith("https://drive.google.com")) {
            // This will fail if Google API key is not defined
            if (getApiKey() === undefined) {
                throw Error("Google drive is referenced, but API key is not defined.  An API key is required for Google Drive access")
@@ -10726,7 +10726,7 @@
 
 
    function isDataURL(obj) {
-       return (isString$2(obj) && obj.startsWith("data:"))
+       return (isString$3(obj) && obj.startsWith("data:"))
    }
 
    function createColumn(columnContainer, className) {
@@ -10952,7 +10952,7 @@
        return list;
    }
 
-   /*! @license DOMPurify 3.2.5 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.2.5/LICENSE */
+   /*! @license DOMPurify 3.2.6 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.2.6/LICENSE */
 
    const {
      entries,
@@ -11156,7 +11156,7 @@
    const TMPLIT_EXPR = seal(/\$\{[\w\W]*/gm); // eslint-disable-line unicorn/better-regex
    const DATA_ATTR = seal(/^data-[\-\w.\u00B7-\uFFFF]+$/); // eslint-disable-line no-useless-escape
    const ARIA_ATTR = seal(/^aria-[\-\w]+$/); // eslint-disable-line no-useless-escape
-   const IS_ALLOWED_URI = seal(/^(?:(?:(?:f|ht)tps?|mailto|tel|callto|sms|cid|xmpp):|[^a-z]|[a-z+.\-]+(?:[^a-z+.\-:]|$))/i // eslint-disable-line no-useless-escape
+   const IS_ALLOWED_URI = seal(/^(?:(?:(?:f|ht)tps?|mailto|tel|callto|sms|cid|xmpp|matrix):|[^a-z]|[a-z+.\-]+(?:[^a-z+.\-:]|$))/i // eslint-disable-line no-useless-escape
    );
    const IS_SCRIPT_OR_DATA = seal(/^(?:\w+script|data):/i);
    const ATTR_WHITESPACE = seal(/[\u0000-\u0020\u00A0\u1680\u180E\u2000-\u2029\u205F\u3000]/g // eslint-disable-line no-control-regex
@@ -11253,7 +11253,7 @@
    function createDOMPurify() {
      let window = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : getGlobal();
      const DOMPurify = root => createDOMPurify(root);
-     DOMPurify.version = '3.2.5';
+     DOMPurify.version = '3.2.6';
      DOMPurify.removed = [];
      if (!window || !window.document || window.document.nodeType !== NODE_TYPE.document || !window.Element) {
        // Not running in a browser, provide a factory function
@@ -11492,8 +11492,8 @@
        URI_SAFE_ATTRIBUTES = objectHasOwnProperty(cfg, 'ADD_URI_SAFE_ATTR') ? addToSet(clone(DEFAULT_URI_SAFE_ATTRIBUTES), cfg.ADD_URI_SAFE_ATTR, transformCaseFunc) : DEFAULT_URI_SAFE_ATTRIBUTES;
        DATA_URI_TAGS = objectHasOwnProperty(cfg, 'ADD_DATA_URI_TAGS') ? addToSet(clone(DEFAULT_DATA_URI_TAGS), cfg.ADD_DATA_URI_TAGS, transformCaseFunc) : DEFAULT_DATA_URI_TAGS;
        FORBID_CONTENTS = objectHasOwnProperty(cfg, 'FORBID_CONTENTS') ? addToSet({}, cfg.FORBID_CONTENTS, transformCaseFunc) : DEFAULT_FORBID_CONTENTS;
-       FORBID_TAGS = objectHasOwnProperty(cfg, 'FORBID_TAGS') ? addToSet({}, cfg.FORBID_TAGS, transformCaseFunc) : {};
-       FORBID_ATTR = objectHasOwnProperty(cfg, 'FORBID_ATTR') ? addToSet({}, cfg.FORBID_ATTR, transformCaseFunc) : {};
+       FORBID_TAGS = objectHasOwnProperty(cfg, 'FORBID_TAGS') ? addToSet({}, cfg.FORBID_TAGS, transformCaseFunc) : clone({});
+       FORBID_ATTR = objectHasOwnProperty(cfg, 'FORBID_ATTR') ? addToSet({}, cfg.FORBID_ATTR, transformCaseFunc) : clone({});
        USE_PROFILES = objectHasOwnProperty(cfg, 'USE_PROFILES') ? cfg.USE_PROFILES : false;
        ALLOW_ARIA_ATTR = cfg.ALLOW_ARIA_ATTR !== false; // Default true
        ALLOW_DATA_ATTR = cfg.ALLOW_DATA_ATTR !== false; // Default true
@@ -11858,7 +11858,7 @@
          allowedTags: ALLOWED_TAGS
        });
        /* Detect mXSS attempts abusing namespace confusion */
-       if (currentNode.hasChildNodes() && !_isNode(currentNode.firstElementChild) && regExpTest(/<[/\w!]/g, currentNode.innerHTML) && regExpTest(/<[/\w!]/g, currentNode.textContent)) {
+       if (SAFE_FOR_XML && currentNode.hasChildNodes() && !_isNode(currentNode.firstElementChild) && regExpTest(/<[/\w!]/g, currentNode.innerHTML) && regExpTest(/<[/\w!]/g, currentNode.textContent)) {
          _forceRemove(currentNode);
          return true;
        }
@@ -12010,7 +12010,8 @@
            value: attrValue
          } = attr;
          const lcName = transformCaseFunc(name);
-         let value = name === 'value' ? attrValue : stringTrim(attrValue);
+         const initValue = attrValue;
+         let value = name === 'value' ? initValue : stringTrim(initValue);
          /* Execute a hook if present */
          hookEvent.attrName = lcName;
          hookEvent.attrValue = value;
@@ -12036,10 +12037,9 @@
          if (hookEvent.forceKeepAttr) {
            continue;
          }
-         /* Remove attribute */
-         _removeAttribute(name, currentNode);
          /* Did the hooks approve of the attribute? */
          if (!hookEvent.keepAttr) {
+           _removeAttribute(name, currentNode);
            continue;
          }
          /* Work around a security issue in jQuery 3.0 */
@@ -12056,6 +12056,7 @@
          /* Is `value` valid for this attribute? */
          const lcTag = transformCaseFunc(currentNode.nodeName);
          if (!_isValidAttribute(lcTag, lcName, value)) {
+           _removeAttribute(name, currentNode);
            continue;
          }
          /* Handle attributes that require Trusted Types */
@@ -12076,19 +12077,23 @@
            }
          }
          /* Handle invalid data-* attribute set by try-catching it */
-         try {
-           if (namespaceURI) {
-             currentNode.setAttributeNS(namespaceURI, name, value);
-           } else {
-             /* Fallback to setAttribute() for browser-unrecognized namespaces e.g. "x-schema". */
-             currentNode.setAttribute(name, value);
-           }
-           if (_isClobbered(currentNode)) {
-             _forceRemove(currentNode);
-           } else {
-             arrayPop(DOMPurify.removed);
+         if (value !== initValue) {
+           try {
+             if (namespaceURI) {
+               currentNode.setAttributeNS(namespaceURI, name, value);
+             } else {
+               /* Fallback to setAttribute() for browser-unrecognized namespaces e.g. "x-schema". */
+               currentNode.setAttribute(name, value);
+             }
+             if (_isClobbered(currentNode)) {
+               _forceRemove(currentNode);
+             } else {
+               arrayPop(DOMPurify.removed);
+             }
+           } catch (_) {
+             _removeAttribute(name, currentNode);
            }
-         } catch (_) {}
+         }
        }
        /* Execute a hook if present */
        _executeHooks(hooks.afterSanitizeAttributes, currentNode, null);
@@ -16909,7 +16914,7 @@
     */
 
