igv 3.3.0 → 3.4.0

package/dist/igv.esm.js

@@ -373,7 +373,7 @@ class Dialog {
  * @param x
  * @returns {boolean}
  */
-function isString$2(x) {
+function isString$3(x) {
     return typeof x === "string" || x instanceof String
 }
 
@@ -473,7 +473,7 @@ function getFilename$2(urlOrFile) {
 
     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);
@@ -10678,7 +10678,7 @@ const isNumber = function (num) {
 };
 
 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")
@@ -10720,7 +10720,7 @@ function prettyBasePairNumber(raw) {
 
 
 function isDataURL(obj) {
-    return (isString$2(obj) && obj.startsWith("data:"))
+    return (isString$3(obj) && obj.startsWith("data:"))
 }
 
 function createColumn(columnContainer, className) {
@@ -10946,7 +10946,7 @@ function createMenuElements$1(itemList, popover) {
     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,
@@ -11150,7 +11150,7 @@ const ERB_EXPR = seal(/<%[\w\W]*|[\w\W]*%>/gm);
 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
@@ -11247,7 +11247,7 @@ const _createHooksMap = function _createHooksMap() {
 function createDOMPurify() {
   let window = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : getGlobal();
   const DOMPurify = root => createDOMPurify(root);
-  DOMPurify.version = '3.2.5';
+  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
@@ -11486,8 +11486,8 @@ function createDOMPurify() {
     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
@@ -11852,7 +11852,7 @@ function createDOMPurify() {
       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;
     }
@@ -12004,7 +12004,8 @@ function createDOMPurify() {
         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;
@@ -12030,10 +12031,9 @@ function createDOMPurify() {
       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 */
@@ -12050,6 +12050,7 @@ function createDOMPurify() {
       /* 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 */
@@ -12070,19 +12071,23 @@ function createDOMPurify() {
         }
       }
       /* 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);
@@ -16903,7 +16908,7 @@ function findFeatureAfterCenter(featureList, center, direction = true) {
  */
 
 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 {
@@ -16975,7 +16980,7 @@ class TrackBase {
             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);
         }
 
@@ -20897,7 +20902,7 @@ class FeatureFileReader {
  * THE SOFTWARE.
  */
 
-const isString$1 = isString$2;
+const isString$2 = isString$3;
 
 
 class CustomServiceReader {
@@ -20936,7 +20941,7 @@ class CustomServiceReader {
         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;
@@ -23019,7 +23024,7 @@ class BWReader {
                     // 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
                         }
                     }
@@ -23317,7 +23322,7 @@ class BWReader {
 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();
@@ -27643,7 +27648,7 @@ class FeatureTrack extends TrackBase {
                         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>`;
@@ -28287,7 +28292,7 @@ class BlatTrack extends FeatureTrack {
     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;
@@ -28304,7 +28309,7 @@ class BlatTrack extends FeatureTrack {
         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,
@@ -28379,7 +28384,7 @@ async function createBlatTrack({sequence, browser, name, title}) {
 
     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});
 
@@ -30609,13 +30614,6 @@ class TrackDbHub {
         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;
@@ -30955,6 +30953,7 @@ function parseMetadata(metadata) {
 
 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"],
@@ -30991,12 +30990,16 @@ class Hub {
         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;
         }
     }
 
@@ -31098,6 +31101,10 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
             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 {
@@ -31491,8 +31498,8 @@ function getHost(url) {
     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 = {
 
@@ -31517,7 +31524,7 @@ const GenomeUtils = {
                 } 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);
@@ -31547,7 +31554,7 @@ const GenomeUtils = {
     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) {
@@ -31556,7 +31563,7 @@ const GenomeUtils = {
         }
 
         let genomeID;
-        if (isString$2(idOrConfig)) {
+        if (isString$3(idOrConfig)) {
             genomeID = idOrConfig;
         } else if (idOrConfig.genome) {
             genomeID = idOrConfig.genome;
@@ -32502,7 +32509,7 @@ class TrackViewport extends Viewport {
         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) {
@@ -40992,6 +40999,9 @@ function doSortByAttributes(sampleInfo, sampleKeys) {
     return true
 }
 
+/**
+ * Track for segmented copy number, mut, maf and shoebox files.
+ */
 class SegTrack extends TrackBase {
 
     #sortDirections = new Map()
@@ -41139,7 +41149,10 @@ class SegTrack extends TrackBase {
                 }, 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/>');
@@ -41170,12 +41183,75 @@ class SegTrack extends TrackBase {
 
     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
@@ -41183,8 +41259,10 @@ class SegTrack extends TrackBase {
 
         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);
@@ -41199,6 +41277,7 @@ class SegTrack extends TrackBase {
 
         IGVGraphics.fillRect(context, 0, pixelTop, pixelWidth, pixelHeight, {'fillStyle': "rgb(255, 255, 255)"});
 
+
         if (features && features.length > 0) {
 
             this.checkForLog(features);
@@ -41210,14 +41289,15 @@ class SegTrack extends TrackBase {
 
             // 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
 
@@ -41355,7 +41435,7 @@ class SegTrack extends TrackBase {
         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
     }
 
     /**
@@ -41364,16 +41444,38 @@ class SegTrack extends TrackBase {
     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});
         }
@@ -41382,62 +41484,40 @@ class SegTrack extends TrackBase {
         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);
@@ -41506,7 +41586,7 @@ class SegTrack extends TrackBase {
             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: () => {
@@ -41518,7 +41598,6 @@ class SegTrack extends TrackBase {
                         end: Math.floor(genomicLocation + bpWidth)
                     };
                     sortHandler(sort);
-                    this.config.sort = sort;
                 }
             }
         })
@@ -41688,13 +41767,13 @@ class PairedAlignment {
         }
     }
 
