igv 3.1.1 → 3.1.3

package/dist/igv.esm.js

@@ -19431,7 +19431,7 @@ function doPath(ctx, x, y) {
     ctx.closePath();
 }
 
-/*! @license DOMPurify 3.2.1 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.2.1/LICENSE */
+/*! @license DOMPurify 3.2.3 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.2.3/LICENSE */
 
 const {
   entries,
@@ -19606,7 +19606,6 @@ function lookupGetter(object, prop) {
 }
 
 const html$1 = freeze(['a', 'abbr', 'acronym', 'address', 'area', 'article', 'aside', 'audio', 'b', 'bdi', 'bdo', 'big', 'blink', 'blockquote', 'body', 'br', 'button', 'canvas', 'caption', 'center', 'cite', 'code', 'col', 'colgroup', 'content', 'data', 'datalist', 'dd', 'decorator', 'del', 'details', 'dfn', 'dialog', 'dir', 'div', 'dl', 'dt', 'element', 'em', 'fieldset', 'figcaption', 'figure', 'font', 'footer', 'form', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6', 'head', 'header', 'hgroup', 'hr', 'html', 'i', 'img', 'input', 'ins', 'kbd', 'label', 'legend', 'li', 'main', 'map', 'mark', 'marquee', 'menu', 'menuitem', 'meter', 'nav', 'nobr', 'ol', 'optgroup', 'option', 'output', 'p', 'picture', 'pre', 'progress', 'q', 'rp', 'rt', 'ruby', 's', 'samp', 'section', 'select', 'shadow', 'small', 'source', 'spacer', 'span', 'strike', 'strong', 'style', 'sub', 'summary', 'sup', 'table', 'tbody', 'td', 'template', 'textarea', 'tfoot', 'th', 'thead', 'time', 'tr', 'track', 'tt', 'u', 'ul', 'var', 'video', 'wbr']);
-// SVG
 const svg$1 = freeze(['svg', 'a', 'altglyph', 'altglyphdef', 'altglyphitem', 'animatecolor', 'animatemotion', 'animatetransform', 'circle', 'clippath', 'defs', 'desc', 'ellipse', 'filter', 'font', 'g', 'glyph', 'glyphref', 'hkern', 'image', 'line', 'lineargradient', 'marker', 'mask', 'metadata', 'mpath', 'path', 'pattern', 'polygon', 'polyline', 'radialgradient', 'rect', 'stop', 'style', 'switch', 'symbol', 'text', 'textpath', 'title', 'tref', 'tspan', 'view', 'vkern']);
 const svgFilters = freeze(['feBlend', 'feColorMatrix', 'feComponentTransfer', 'feComposite', 'feConvolveMatrix', 'feDiffuseLighting', 'feDisplacementMap', 'feDistantLight', 'feDropShadow', 'feFlood', 'feFuncA', 'feFuncB', 'feFuncG', 'feFuncR', 'feGaussianBlur', 'feImage', 'feMerge', 'feMergeNode', 'feMorphology', 'feOffset', 'fePointLight', 'feSpecularLighting', 'feSpotLight', 'feTile', 'feTurbulence']);
 // List of SVG elements that are disallowed by default.
@@ -19628,8 +19627,8 @@ const xml = freeze(['xlink:href', 'xml:id', 'xlink:title', 'xml:space', 'xmlns:x
 // eslint-disable-next-line unicorn/better-regex
 const MUSTACHE_EXPR = seal(/\{\{[\w\W]*|[\w\W]*\}\}/gm); // Specify template detection regex for SAFE_FOR_TEMPLATES mode
 const ERB_EXPR = seal(/<%[\w\W]*|[\w\W]*%>/gm);
-const TMPLIT_EXPR = seal(/\${[\w\W]*}/gm);
-const DATA_ATTR = seal(/^data-[\-\w.\u00B7-\uFFFF]/); // eslint-disable-line no-useless-escape
+const TMPLIT_EXPR = seal(/\$\{[\w\W]*}/gm); // eslint-disable-line unicorn/better-regex
+const DATA_ATTR = seal(/^data-[\-\w.\u00B7-\uFFFF]+$/); // 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
 );
@@ -19712,10 +19711,23 @@ const _createTrustedTypesPolicy = function _createTrustedTypesPolicy(trustedType
     return null;
   }
 };
+const _createHooksMap = function _createHooksMap() {
+  return {
+    afterSanitizeAttributes: [],
+    afterSanitizeElements: [],
+    afterSanitizeShadowDOM: [],
+    beforeSanitizeAttributes: [],
+    beforeSanitizeElements: [],
+    beforeSanitizeShadowDOM: [],
+    uponSanitizeAttribute: [],