    const fixColor = (colorString) => {
-       if (isString$2(colorString)) {
+       if (isString$3(colorString)) {
            return (colorString.indexOf(",") > 0 && !(colorString.startsWith("rgb(") || colorString.startsWith("rgba("))) ?
                `rgb(${colorString})` : colorString
        } else {
@@ -16981,7 +16986,7 @@
                this.name = config.name || config.label;
            } else if (isFile(config.url)) {
                this.name = config.url.name;
-           } else if (isString$2(config.url) && !config.url.startsWith("data:")) {
+           } else if (isString$3(config.url) && !config.url.startsWith("data:")) {
                this.name = getFilename$2(config.url);
            }
 
@@ -20903,7 +20908,7 @@
     * THE SOFTWARE.
     */
 
-   const isString$1 = isString$2;
+   const isString$2 = isString$3;
 
 
    class CustomServiceReader {
@@ -20942,7 +20947,7 @@
            if (data) {
                if (typeof this.config.parser === "function") {
                    features = this.config.parser(data);
-               } else if (isString$1(data)) {
+               } else if (isString$2(data)) {
                    features = JSON.parse(data);
                } else {
                    features = data;
@@ -22343,7 +22348,7 @@
    }
 
    function getDecoder(definedFieldCount, fieldCount, autoSql, format) {
-
+   //biggenepred
        if ("biginteract" === format || (autoSql && ('chromatinInteract' === autoSql.table || 'interact' === autoSql.table))) {
            return decodeInteract
        } else {
@@ -22390,9 +22395,20 @@
                    const extraStart = definedFieldCount;
                    for (let i = extraStart; i < fieldCount; i++) {
                        if (i < autoSql.fields.length) {
+
                            const name = autoSql.fields[i].name;
-                           const value = tokens[i - 3];
-                           feature[name] = value;
+
+                           if (name === "exonFrames") {
+                               const frameOffsets = tokens[i - 3].replace(/,$/, '').split(',');
+                               for (let i = 0; i < feature.exons.length; i++) {
+                                   const exon = feature.exons[i];
+                                   const fo = parseInt(frameOffsets[i]);
+                                   if (fo != -1) exon.readingFrame = fo;
+                               }
+                           } else {
+                               const value = tokens[i - 3];
+                               feature[name] = value;
+                           }
                        }
                    }
                }
@@ -22438,6 +22454,7 @@
 
            return feature
        }
+
    }
 
    function findUTRs(exons, cdStart, cdEnd) {
@@ -23025,14 +23042,14 @@
                        // TODO -- align all feature attribute names with UCSC, an use specific column
                        for (let key of Object.keys(f)) {
                            const v = f[key];
-                           if (isString$2(v) && v.toLowerCase() === term.toLowerCase()) {
+                           if (isString$3(v) && v.toLowerCase() === term.toLowerCase()) {
                                return true
                            }
                        }
                        return false
                    });
                    if (matching.length > 0) {
-                       return matching.reduce((l, f) => (l.end - l.start) > (f.end - f.start) ? l : f, features[0])
+                       return matching.reduce((l, f) => (l.end - l.start) > (f.end - f.start) ? l : f, matching[0])
                    } else {
                        return undefined
                    }
@@ -23323,7 +23340,7 @@
    class ZoomLevelHeader {
        constructor(index, byteBuffer) {
            this.index = index;
-           this.reductionLevel = byteBuffer.getInt();
+           this.reductionLevel = byteBuffer.getUInt();
            this.reserved = byteBuffer.getInt();
            this.dataOffset = byteBuffer.getLong();
            this.indexOffset = byteBuffer.getLong();
@@ -26926,7 +26943,7 @@
            let aaLetter;
            if (undefined === aminoAcidLetter) {
 
-               if(sequenceInterval.hasSequence(start, end)) {
+               if (sequenceInterval.hasSequence(start, end)) {
 
                    const sequence = sequenceInterval.getSequence(start, end);
                    if (sequence && 3 === sequence.length) {
@@ -27062,7 +27079,8 @@
        try {
            ctx.save();
 
-           let name = feature.name;
+           const labelField = this.config.labelField ? this.config.labelField : 'name';
+           let name = feature[labelField];
            if (name === undefined && feature.gene) name = feature.gene.name;
            if (name === undefined) name = feature.id || feature.ID;
            if (!name || name === '.') return
@@ -27095,20 +27113,13 @@
            if (options.labelAllFeatures || xleft > lastLabelX || selected) {
                options.rowLastLabelX[feature.row] = xright;
 
-               if ('y' === options.axis) {
-                   // TODO -- is this ever used?
-                   ctx.save();
-                   IGVGraphics.labelTransformWithContext(ctx, centerX);
-                   IGVGraphics.fillText(ctx, name, centerX, labelY, geneFontStyle, transform);
-                   ctx.restore();
-               } else {
-                   ctx.clearRect(
-                       centerX - textMetrics.width / 2 - 1,
-                       labelY - textMetrics.actualBoundingBoxAscent - 1,
-                       textMetrics.width + 2,
-                       textMetrics.actualBoundingBoxAscent + textMetrics.actualBoundingBoxDescent + 2);
-                   IGVGraphics.fillText(ctx, name, centerX, labelY, geneFontStyle, transform);
-               }
+               ctx.clearRect(
+                   centerX - textMetrics.width / 2 - 1,
+                   labelY - textMetrics.actualBoundingBoxAscent - 1,
+                   textMetrics.width + 2,
+                   textMetrics.actualBoundingBoxAscent + textMetrics.actualBoundingBoxDescent + 2);
+               IGVGraphics.fillText(ctx, name, centerX, labelY, geneFontStyle, transform);
+
            }
 