-    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
     }
@@ -43408,7 +43487,7 @@ class BamAlignment {
     isNegativeStrand() {
         return (this.flags & READ_STRAND_FLAG$2) !== 0
     }
-    
+
     isMateNegativeStrand() {
         return (this.flags & MATE_STRAND_FLAG$2) !== 0
     }
@@ -43456,7 +43535,7 @@ class BamAlignment {
         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).
@@ -43539,15 +43618,20 @@ class BamAlignment {
             }
         }
 
-        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)});
@@ -43555,18 +43639,18 @@ class BamAlignment {
         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}%`);
                     }
                 }
@@ -43656,7 +43740,7 @@ class BamAlignment {
             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 {
@@ -43669,7 +43753,7 @@ class BamAlignment {
         return this.baseModificationSets
     }
 
-     getGroupValue( groupBy, tag, expectedPairOrientation) {
+    getGroupValue(groupBy, tag, expectedPairOrientation) {
 
         const al = this;
         switch (groupBy) {
@@ -43706,7 +43790,7 @@ class BamAlignment {
         }
     }
 
-    positionToReadIndex( position) {
+    positionToReadIndex(position) {
         const block = blockAtGenomicLocation(this.blocks, position);
         if (block) {
             return (position - block.start) + block.seqOffset
@@ -45685,7 +45769,7 @@ function inferFileFormatFromName(fn) {
 
 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)
@@ -45844,7 +45928,7 @@ class BamSource {
             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}`);
@@ -48156,7 +48240,7 @@ class AlignmentTrack extends TrackBase {
         highlightColor: undefined,
         minTLEN: undefined,
         maxTLEN: undefined,
-        tagColorPallete: "Set1"
+        tagColorPallete: "Set1",
     }
 
     _colorTables = new Map()
@@ -48171,6 +48255,18 @@ class AlignmentTrack extends TrackBase {
             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;
@@ -48731,7 +48827,7 @@ class AlignmentTrack extends TrackBase {
 
     popupData(clickState) {
         const clickedObject = this.getClickedObject(clickState);
-        return clickedObject ? clickedObject.popupData(clickState.genomicLocation) : undefined
+        return clickedObject?.popupData(clickState.genomicLocation, this.hiddenTags, this.showTags)
     };
 
     /**
@@ -48762,7 +48858,10 @@ class AlignmentTrack extends TrackBase {
             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));
@@ -49488,14 +49587,19 @@ class AlignmentTrack extends TrackBase {
             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
         }
@@ -65712,7 +65816,7 @@ function autoscale(chr, featureArrays) {
  * THE SOFTWARE.
  */
 
-const isString = isString$2;
+const isString$1 = isString$3;
 
 const DEFAULT_VISIBILITY_WINDOW = 1000000;
 const TOP_MARGIN = 10;
@@ -65835,7 +65939,7 @@ class VariantTrack extends TrackBase {
         }
         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();
@@ -69719,6 +69823,9 @@ const trackFunctions =
         ['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*
@@ -70211,7 +70318,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.3.0";
+const _version = "3.4.0";
 function version() {
     return _version
 }
@@ -70262,7 +70369,7 @@ class ChromosomeSelectWidget {
                 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);
@@ -72067,6 +72174,26 @@ class ROIMenu {
         }
 
 
+        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/>',
@@ -72075,7 +72202,7 @@ class ROIMenu {
                     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();
@@ -73248,6 +73375,189 @@ class CytobandFile {
 
 }
 
+/**
+ * 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"],
@@ -73269,6 +73579,7 @@ class Genome {
 
     static async createGenome(options, browser) {
 
+        updateReference(options);
         const genome = new Genome(options, browser);
         await genome.init();
         return genome
@@ -73292,7 +73603,6 @@ class Genome {
         // 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) {
@@ -73336,10 +73646,14 @@ class Genome {
                 } 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
@@ -73612,7 +73926,7 @@ function trimSmallChromosomes(chromosomes) {
 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
@@ -74345,7 +74659,7 @@ class Browser {
         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 {
@@ -74424,7 +74738,7 @@ class Browser {
             return
         }
 
-        const genomeConfig = isString$2(genomeOrReference) ?
+        const genomeConfig = isString$3(genomeOrReference) ?
             await GenomeUtils.expandReference(this.alert, genomeOrReference) :
             genomeOrReference;
 
@@ -74546,7 +74860,7 @@ class Browser {
     }
 
     /**
-     * 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
@@ -74611,7 +74925,7 @@ class Browser {
 
         // 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)) {
@@ -74621,11 +74935,11 @@ class Browser {
         }
 
         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 {
@@ -74792,7 +75106,7 @@ class Browser {
     async #loadTrackHelper(config) {
 
         // config might be json
-        if (isString$2(config)) {
+        if (isString$3(config)) {
             config = JSON.parse(config);
         }
 
@@ -74922,7 +75236,7 @@ class Browser {
 
         // Resolve function and promise urls
         let url = await resolveURL(config.url || config.fastaURL);
-        if (isString$2(url)) {
+        if (isString$3(url)) {
             url = url.trim();
         }
 
@@ -74970,7 +75284,7 @@ class Browser {
                     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";