+    uponSanitizeElement: [],
+    uponSanitizeShadowNode: []
+  };
+};
 function createDOMPurify() {
   let window = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : getGlobal();
   const DOMPurify = root => createDOMPurify(root);
-  DOMPurify.version = '3.2.1';
+  DOMPurify.version = '3.2.3';
   DOMPurify.removed = [];
   if (!window || !window.document || window.document.nodeType !== NODE_TYPE.document) {
     // Not running in a browser, provide a factory function
@@ -19768,7 +19780,7 @@ function createDOMPurify() {
   const {
     importNode
   } = originalDocument;
-  let hooks = {};
+  let hooks = _createHooksMap();
   /**
    * Expose whether this browser supports running the full DOMPurify.
    */
@@ -20197,8 +20209,8 @@ function createDOMPurify() {
       });
     }
     element.removeAttribute(name);
-    // We void attribute values for unremovable "is"" attributes
-    if (name === 'is' && !ALLOWED_ATTR[name]) {
+    // We void attribute values for unremovable "is" attributes
+    if (name === 'is') {
       if (RETURN_DOM || RETURN_DOM_FRAGMENT) {
         try {
           _forceRemove(element);
@@ -20289,11 +20301,8 @@ function createDOMPurify() {
   const _isNode = function _isNode(value) {
     return typeof Node === 'function' && value instanceof Node;
   };
-  function _executeHook(entryPoint, currentNode, data) {
-    if (!hooks[entryPoint]) {
-      return;
-    }
-    arrayForEach(hooks[entryPoint], hook => {
+  function _executeHooks(hooks, currentNode, data) {
+    arrayForEach(hooks, hook => {
       hook.call(DOMPurify, currentNode, data, CONFIG);
     });
   }
@@ -20309,7 +20318,7 @@ function createDOMPurify() {
   const _sanitizeElements = function _sanitizeElements(currentNode) {
     let content = null;
     /* Execute a hook if present */
-    _executeHook('beforeSanitizeElements', currentNode, null);
+    _executeHooks(hooks.beforeSanitizeElements, currentNode, null);
     /* Check if element is clobbered or can clobber */
     if (_isClobbered(currentNode)) {
       _forceRemove(currentNode);
@@ -20318,7 +20327,7 @@ function createDOMPurify() {
     /* Now let's check the element's type and name */
     const tagName = transformCaseFunc(currentNode.nodeName);
     /* Execute a hook if present */
-    _executeHook('uponSanitizeElement', currentNode, {
+    _executeHooks(hooks.uponSanitizeElement, currentNode, {
       tagName,
       allowedTags: ALLOWED_TAGS
     });
@@ -20389,7 +20398,7 @@ function createDOMPurify() {
       }
     }
     /* Execute a hook if present */
-    _executeHook('afterSanitizeElements', currentNode, null);
+    _executeHooks(hooks.afterSanitizeElements, currentNode, null);
     return false;
   };
   /**
@@ -20450,12 +20459,12 @@ function createDOMPurify() {
    */
   const _sanitizeAttributes = function _sanitizeAttributes(currentNode) {
     /* Execute a hook if present */
-    _executeHook('beforeSanitizeAttributes', currentNode, null);
+    _executeHooks(hooks.beforeSanitizeAttributes, currentNode, null);
     const {
       attributes
     } = currentNode;
     /* Check if we have attributes; if not we might have a text node */
-    if (!attributes) {
+    if (!attributes || _isClobbered(currentNode)) {
       return;
     }
     const hookEvent = {
@@ -20481,7 +20490,7 @@ function createDOMPurify() {
       hookEvent.attrValue = value;
       hookEvent.keepAttr = true;
       hookEvent.forceKeepAttr = undefined; // Allows developers to see this is a property they can set