        } finally {
@@ -27522,7 +27533,11 @@
            // If drawing amino acids fetch cached sequence interval.  It is not needed if track does not support AA, but
            // costs nothing since only a reference to a cached object is fetched.
            if (bpPerPixel < aminoAcidSequenceRenderThreshold) {
-               options.sequenceInterval = this.browser.genome.getSequenceInterval(referenceFrame.chr, bpStart, bpEnd);
+               // Restrict the range requested to the limits: 1-chromosome.bpLength
+               const chromosome = this.browser.genome.getChromosome(referenceFrame.chr);
+               const chromosomeEnd = chromosome.bpLength;
+               options.sequenceInterval = this.browser.genome.getSequenceInterval(referenceFrame.chr,
+                   bpStart > 0 ? bpStart : 0, bpEnd > chromosomeEnd ? chromosomeEnd : bpEnd);
            }
 
 
@@ -27649,7 +27664,7 @@
                            fd.name &&
                            fd.name.toLowerCase() === "name" &&
                            fd.value &&
-                           isString$2(fd.value) &&
+                           isString$3(fd.value) &&
                            !fd.value.startsWith("<")) {
                            const href = infoURL.replace("$$", feature.name);
                            fd.value = `<a target=_blank href=${href}>${fd.value}</a>`;
@@ -28293,7 +28308,7 @@
        async postInit() {
            if(!this.featureSource) {
                // This will be the case when restoring from a session
-               const db = this.browser.genome.id;   // TODO -- blat specific property
+               const db = this.browser.genome.ucscID;   // TODO -- blat specific property
                const url = this.browser.config["blatServerURL"];
                const features = await blat({url, userSeq: this.sequence, db});
                this._features = features;
@@ -28310,7 +28325,7 @@
            if (undefined === this.table) {
 
                const rows = this._features.map(f => [
-                   f.chr,
+                   this.browser.genome.getChromosomeDisplayName(f.chr),
                    (f.start + 1),
                    f.end,
                    f.strand,
@@ -28385,7 +28400,7 @@
 
        try {
 
-           const db = browser.genome.id;   // TODO -- blat specific property
+           const db = browser.genome.ucscID;   // TODO -- blat specific property
            const url = browser.config["blatServerURL"] || defaultBlatServer;
            const features = await blat({url, userSeq: sequence, db});
 
@@ -28627,7 +28642,7 @@
                }
 
                items.push({
-                   label: 'BLAT read sequence',
+                   label: 'BLAT visible sequence',
                    click: async () => {
                        let sequence = await this.browser.genome.getSequence(chr, start, end);
                        if (sequence) {
@@ -30615,13 +30630,6 @@
            this.trackStanzas = trackStanzas;
        }
 
-       findCytobandURL() {
-           for (const t of this.trackStanzas) {
-               if (t.name === "cytoBandIdeo" && t.hasProperty("bigDataUrl")) {
-                   return t.getProperty("bigDataUrl")
-               }
-           }
-       }
 
        getSupportedTrackCount() {
            let count = 0;
@@ -30961,6 +30969,7 @@
 
    const idMappings = new Map([
        ["hg38", "GCF_000001405.40"],
+       ["hg38_1kg", "GCF_000001405.40"],
        ["mm39", "GCF_000001635.27"],
        ["mm10", "GCF_000001635.26"],
        ["bosTau9", "GCF_002263795.1"],
@@ -30997,12 +31006,16 @@
            this.genomeStanzas = genomeStanzas;
            this.trackStanzas = trackStanzas;
            this.groupStanzas = groupStanzas;
+           this.cytobandStanza = null;
            this.trackHubMap = new Map();
 
            // trackStanzas will not be null if this is a "onefile" hub
            if (trackStanzas) {
                const genomeId = genomeStanzas[0].getProperty("genome"); // Assumption here this is a single genome hub
                this.trackHubMap.set(genomeId, new TrackDbHub(trackStanzas, groupStanzas));
+
+               // Search for cytoband track.  This supports a special but important case -- Genark assembly hubs
+               this.cytobandStanza = this.trackStanzas.find(t => t.name === "cytoBandIdeo" && t.hasProperty("bigDataUrl")) || null;
            }
        }
 
@@ -31104,6 +31117,10 @@
                config.twoBitBptURL = genomeStanza.getProperty("twoBitBptUrl");
            }
 
+           if(this.cytobandStanza){
+               config.cytobandBbURL = this.cytobandStanza.getProperty("bigDataUrl");
+           }
+
            if (this.hubStanza.hasProperty("longLabel")) {
                config.description = this.hubStanza.getProperty("longLabel").replace("/", "\n");
            } else {
@@ -31263,7 +31280,6 @@
            if (t.hasProperty("searchTrix")) {
                config.trixURL = t.getProperty("searchTrix");
            }
-
            if (t.hasProperty("group")) {
                config._group = t.getProperty("group");
                if (this.groupPriorityMap && this.groupPriorityMap.has(config._group)) {
@@ -31272,6 +31288,12 @@
                    this.groupPriorityMap.set(config._group, nextPriority);
                }
            }
+           const labelFields = t.hasProperty("defaultLabelFields") ?
+               t.getProperty("defaultLabelFields") :
+               t.getProperty("labelFields");
+           if (labelFields) {
+               config.labelField = labelFields.split(",")[0];
+           }
 
            return config
        }
@@ -31412,9 +31434,9 @@
                }
 
 
-               const i = line.indexOf(' ');
-               const key = line.substring(0, i).trim();
-               let value = line.substring(i + 1).trim();
+               const index = line.indexOf(' ');
+               const key = line.substring(0, index).trim();
+               let value = line.substring(index + 1).trim();
 
                if (key === "type") {
                    // The "type" property contains format and sometimes other information. For example, data range
@@ -31497,8 +31519,8 @@
        return host
    }
 
-   const DEFAULT_GENOMES_URL = "https://igv.org/genomes/genomes.json";
-   const BACKUP_GENOMES_URL = "https://raw.githubusercontent.com/igvteam/igv-genomes/refs/heads/main/dist/genomes.json";
+   const DEFAULT_GENOMES_URL = "https://igv.org/genomes/genomes3.json";
+   const BACKUP_GENOMES_URL = "https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/genomes/web/genomes.json";
 
    const GenomeUtils = {
 
@@ -31523,7 +31545,7 @@
                    } catch (error) {
                        try {
                            console.error("Error initializing default genomes:", error);
-                           const jsonArray = await igvxhr.loadJson(BACKUP_GENOMES_URL, {timeout: 2000});
+                           const jsonArray = await igvxhr.loadJson(BACKUP_GENOMES_URL, {timeout: 10000});
                            processJson(jsonArray, table);
                        } catch (e) {
                            console.error("Error initializing backup genomes:", error);
@@ -31553,7 +31575,7 @@
        expandReference: async function (alert, idOrConfig) {
 
