npm - igv - Versions diffs - 3.3.0 → 3.4.0 - Mend

igv 3.3.0 → 3.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (8) hide show

package/dist/igv.js CHANGED Viewed

@@ -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;
@@ -23025,7 +23030,7 @@
                        // 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
                            }
                        }
@@ -23323,7 +23328,7 @@
    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();
@@ -27649,7 +27654,7 @@
                            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 +28298,7 @@
        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 +28315,7 @@
            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 +28390,7 @@
        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});
@@ -30615,13 +30620,6 @@
            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 +30959,7 @@
    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 +30996,16 @@
            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 +31107,10 @@
                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 {
@@ -31497,8 +31504,8 @@
        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 +31530,7 @@
                    } 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 +31560,7 @@
        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 +31569,7 @@
            }
            let genomeID;
-           if (isString$2(idOrConfig)) {
+           if (isString$3(idOrConfig)) {
                genomeID = idOrConfig;
            } else if (idOrConfig.genome) {
                genomeID = idOrConfig.genome;
@@ -32508,7 +32515,7 @@
            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 +41005,9 @@
        return true
    }
+   /**
+    * Track for segmented copy number, mut, maf and shoebox files.
+    */
    class SegTrack extends TrackBase {
        #sortDirections = new Map()
@@ -41145,7 +41155,10 @@
                    }, 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 +41189,75 @@
        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 +41265,10 @@
            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 +41283,7 @@
            IGVGraphics.fillRect(context, 0, pixelTop, pixelWidth, pixelHeight, {'fillStyle': "rgb(255, 255, 255)"});
            if (features && features.length > 0) {
                this.checkForLog(features);
@@ -41216,14 +41295,15 @@
                // 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 +41441,7 @@
            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 +41450,38 @@
        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 +41490,40 @@
            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 +41592,7 @@
                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 +41604,6 @@
                            end: Math.floor(genomicLocation + bpWidth)
                        };
                        sortHandler(sort);
-                       this.config.sort = sort;
                    }
                }
            })
@@ -41694,13 +41773,13 @@
            }
        }
-       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 +43493,7 @@
        isNegativeStrand() {
            return (this.flags & READ_STRAND_FLAG$2) !== 0
        }
        isMateNegativeStrand() {
            return (this.flags & MATE_STRAND_FLAG$2) !== 0
        }
@@ -43462,7 +43541,7 @@
            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 +43624,20 @@
                }
            }
-           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$1(1 + genomicLocation)});
@@ -43561,18 +43645,18 @@
            nameValues.push({name: 'Base Quality:', value: this.readBaseQualityAt(genomicLocation)});
            const bmSets = this.getBaseModificationSets();
-           if(bmSets) {
+           if (bmSets) {
                const i = this.positionToReadIndex(genomicLocation);
-               if(undefined !== i) {
+               if (undefined !== i) {
                    let found = false;
                    for (let bmSet of bmSets) {
                        if (bmSet.containsPosition(i)) {
-                           if(!found) {
+                           if (!found) {
                                nameValues.push('<hr/>');
                                nameValues.push('<b>Base modifications:</b>');
                                found = true;
                            }
-                           const lh = Math.round((100/255) * byteToUnsignedInt(bmSet.likelihoods.get(i)));
+                           const lh = Math.round((100 / 255) * byteToUnsignedInt(bmSet.likelihoods.get(i)));
                            nameValues.push(`${bmSet.fullName()} @ likelihood =  ${lh}%`);
                        }
                    }
@@ -43662,7 +43746,7 @@
                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 +43759,7 @@
            return this.baseModificationSets
        }
-        getGroupValue( groupBy, tag, expectedPairOrientation) {
+       getGroupValue(groupBy, tag, expectedPairOrientation) {
            const al = this;
            switch (groupBy) {
@@ -43712,7 +43796,7 @@
            }
        }
-       positionToReadIndex( position) {
+       positionToReadIndex(position) {
            const block = blockAtGenomicLocation(this.blocks, position);
            if (block) {
                return (position - block.start) + block.seqOffset
@@ -45691,7 +45775,7 @@
    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 +45934,7 @@
                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 +48246,7 @@
            highlightColor: undefined,
            minTLEN: undefined,
            maxTLEN: undefined,
-           tagColorPallete: "Set1"
+           tagColorPallete: "Set1",
        }
        _colorTables = new Map()
@@ -48177,6 +48261,18 @@
                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 +48833,7 @@
        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 +48864,10 @@
                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));
@@ -49494,14 +49593,19 @@
                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 +65822,7 @@ ${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 +65945,7 @@ ${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 +69829,9 @@ ${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 +70324,7 @@ ${indent}columns: ${matrix.columns}
        })
    }
-   const _version = "3.3.0";
+   const _version = "3.4.0";
    function version() {
        return _version
    }
@@ -70268,7 +70375,7 @@ ${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 +72180,26 @@ ${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 +72208,7 @@ ${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 +73381,189 @@ ${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 +73585,7 @@ ${indent}columns: ${matrix.columns}
        static async createGenome(options, browser) {
+           updateReference(options);
            const genome = new Genome(options, browser);
            await genome.init();
            return genome
@@ -73298,7 +73609,6 @@ ${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 +73652,14 @@ ${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 +73932,7 @@ ${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 +74665,7 @@ ${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 +74744,7 @@ ${indent}columns: ${matrix.columns}
                return
            }
-           const genomeConfig = isString$2(genomeOrReference) ?
+           const genomeConfig = isString$3(genomeOrReference) ?
                await GenomeUtils.expandReference(this.alert, genomeOrReference) :
                genomeOrReference;
@@ -74552,7 +74866,7 @@ ${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
@@ -74617,7 +74931,7 @@ ${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 +74941,11 @@ ${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 +75112,7 @@ ${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 +75242,7 @@ ${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 +75290,7 @@ ${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";