-      _executeHook('uponSanitizeAttribute', currentNode, hookEvent);
+      _executeHooks(hooks.uponSanitizeAttribute, currentNode, hookEvent);
       value = hookEvent.attrValue;
       /* Full DOM Clobbering protection via namespace isolation,
        * Prefix id and name attributes with `user-content-`
@@ -20556,7 +20565,7 @@ function createDOMPurify() {
       } catch (_) {}
     }
     /* Execute a hook if present */
-    _executeHook('afterSanitizeAttributes', currentNode, null);
+    _executeHooks(hooks.afterSanitizeAttributes, currentNode, null);
   };
   /**
    * _sanitizeShadowDOM
@@ -20567,23 +20576,21 @@ function createDOMPurify() {
     let shadowNode = null;
     const shadowIterator = _createNodeIterator(fragment);
     /* Execute a hook if present */
-    _executeHook('beforeSanitizeShadowDOM', fragment, null);
+    _executeHooks(hooks.beforeSanitizeShadowDOM, fragment, null);
     while (shadowNode = shadowIterator.nextNode()) {
       /* Execute a hook if present */
-      _executeHook('uponSanitizeShadowNode', shadowNode, null);
+      _executeHooks(hooks.uponSanitizeShadowNode, shadowNode, null);
       /* Sanitize tags and elements */
-      if (_sanitizeElements(shadowNode)) {
-        continue;
-      }
+      _sanitizeElements(shadowNode);
+      /* Check attributes next */
+      _sanitizeAttributes(shadowNode);
       /* Deep shadow DOM detected */
       if (shadowNode.content instanceof DocumentFragment) {
         _sanitizeShadowDOM(shadowNode.content);
       }
-      /* Check attributes, sanitize if necessary */
-      _sanitizeAttributes(shadowNode);
     }
     /* Execute a hook if present */
-    _executeHook('afterSanitizeShadowDOM', fragment, null);
+    _executeHooks(hooks.afterSanitizeShadowDOM, fragment, null);
   };
   // eslint-disable-next-line complexity
   DOMPurify.sanitize = function (dirty) {
@@ -20669,15 +20676,13 @@ function createDOMPurify() {
     /* Now start iterating over the created document */
     while (currentNode = nodeIterator.nextNode()) {
       /* Sanitize tags and elements */
-      if (_sanitizeElements(currentNode)) {
-        continue;
-      }
+      _sanitizeElements(currentNode);
+      /* Check attributes next */
+      _sanitizeAttributes(currentNode);
       /* Shadow DOM detected, sanitize it */
       if (currentNode.content instanceof DocumentFragment) {
         _sanitizeShadowDOM(currentNode.content);
       }
-      /* Check attributes, sanitize if necessary */
-      _sanitizeAttributes(currentNode);
     }
     /* If we sanitized `dirty` in-place, return it. */
     if (IN_PLACE) {
@@ -20741,21 +20746,16 @@ function createDOMPurify() {
     if (typeof hookFunction !== 'function') {
       return;
     }
-    hooks[entryPoint] = hooks[entryPoint] || [];
     arrayPush(hooks[entryPoint], hookFunction);
   };
   DOMPurify.removeHook = function (entryPoint) {
-    if (hooks[entryPoint]) {
-      return arrayPop(hooks[entryPoint]);
-    }
+    return arrayPop(hooks[entryPoint]);
   };
   DOMPurify.removeHooks = function (entryPoint) {
-    if (hooks[entryPoint]) {
-      hooks[entryPoint] = [];
-    }
+    hooks[entryPoint] = [];
   };
   DOMPurify.removeAllHooks = function () {
-    hooks = {};
+    hooks = _createHooksMap();
   };
   return DOMPurify;
 }
@@ -28388,7 +28388,7 @@ class VcfParser {
         while ((line = await dataWrapper.nextLine()) !== undefined) {
             if (line && !line.startsWith("#")) {
 