            // idOrConfig might be a json string?  I'm actually not sure how this arises.
-           if (isString$2(idOrConfig) && idOrConfig.startsWith("{")) {
+           if (isString$3(idOrConfig) && idOrConfig.startsWith("{")) {
                try {
                    idOrConfig = JSON.parse(idOrConfig);
                } catch (e) {
@@ -31562,7 +31584,7 @@
            }
 
            let genomeID;
-           if (isString$2(idOrConfig)) {
+           if (isString$3(idOrConfig)) {
                genomeID = idOrConfig;
            } else if (idOrConfig.genome) {
                genomeID = idOrConfig.genome;
@@ -32508,7 +32530,7 @@
            let track = this.trackView.track;
            const dataList = track.popupData(clickState);
 
-           const popupClickHandlerResult = this.browser.fireEvent('trackclick', [track, dataList]);
+           const popupClickHandlerResult = this.browser.fireEvent('trackclick', [track, dataList, clickState.genomicLocation]);
 
            let content;
            if (undefined === popupClickHandlerResult || true === popupClickHandlerResult) {
@@ -40998,6 +41020,9 @@
        return true
    }
 
+   /**
+    * Track for segmented copy number, mut, maf and shoebox files.
+    */
    class SegTrack extends TrackBase {
 
        #sortDirections = new Map()
@@ -41145,7 +41170,10 @@
                    }, e);
                }
 
-               menuItems.push({ element: createElementWithString('<div>Set color scale threshold</div>'), dialog: dialogPresentationHandler});
+               menuItems.push({
+                   element: createElementWithString('<div>Set color scale threshold</div>'),
+                   dialog: dialogPresentationHandler
+               });
            }
 
            menuItems.push('<hr/>');
@@ -41176,12 +41204,75 @@
 
        getSamples() {
            return {
-               names: this.sampleKeys,
+               names: this.filteredSampleKeys,
                height: this.sampleHeight,
                yOffset: 0
            }
        }
 
+       /**
+        * Set the sample filter object.  This is used to filter samples from the set based on values over a specified
+        * genomic region.   The values compared depend on the track data type:
+        *   - "seg" and "shoebox" -- average value over the region
+        *   - "mut" and "maf" -- count of features overlapping the region
+        *
+        * The method is asynchronous because it may need to fetch data from the server to compute the scores.
+        * Computed scores are stored and used to filter the sample keys on demand.
+        *
+        * @param filterObject
+        * @returns {Promise<void>}
+        */
+       async setSampleFilter(filterObject) {
+           if (!filterObject) {
+               this.config.filterObject = undefined;
+               this.filterObject = undefined;
+               this.trackView.repaintViews();
+           } else {
+               const filterObjectCopy = Object.assign({}, filterObject);
+               this.config.filterObject = filterObjectCopy;
+
+               filterObject.scores = await this.computeRegionScores(filterObject);
+               this.filterObject = filterObject;
+               this.trackView.checkContentHeight();
+               this.trackView.repaintViews();
+           }
+           // TODO - store filter object in session
+       }
+
+
+       /**
+        * Filter function for sample keys.
+        *
+        * @param sampleKey
+        * @returns {boolean}
+        */
+       filter(sampleKey) {
+           if (this.filterObject) {
+               const filterObject = this.filterObject;
+               const scores = filterObject.scores;
+               const score = scores[sampleKey];
+
+               if (this.type === 'seg') {
+                   if (filterObject.op === '>') {
+                       return score > filterObject.value
+                   } else if (filterObject.op === '<') {
+                       return score < filterObject.value
+                   }
+               } else if (this.type === 'mut' || this.type === 'maf') {
+                   return 'HAS' === filterObject.op ? score : !score
+               }
+           }
+           // else if (this.config.sampleFilter) {
+           //     return this.config.sampleFilter(sampleKey)
+           // }
+           return true
+       }
+
+       get filteredSampleKeys() {
+           return this.sampleKeys.filter(sampleKey => this.filter(sampleKey))
+       }
+
+
        async getFeatures(chr, start, end) {
            const features = await this.featureSource.getFeatures({chr, start, end});
            // New segments could conceivably add new samples
@@ -41189,8 +41280,10 @@
 
            if (this.initialSort) {
                const sort = this.initialSort;
+
                if (sort.option === undefined || sort.option.toUpperCase() === "VALUE") {
-                   this.sortByValue(sort, features);
+                   const sortFeatures = (sort.chr === chr && sort.start >= start && sort.end <= end) ? features : undefined;
+                   this.sortByValue(sort, sortFeatures);
                } else if ("ATTRIBUTE" === sort.option.toUpperCase() && sort.attribute) {
                    const sortDirection = "DESC" === sort.direction ? 1 : -1;
                    this.sortByAttribute(sort.attribute, sortDirection);
@@ -41205,6 +41298,7 @@
 
            IGVGraphics.fillRect(context, 0, pixelTop, pixelWidth, pixelHeight, {'fillStyle': "rgb(255, 255, 255)"});
 
+
            if (features && features.length > 0) {
 
                this.checkForLog(features);
@@ -41216,14 +41310,15 @@
 
                // Create a map for fast id -> row lookup
                const samples = {};
-               this.sampleKeys.forEach(function (id, index) {
+               const filteredKeys = this.filteredSampleKeys;
+               filteredKeys.forEach(function (id, index) {
                    samples[id] = index;
                });
 
                let border;
                switch (this.displayMode) {
                    case "FILL":
-                       this.sampleHeight = pixelHeight / this.sampleKeys.length;
+                       this.sampleHeight = pixelHeight / filteredKeys.length;
                        border = 0;
                        break
 
@@ -41361,7 +41456,7 @@
            if (!features) return 0
            const sampleHeight = ("SQUISHED" === this.displayMode) ? this.squishedRowHeight : this.expandedRowHeight;
            this.updateSampleKeys(features);
-           return this.sampleKeys.length * sampleHeight
+           return this.filteredSampleKeys.length * sampleHeight
        }
 