-                const tokens = line.split("\t");
+                const tokens = line.trim().split("\t");
                 if (tokens.length === nExpectedColumns) {
                     const variant = new Variant(tokens);
                     variant.header = this.header;       // Keep a pointer to the header to interpret fields for popup text
@@ -33157,7 +33157,7 @@ class BWReader {
         if (this.type === "bigwig") {
             return "wig"
         } else {
-            return this.autoSql && this.autoSql.table === "chromatinInteract" ? "interact" : "annotation"
+            return this.autoSql && ("interact" === this.autoSql.table || "chromatinInteract" === this.autoSql.table) ? "interact" : "annotation"
         }
     }
 
@@ -34847,7 +34847,7 @@ class TextFeatureSource extends BaseFeatureSource {
         // indicating whole chromosome should be read at once.
         if ((!visibilityWindow || visibilityWindow <= 0) && this.config.expandQuery !== false) {
             // Whole chromosome
-            const chromosome = this.genome ? this.genome.getChromosome(queryChr) : undefined;
+            const chromosome = this.genome ? this.genome.getChromosome(chr) : undefined;
             intervalStart = 0;
             intervalEnd = Math.max(chromosome ? chromosome.bpLength : Number.MAX_SAFE_INTEGER, end);
         } else if (visibilityWindow > (end - start) && this.config.expandQuery !== false) {
@@ -40057,8 +40057,8 @@ class TrackViewport extends Viewport {
     checkZoomIn() {
 
         const zoomedOutOfWindow = () => {
-            if (this.referenceFrame.chr.toLowerCase() === "all" && !this.trackView.track.supportsWholeGenome) {
-                return true
+            if (this.referenceFrame.chr.toLowerCase() === "all") {
+                return !this.trackView.track.supportsWholeGenome
             } else {
                 const visibilityWindow = this.trackView.track.visibilityWindow;
                 return (
@@ -60022,7 +60022,7 @@ class InteractionTrack extends TrackBase {
     }
 
     get supportsWholeGenome() {
-        return true
+        return typeof this.featureSource.supportsWholeGenome === 'function' ? this.featureSource.supportsWholeGenome() : true;
     }
 
     async getFeatures(chr, start, end) {
@@ -72568,7 +72568,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.1.1";
+const _version = "3.1.3";
 function version() {
     return _version
 }
@@ -75186,6 +75186,188 @@ async function translateSession(juiceboxSession) {
 