        /**
@@ -41370,16 +41465,38 @@
        async sortByValue(sort, featureList) {
 
            const chr = sort.chr;
+           const start = sort.position !== undefined ? sort.position - 1 : sort.start;
+           const end = sort.end === undefined ? start + 1 : sort.end;
+           const scores = await this.computeRegionScores({chr, start, end}, featureList);
+           const d2 = (sort.direction === "ASC" ? 1 : -1);
+
+           this.sampleKeys.sort(function (a, b) {
+               let s1 = scores[a];
+               let s2 = scores[b];
+               if (!s1) s1 = d2 * Number.MAX_VALUE;
+               if (!s2) s2 = d2 * Number.MAX_VALUE;
+               if (s1 === s2) return 0
+               else if (s1 > s2) return d2
+               else return d2 * -1
+           });
+
+           this.config.sort = sort;
+           this.trackView.repaintViews();
+       }
+
+
+       async computeRegionScores(filterObject, featureList) {
+
+           const chr = filterObject.chr;
            let start, end;
-           if (sort.position) {
-               start = sort.position - 1;
+           if (filterObject.position) {
+               start = filterObject.position - 1;
                end = start + 1;
            } else {
-               start = sort.start;
-               end = sort.end;
+               start = filterObject.start;
+               end = filterObject.end;
            }
 
-
            if (!featureList) {
                featureList = await this.featureSource.getFeatures({chr, start, end});
            }
@@ -41388,62 +41505,40 @@
            this.updateSampleKeys(featureList);
 
            const scores = {};
-           const d2 = (sort.direction === "ASC" ? 1 : -1);
+           const bpLength = end - start + 1;
+
+           const mutationTypes = filterObject.value ? new Set(filterObject.value) : undefined;
+
+           for (let segment of featureList) {
+               if (segment.end < start) continue
+               if (segment.start > end) break
+               const sampleKey = segment.sampleKey || segment.sample;
+
+               if ("mut" === this.type) {
+                   if (mutationTypes) {
+                       const mutationType = segment.getAttribute("Variant_Classification");
+                       if (mutationTypes.has(mutationType)) {
+                           // Just count features overlapping region per sample
+                           scores[sampleKey] = (scores[sampleKey] || 0) + 1;
+                       }
+                   } else {
+                       // Just count features overlapping region per sample
+                       scores[sampleKey] = (scores[sampleKey] || 0) + 1;
+                   }
+               } else {
 
-           const sortSeg = () => {
-               // Compute weighted average score for each sample
-               const bpLength = end - start + 1;
-               for (let segment of featureList) {
-                   if (segment.end < start) continue
-                   if (segment.start > end) break
                    const min = Math.max(start, segment.start);
                    const max = Math.min(end, segment.end);
                    const f = (max - min) / bpLength;
-                   const sampleKey = segment.sampleKey || segment.sample;
-                   const s = scores[sampleKey] || 0;
-                   scores[sampleKey] = s + f * segment.value;
-               }
-
-               // Now sort sample names by score
-               this.sampleKeys.sort(function (a, b) {
-                   let s1 = scores[a];
-                   let s2 = scores[b];
-                   if (!s1) s1 = d2 * Number.MAX_VALUE;
-                   if (!s2) s2 = d2 * Number.MAX_VALUE;
-                   if (s1 === s2) return 0
-                   else if (s1 > s2) return d2
-                   else return d2 * -1
-               });
-           };
-
-           const sortMut = () => {
-               // Compute weighted average score for each sample
-               for (let segment of featureList) {
-                   if (segment.end < start) continue
-                   if (segment.start > end) break
-                   const sampleKey = segment.sampleKey || segment.sample;
-                   if (!scores.hasOwnProperty(sampleKey) || segment.value.localeCompare(scores[sampleKey]) > 0) {
-                       scores[sampleKey] = segment.value;
-                   }
-               }
-               // Now sort sample names by score
-               this.sampleKeys.sort(function (a, b) {
-                   let sa = scores[a] || "";
-                   let sb = scores[b] || "";
-                   return d2 * (sa.localeCompare(sb))
-               });
-           };
-
-           if ("mut" === this.type) {
-               sortMut();
-           } else {
-               sortSeg();
+                   scores[sampleKey] = (scores[sampleKey] || 0) + f * segment.value;
+               }
            }
 
-           this.trackView.repaintViews();
+           return scores
 
        }
 
+
        sortByAttribute(attribute, sortDirection) {
 
            this.sampleKeys = this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys, attribute, sortDirection);
@@ -41512,7 +41607,7 @@
                const dirLabel = direction === "DESC" ? "descending" : "ascending";
                const sortLabel = this.type === 'seg' || this.type === 'shoebox' ?
                    `Sort by value (${dirLabel})` :
-                   `Sort by type (${dirLabel})`;
+                   `Sort by count (${dirLabel})`;
                return {
                    label: sortLabel,
                    click: () => {
@@ -41524,7 +41619,6 @@
                            end: Math.floor(genomicLocation + bpWidth)
                        };
                        sortHandler(sort);
-                       this.config.sort = sort;
                    }
                }
            })
@@ -41694,13 +41788,13 @@
            }
        }
 
-       popupData(genomicLocation) {
+       popupData(genomicLocation, hiddenTags, showTags) {
 
-           let nameValues = this.firstAlignment.popupData(genomicLocation);
+           let nameValues = this.firstAlignment.popupData(genomicLocation, hiddenTags, showTags);
 
            if (this.secondAlignment) {
                nameValues.push("-------------------------------");
-               nameValues = nameValues.concat(this.secondAlignment.popupData(genomicLocation));
+               nameValues = nameValues.concat(this.secondAlignment.popupData(genomicLocation, hiddenTags, showTags));
            }
            return nameValues
        }
@@ -43414,7 +43508,7 @@
        isNegativeStrand() {
            return (this.flags & READ_STRAND_FLAG$2) !== 0
        }
-       
+
        isMateNegativeStrand() {
            return (this.flags & MATE_STRAND_FLAG$2) !== 0
        }
@@ -43462,7 +43556,7 @@
            return (genomicLocation >= s && genomicLocation <= (s + l))
        }
 
-       popupData(genomicLocation) {
+       popupData(genomicLocation, hiddenTags, showTags) {
 
            // if the user clicks on a base next to an insertion, show just the
            // inserted bases in a popup (like in desktop IGV).
@@ -43545,15 +43639,20 @@
                }
            }
 
-           const hiddenTags = new Set(['SA', 'MD']);
            nameValues.push('<hr/>');
            for (let key in tagDict) {
-               if (!hiddenTags.has(key)) {
+               if (showTags?.has(key)) {
+                   nameValues.push({name: key, value: tagDict[key]});
+               } else if (showTags) {
+                   hiddenTags.add(key);
+               } else if (!hiddenTags.has(key)) {
                    nameValues.push({name: key, value: tagDict[key]});
                }
            }
 
-           nameValues.push({name: 'Hidden Tags', value: 'SA, MD'});
+           if (hiddenTags && hiddenTags.size > 0) {
+               nameValues.push({name: 'Hidden Tags', value: Array.from(hiddenTags).join(", ")});
+           }
 
            nameValues.push('<hr/>');
            nameValues.push({name: 'Genomic Location: ', value: numberFormatter$1(1 + genomicLocation)});
@@ -43561,18 +43660,18 @@
            nameValues.push({name: 'Base Quality:', value: this.readBaseQualityAt(genomicLocation)});
 
            const bmSets = this.getBaseModificationSets();
-           if(bmSets) {
+           if (bmSets) {
                const i = this.positionToReadIndex(genomicLocation);
-               if(undefined !== i) {
+               if (undefined !== i) {
                    let found = false;
                    for (let bmSet of bmSets) {
                        if (bmSet.containsPosition(i)) {
-                           if(!found) {
+                           if (!found) {
                                nameValues.push('<hr/>');
                                nameValues.push('<b>Base modifications:</b>');
                                found = true;
                            }
-                           const lh = Math.round((100/255) * byteToUnsignedInt(bmSet.likelihoods.get(i)));
+                           const lh = Math.round((100 / 255) * byteToUnsignedInt(bmSet.likelihoods.get(i)));
                            nameValues.push(`${bmSet.fullName()} @ likelihood =  ${lh}%`);
                        }
                    }
@@ -43662,7 +43761,7 @@
                const mm = this.tagDict["MM"] || this.tagDict["Mm"];
                const ml = this.tagDict["ML"] || this.tagDict["Ml"];
 
-               if (isString$2(mm) && (!ml || Array.isArray(ml))) { // minimal validation, 10X uses these reserved tags for something completely different
+               if (isString$3(mm) && (!ml || Array.isArray(ml))) { // minimal validation, 10X uses these reserved tags for something completely different
                    if (mm.length === 0) {
                        this.baseModificationSets = EMPTY_SET;
                    } else {
@@ -43675,7 +43774,7 @@
            return this.baseModificationSets
        }
 
-        getGroupValue( groupBy, tag, expectedPairOrientation) {
+       getGroupValue(groupBy, tag, expectedPairOrientation) {
 
            const al = this;
            switch (groupBy) {
@@ -43712,7 +43811,7 @@
            }
        }
 
-       positionToReadIndex( position) {
+       positionToReadIndex(position) {
            const block = blockAtGenomicLocation(this.blocks, position);
            if (block) {
                return (position - block.start) + block.seqOffset
@@ -45691,7 +45790,7 @@
 
    function inferIndexPath(url, extension) {
 
-       if (isString$2(url)) {
+       if (isString$3(url)) {
            if (url.includes("?")) {
                const idx = url.indexOf("?");
                return url.substring(0, idx) + "." + extension + url.substring(idx)
@@ -45850,7 +45949,7 @@
                this.bamReader = new CramReader(config, genome, browser);
            } else {
                if (!this.config.indexURL && config.indexed !== false) {
-                   if (isString$2(this.config.url)) {
+                   if (isString$3(this.config.url)) {
                        const indexPath = inferIndexPath(this.config.url, "bai");
                        if (indexPath) {
                            console.warn(`Warning: no indexURL specified for ${this.config.url}.  Guessing ${indexPath}`);
@@ -48162,7 +48261,7 @@
            highlightColor: undefined,
            minTLEN: undefined,
            maxTLEN: undefined,
-           tagColorPallete: "Set1"
+           tagColorPallete: "Set1",
        }
 
        _colorTables = new Map()
@@ -48177,6 +48276,18 @@
                this.colorTable = new ColorTable(config.tagColorTable);
            }
 
+           // Only one of showTags / hideTags should be specified.  If both are specified showTags takes precedence.
+           if (config.showTags && config.hideTags) {
+               console.warn("Both showTags and hideTags specified.  showTags will be used.");
+           }
+           if (config.showTags) {
+               this.showTags = new Set(config.showTags);
+               this.hiddenTags = new Set();
+           } else {
+               this.hiddenTags = new Set(config.hideTags || ["SA", "MD"]);
+           }
+
+
            // Backward compatibility overrides
            if (config.largeFragmentLengthColor) this.largeTLENColor = config.largeFragmentLengthColor;
            if (config.pairOrienation) this.expectedPairOrientation = config.pairOrientation;
@@ -48737,7 +48848,7 @@
 
        popupData(clickState) {
            const clickedObject = this.getClickedObject(clickState);
-           return clickedObject ? clickedObject.popupData(clickState.genomicLocation) : undefined
+           return clickedObject?.popupData(clickState.genomicLocation, this.hiddenTags, this.showTags)
        };
 
        /**
@@ -48768,7 +48879,10 @@
                colorByMenuItems.push({key: 'tlen', label: 'insert size (TLEN)'});
                colorByMenuItems.push({key: 'unexpectedPair', label: 'pair orientation & insert size (TLEN)'});
            }
-           colorByMenuItems.push({key: 'tag', label: 'tag'});
+           if(this.colorBy && this.colorBy.startsWith("tag:")) {
+               colorByMenuItems.push({key: this.colorBy, label: this.colorBy});
+           }
+           colorByMenuItems.push({key: 'tag', label: 'tag...'});
            for (let item of colorByMenuItems) {
                const selected = (this.colorBy === undefined && item.key === 'none') || this.colorBy === item.key;
                menuItems.push(this.colorByCB(item, selected));
@@ -49284,7 +49398,7 @@
 
                        if (seqstring.length < maxSequenceSize$1) {
                            list.push({
-                               label: 'BLAT read sequence',
+                               label: 'BLAT visible sequence',
                                click: () => {
                                    const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(seqstring) : seqstring;
                                    const name = `${clickedAlignment.readName} - blat`;
@@ -49494,14 +49608,19 @@
                case "tag":
                    const tagValue = alignment.tags()[tag];
                    if (tagValue !== undefined) {
-                       if (this.bamColorTag === tag) {
+
+                       // If the tag value can be interpreted as a color, use it
+                       if(typeof tagValue.startsWith === 'function') {
                            color = IGVColor.createColorStringSafe(tagValue);
                        }
-                       if (!this.colorTable) {
-                           this.colorTable = new PaletteColorTable(this.tagColorPallete);
-                       }
-                       color = this.colorTable.getColor(tagValue);
 
+                       // Tag value is not a color, use a color table
+                       if (!color) {
+                           if (!this.colorTable) {
+                               this.colorTable = new PaletteColorTable(this.tagColorPallete);
+                           }
+                           color = this.colorTable.getColor(tagValue);
+                       }
                    }
                    break
            }
@@ -65718,7 +65837,7 @@ ${indent}columns: ${matrix.columns}
     * THE SOFTWARE.
     */
 