 }
 
+/**
+ * Default chromosome aliases, mostly 1<->chr1 etc.  Used if chrom alias file is not supplied.
+ *
+ */
+
+class ChromAliasDefaults {
+
+    aliasRecordCache = new Map()
+
+    constructor(id, chromosomeNames) {
+        this.genomeID = id;
+        this.update(id, chromosomeNames);
+    }
+
+    async preload() {
+        // no-op
+    }
+
+    /**
+     * Return the canonical chromosome name for the alias.  If none found return the alias
+     *
+     * @param alias
+     * @returns {*}
+     */
+    getChromosomeName(alias) {
+        return this.aliasRecordCache.has(alias) ? this.aliasRecordCache.get(alias).chr : alias
+    }
+
+    /**
+     * Return an alternate chromosome name (alias).
+     *
+     * @param chr
+     * @param nameSet -- The name set, e.g. "ucsc"
+     * @returns {*|undefined}
+     */
+    getChromosomeAlias(chr, nameSet) {
+        const aliasRecord = this.aliasRecordCache.get(chr);
+        return aliasRecord ? aliasRecord[nameSet] || chr : chr
+    }
+
+    update(id, chromosomeNames) {
+
+        if (chromosomeNames) {
+            const aliasRecords = [];
+            for (let name of chromosomeNames) {
+
+                if(this.aliasRecordCache.has(name)) {
+                    continue;
+                }
+
+                const record = {chr: name};
+                aliasRecords.push(record);
+
+                if (name.startsWith("gi|")) {
+                    // NCBI
+                    const alias = ChromAliasDefaults.getNCBIName(name);
+                    record["ncbi-gi-versioned"] = alias;
+
+                    // Also strip version number out, if present
+                    const dotIndex = alias.lastIndexOf('.');
+                    if (dotIndex > 0) {
+                        const alias = alias.substring(0, dotIndex);
+                        record["ncbi-gi"] = alias;
+                    }
+                } else {
+
+                    if (name === "chrM") {
+                        record["ncbi"] = "MT";
+                    } else if (name === "MT") {
+                        record["ucsc"] = "chrM";
+                    } else if (name.toLowerCase().startsWith("chr") && Number.isInteger(Number(name.substring(3)))) {
+                        record["ncbi"] = name.substring(3);
+                    } else if (Number.isInteger(Number(name))) {
+                        record["ucsc"] = "chr" + name;
+                    }
+
+                    // Special cases for human and mouse
+                    if (id.startsWith("hg") || id.startsWith("GRCh") || id === "1kg_ref" || id === "b37") {
+                        switch (name) {
+                            case "23":
+                                record["ucsc"] = "chrX";
+                                record["assembly"] = "X";
+                                break
+                            case "24":
+                                record["ucsc"] = "chrY";
+                                record["assembly"] = "Y";
+                                break
+                            case "chrX":
+                                record["ncbi"] = "23";
+                                record["assembly"] = "X";
+                                break
+                            case "chrY":
+                                record["ncbi"] = "24";
+                                record["assembly"] = "Y";
+                                break
+                            case "X":
+                                record["ucsc"] = "chrX";
+                                record["ncbi"] = "23";
+                                break
+                            case "Y":
+                                record["ucsc"] = "chrY";
+                                record["ncbi"] = "24";
+                                break
+
+                        }
+                    } else if (id.startsWith("mm") || id.startsWith("GRCm") || id.startsWith("rheMac")) {
+                        switch (name) {
+                            case "21":
+                                record["ucsc"] = "chrX";
+                                record["assembly"] = "X";
+                                break
+                            case "22":
+                                record["ucsc"] = "chrY";
+                                record["assembly"] = "Y";
+                                break
+                            case "chrX":
+                                record["ncbi"] = "21";
+                                record["assembly"] = "X";
+                                break
+                            case "chrY":
+                                record["ncbi"] = "22";
+                                record["assembly"] = "Y";
+                                break
+                            case "X":
+                                record["ucsc"] = "chrX";
+                                record["ncbi"] = "21";
+                                break
+                            case "Y":
+                                record["ucsc"] = "chrY";
+                                record["ncbi"] = "22";
+                                break
+
+                        }
+                    }
+                }
+            }
+
+
+            for (let rec of aliasRecords) {
+                ChromAliasDefaults.addCaseAliases(rec);
+                for (let a of Object.values(rec)) {
+                    this.aliasRecordCache.set(a, rec);
+                }
+            }
+
+        }
+    }
+
+    search(alias) {
+        return this.aliasRecordCache.get(alias)
+
+    }
+
+    /**
+     * Extract the user friendly name from an NCBI accession
+     * example: gi|125745044|ref|NC_002229.3|  =>  NC_002229.3
+     */
+    static getNCBIName(name) {
+        const tokens = name.split("\\|");
+        return tokens[tokens.length - 1]
+    }
+
+    static addCaseAliases(aliasRecord) {
+
+            // Add some aliases for case insensitivy
+            const upper = aliasRecord.chr.toUpperCase();
+            const lower = aliasRecord.chr.toLowerCase();
+            const cap = aliasRecord.chr.charAt(0).toUpperCase() + aliasRecord.chr.slice(1);
+            if(aliasRecord.chr !== upper) {
+                aliasRecord["_uppercase"] = upper;
+            }
+            if(aliasRecord.chr !== lower) {
+                aliasRecord["_lowercase"] = lower;
+            }
+            if(aliasRecord.chr !== cap) {
+                aliasRecord["_cap"] = cap;
+            }
+
+    }
+
+}
+
 /**
  * Chromosome alias source backed by a UCSC bigbed file
  *
@@ -75248,6 +75430,7 @@ class ChromAliasBB {
         if (!this.aliasRecordCache.has(alias)) {
             const aliasRecord = await this.reader.search(alias);
             if (aliasRecord) {
+                ChromAliasDefaults.addCaseAliases(aliasRecord);
                 for (let key of Object.keys(aliasRecord)) {
                     if ("start" !== key && "end" !== key) {
                         this.aliasRecordCache.set(aliasRecord[key], aliasRecord);
@@ -75338,14 +75521,16 @@ class ChromAliasFile {
                 }
 
                 const aliasRecord = {chr};
+                ChromAliasDefaults.addCaseAliases(aliasRecord);
                 for (let i = 0; i < tokens.length; i++) {
                     const key = this.headings ? this.headings[i] : i;
                     aliasRecord[key] = tokens[i];
-                    this.aliasRecordCache.set(tokens[i], aliasRecord);
                 }
 