-   const isString = isString$2;
+   const isString$1 = isString$3;
 
    const DEFAULT_VISIBILITY_WINDOW = 1000000;
    const TOP_MARGIN = 10;
@@ -65841,7 +65960,7 @@ ${indent}columns: ${matrix.columns}
            }
            if (undefined === this.visibilityWindow && this.config.indexed !== false) {
                const fn = isFile(this.config.url) ? this.config.url.name : this.config.url;
-               if (isString(fn) && fn.toLowerCase().includes("gnomad")) {
+               if (isString$1(fn) && fn.toLowerCase().includes("gnomad")) {
                    this.visibilityWindow = 1000;  // these are known to be very dense
                } else if (typeof this.featureSource.defaultVisibilityWindow === 'function') {
                    this.visibilityWindow = await this.featureSource.defaultVisibilityWindow();
@@ -69725,6 +69844,9 @@ ${indent}columns: ${matrix.columns}
            ['image', (config, browser) => new ImageTrack(config, browser)]
        ]);
 
+   function knownTrackTypes () {
+       return new Set(trackFunctions.keys())
+   }
 
    /**
     * Return a track of the given type, passing configuration and a point to the IGV "Browser" object to its constructor function*
@@ -70217,7 +70339,7 @@ ${indent}columns: ${matrix.columns}
        })
    }
 
-   const _version = "3.3.0";
+   const _version = "3.4.1";
    function version() {
        return _version
    }
@@ -70268,7 +70390,7 @@ ${indent}columns: ${matrix.columns}
                    if (this.select.value.trim().toLowerCase() === "all" || this.select.value === "*") {
                        if (browser.genome.wholeGenomeView) {
                            const wgChr = browser.genome.getChromosome("all");
-                           return {chr: "all", start: 0, end: wgChr.bpLength}
+                           browser.updateLoci([{chr: "all", start: 0, end: wgChr.bpLength}]);
                        }
                    } else {
                        const chromosome = await browser.genome.loadChromosome(this.select.value);
@@ -72073,6 +72195,26 @@ ${indent}columns: ${matrix.columns}
            }
 
 
+           const found = this.browser.findTracks(track => typeof track.sortByValue === 'function');
+           if (found.length > 0) {
+               const { chr, start, end } = feature;
+               items.push(
+                   '<hr/>',
+                   {
+                       label: 'Sort by value (ascending)',
+                       click: () => Promise.all(found.map(track => track.sortByValue({ option: 'VALUE', direction: 'ASC', chr, start, end })))
+                   });
+
+               items.push(
+                   '<hr/>',
+                   {
+                       label: 'Sort by value (descending)',
+                       click: () => Promise.all(found.map(track => track.sortByValue({ option: 'VALUE', direction: 'DESC', chr, start, end })))
+                   });
+
+           }
+
+
            if (roiSet.isUserDefined) {
                items.push(
                    '<hr/>',
@@ -72081,7 +72223,7 @@ ${indent}columns: ${matrix.columns}
                        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();
@@ -73254,6 +73396,189 @@ ${indent}columns: ${matrix.columns}
 
    }
 
+   /**
+    * Update deprecated fasta & index urls in the reference object.
+    */
+
+   const isString = (x) => {
+       return (x && typeof x === "string") || x instanceof String
+   };
+
+   /**
+    * Replaces deprecated s3 fasta URLs with twoBitURLs.  The purpose here is to rescue references from saved sessions
+    * that contain pointers to deprectated IGV s3 buckets.  These buckets will eventually be deleted
+    *
+    * @param reference
+    */
+   function updateReference(reference) {
+
+       if (!(requiresUpdate(reference) && updates[reference.id])) {
+           return
+       }
+
+       const updatedReference = updates[reference.id];
+       if (updatedReference) {
+           delete reference.fastaURL;
+           if (reference.indexURL) delete reference.indexURL;
+           reference.twoBitURL = updatedReference.twoBitURL;
+           if (updatedReference.twoBitBptURL) reference.twoBitBptURL = updatedReference.twoBitBptURL;
+           if (updatedReference.chromSizesURL) reference.chromSizesURL = updatedReference.chromSizesURL;
+       }
+   }
+
+   function requiresUpdate(reference) {
+       return isString(reference.fastaURL) &&
+           (reference.fastaURL.startsWith("https://igv.org") ||
+               ["igv.org.genomes", "igv.broadinstitute.org", "igv.genepattern.org", "igvdata.broadinstitute.org",
+                   "igv-genepattern-org"].some(bucket => reference.fastaURL.includes(bucket)))
+   }
+
+   const updates = {
+       "hs1": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit",
+           "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit.bpt",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chrom.sizes.txt"
+       },
+       "hg38": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes"
+       },
+       "hg19": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes"
+       },
+       "hg18": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/hg18.chrom.sizes"
+       },
+       "mm39": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes"
+       },
+       "mm10": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes"
+       },
+       "mm9": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.chrom.sizes"
+       },
+       "rn7": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/227/675/GCF_015227675.2/GCF_015227675.2.2bit",
+           "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/227/675/GCF_015227675.2/GCF_015227675.2.2bit.bpt",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/227/675/GCF_015227675.2/GCF_015227675.2.chrom.sizes.txt"
+       },
+       "rn6": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/895/GCF_000001895.5/GCF_000001895.5.2bit",
+           "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/895/GCF_000001895.5/GCF_000001895.5.2bit.bpt",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/895/GCF_000001895.5/GCF_000001895.5.chrom.sizes.txt"
+       },
+       "gorGor6": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.chrom.sizes"
+       },
+       "gorGor4": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/bigZips/gorGor4.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/bigZips/gorGor4.chrom.sizes"
+       },
+       "panTro6": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chrom.sizes"
+       },
+       "panTro5": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro5/bigZips/panTro5.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro5/bigZips/panTro5.chrom.sizes"
+       },
+       "panTro4": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro4/bigZips/panTro4.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro4/bigZips/panTro4.chrom.sizes"
+       },
+       "macFas5": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.chrom.sizes"
+       },
+       "panPan2": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panPan2/bigZips/panPan2.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panPan2/bigZips/panPan2.chrom.sizes"
+       },
+       "canFam6": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chrom.sizes"
+       },
+       "canFam5": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.chrom.sizes"
+       },
+       "canFam4": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.chrom.sizes"
+       },
+       "canFam3": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam3/bigZips/canFam3.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam3/bigZips/canFam3.chrom.sizes"
+       },
+       "bosTau9": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.chrom.sizes"
+       },
+       "bosTau8": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.chrom.sizes"
+       },
+       "susScr11": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.chrom.sizes"
+       },
+       "galGal6": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.chrom.sizes"
+       },
+       "danRer11": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.chrom.sizes"
+       },
+       "danRer10": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.chrom.sizes"
+       },
+       "ce11": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.chrom.sizes"
+       },
+       "dm6": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.chrom.sizes"
+       },
+       "dm3": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes"
+       },
+       "sacCer3": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit",
+           "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit.bpt",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.chrom.sizes.txt"
+       },
+       "GCF_000002945.1": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit",
+           "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit.bpt",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chrom.sizes.txt"
+       },
+       "GCF_009858895.2": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.2bit",
+           "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.2bit.bpt",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.chrom.sizes.txt"
+       },
+       "tair10": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.2bit",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.chrom.sizes.txt"
+       },
+       "GCA_000022165.1": {
+           "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/022/165/GCA_000022165.1/GCA_000022165.1.2bit",
+           "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/022/165/GCA_000022165.1/GCA_000022165.1.2bit.bpt",
+           "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/022/165/GCA_000022165.1/GCA_000022165.1.chrom.sizes.txt"
+       }
+   };
+
    const ucsdIDMap = new Map([
        ["1kg_ref", "hg18"],
        ["1kg_v37", "hg19"],
@@ -73275,6 +73600,7 @@ ${indent}columns: ${matrix.columns}
 
        static async createGenome(options, browser) {
 
+           updateReference(options);
            const genome = new Genome(options, browser);
            await genome.init();
            return genome
@@ -73298,7 +73624,6 @@ ${indent}columns: ${matrix.columns}
            // Load sequence
            this.sequence = await loadSequence(config, this.browser);
 
-
            // Load cytobands.  This is optional but required to support the ideogram.  Only needed for whole genome view
            if(false !== config.showIdeogram && false !== config.wholeGenomeView) {
                if (config.cytobandURL) {
@@ -73342,10 +73667,14 @@ ${indent}columns: ${matrix.columns}
                    } else {
                        this.#wgChromosomeNames = config.chromosomeOrder.split(',').map(nm => nm.trim());
                    }
+                   // Trim to remove non-existent chromosomes
+                   await this.chromAlias.preload(this.#wgChromosomeNames);
+                   this.#wgChromosomeNames =
+                       this.#wgChromosomeNames.map(c =>  this.getChromosomeName(c)).filter(c => this.chromosomes.has(c));
                } else {
                    this.#wgChromosomeNames = trimSmallChromosomes(this.chromosomes);
+                   await this.chromAlias.preload(this.#wgChromosomeNames);
                }
-               await this.chromAlias.preload(this.#wgChromosomeNames);
            }
 
            // Optionally create the psuedo chromosome "all" to support whole genome view
@@ -73618,7 +73947,7 @@ ${indent}columns: ${matrix.columns}
    function generateGenomeID(config) {
        if (config.id !== undefined) {
            return config.id
-       } else if (config.fastaURL && isString$2(config.fastaURL) && !config.fastaURL.startsWith("data:")) {
+       } else if (config.fastaURL && isString$3(config.fastaURL) && !config.fastaURL.startsWith("data:")) {
            return config.fastaURL
        } else if (config.fastaURL && config.fastaURL.name) {
            return config.fastaURL.name
@@ -74351,7 +74680,7 @@ ${indent}columns: ${matrix.columns}
            const urlOrFile = options.url || options.file;
 
            let config;
-           if (options.url && isString$2(options.url) && (options.url.startsWith("blob:") || options.url.startsWith("data:"))) {
+           if (options.url && isString$3(options.url) && (options.url.startsWith("blob:") || options.url.startsWith("data:"))) {
                const json = Browser.uncompressSession(options.url);
                config = JSON.parse(json);
            } else {
@@ -74430,7 +74759,7 @@ ${indent}columns: ${matrix.columns}
                return
            }
 
-           const genomeConfig = isString$2(genomeOrReference) ?
+           const genomeConfig = isString$3(genomeOrReference) ?
                await GenomeUtils.expandReference(this.alert, genomeOrReference) :
                genomeOrReference;
 
@@ -74552,7 +74881,7 @@ ${indent}columns: ${matrix.columns}
        }
 
        /**
-        * Load a reference genome object.  This includes the fasta, and optional cytoband, but no tracks.  This method
+        * Load a reference genome object.  This includes the sequence, and optional cytoband, but no tracks.  This method
         * is used by loadGenome and loadSession.
         *
         * @param genomeConfig
@@ -74585,7 +74914,10 @@ ${indent}columns: ${matrix.columns}
 
            const locusFound = await this.search(locus, true);
            if (!locusFound) {
-               throw new Error(`Cannot set initial locus ${locus}`)
+               console.error(`Cannot set initial locus ${locus}`);
+               if(locus !== genome.initialLocus) {
+                   await this.search(genome.initialLocus);
+               }
            }
 
            if (genomeChange) {
@@ -74617,7 +74949,7 @@ ${indent}columns: ${matrix.columns}
 
            // Translate the generic "url" field, used by clients such as igv-webapp
            if (idOrConfig.url) {
-               if (isString$2(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
+               if (isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
                    idOrConfig.hubURL = idOrConfig.url;
                    delete idOrConfig.url;
                } else if ("gbk" === getFileExtension(idOrConfig.url)) {
@@ -74627,11 +74959,11 @@ ${indent}columns: ${matrix.columns}
            }
 
            let genomeConfig;
-           const isHubGenome = idOrConfig.hubURL || (idOrConfig.url && isString$2(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt"));
+           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$2(idOrConfig) || !(idOrConfig.url || idOrConfig.fastaURL || idOrConfig.twoBitURL || idOrConfig.gbkURL)) {
+           } 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 {
@@ -74798,7 +75130,7 @@ ${indent}columns: ${matrix.columns}
        async #loadTrackHelper(config) {
 
            // config might be json
-           if (isString$2(config)) {
+           if (isString$3(config)) {
                config = JSON.parse(config);
            }
 
@@ -74928,7 +75260,7 @@ ${indent}columns: ${matrix.columns}
 
            // Resolve function and promise urls
            let url = await resolveURL(config.url || config.fastaURL);
-           if (isString$2(url)) {
+           if (isString$3(url)) {
                url = url.trim();
            }
 
@@ -74976,7 +75308,7 @@ ${indent}columns: ${matrix.columns}
                        const featureSource = FeatureSource(config, this.genome);
                        config._featureSource = featureSource;    // This is a temp variable, bit of a hack
                        const trackType = await featureSource.trackType();
-                       if (trackType) {
+                       if (trackType && knownTrackTypes().has(trackType)) {
                            type = trackType;
                        } else {
                            type = "annotation";