-                this.aliasRecordCache.set(chr.toLowerCase(), aliasRecord);
-                this.aliasRecordCache.set(chr.toUpperCase(), aliasRecord);
+                for (let a of Object.values(aliasRecord)) {
+                    this.aliasRecordCache.set(a, aliasRecord);
+                }
+
             }
         }
     }
@@ -75503,170 +75688,6 @@ class CytobandFile {
 
 }
 
-/**
- * Default chromosome aliases, mostly 1<->chr1 etc.  Used if chrom alias file is not supplied.
- *
- */
-
-class ChromAliasDefaults {
-
-    aliasRecordCache = new Map()
-
-    constructor(id, chromosomeNames) {
-        this.genomeID = id;
-        this.update(id, chromosomeNames);
-    }
-
-    async preload() {
-        // no-op
-    }
-
-    /**
-     * Return the canonical chromosome name for the alias.  If none found return the alias
-     *
-     * @param alias
-     * @returns {*}
-     */
-    getChromosomeName(alias) {
-        return this.aliasRecordCache.has(alias) ? this.aliasRecordCache.get(alias).chr : alias
-    }
-
-    /**
-     * Return an alternate chromosome name (alias).
-     *
-     * @param chr
-     * @param nameSet -- The name set, e.g. "ucsc"
-     * @returns {*|undefined}
-     */
-    getChromosomeAlias(chr, nameSet) {
-        const aliasRecord = this.aliasRecordCache.get(chr);
-        return aliasRecord ? aliasRecord[nameSet] || chr : chr
-    }
-
-    update(id, chromosomeNames) {
-
-        if (chromosomeNames) {
-            const aliasRecords = [];
-            for (let name of chromosomeNames) {
-
-                if(this.aliasRecordCache.has(name)) {
-                    continue;
-                }
-
-                const record = {chr: name};
-                aliasRecords.push(record);
-
-                if (name.startsWith("gi|")) {
-                    // NCBI
-                    const alias = ChromAliasDefaults.getNCBIName(name);
-                    record["ncbi-gi-versioned"] = alias;
-
-                    // Also strip version number out, if present
-                    const dotIndex = alias.lastIndexOf('.');
-                    if (dotIndex > 0) {
-                        const alias = alias.substring(0, dotIndex);
-                        record["ncbi-gi"] = alias;
-                    }
-                } else {
-
-                    if (name === "chrM") {
-                        record["ncbi"] = "MT";
-                    } else if (name === "MT") {
-                        record["ucsc"] = "chrM";
-                    } else if (name.toLowerCase().startsWith("chr") && Number.isInteger(Number(name.substring(3)))) {
-                        record["ncbi"] = name.substring(3);
-                    } else if (Number.isInteger(Number(name))) {
-                        record["ucsc"] = "chr" + name;
-                    }
-
-                    // Special cases for human and mouse
-                    if (id.startsWith("hg") || id.startsWith("GRCh") || id === "1kg_ref" || id === "b37") {
-                        switch (name) {
-                            case "23":
-                                record["ucsc"] = "chrX";
-                                record["assembly"] = "X";
-                                break
-                            case "24":
-                                record["ucsc"] = "chrY";
-                                record["assembly"] = "Y";
-                                break
-                            case "chrX":
-                                record["ncbi"] = "23";
-                                record["assembly"] = "X";
-                                break
-                            case "chrY":
-                                record["ncbi"] = "24";
-                                record["assembly"] = "Y";
-                                break
-                            case "X":
-                                record["ucsc"] = "chrX";
-                                record["ncbi"] = "23";
-                                break
-                            case "Y":
-                                record["ucsc"] = "chrY";
-                                record["ncbi"] = "24";
-                                break
-
-                        }
-                    } else if (id.startsWith("mm") || id.startsWith("GRCm") || id.startsWith("rheMac")) {
-                        switch (name) {
-                            case "21":
-                                record["ucsc"] = "chrX";
-                                record["assembly"] = "X";
-                                break
-                            case "22":
-                                record["ucsc"] = "chrY";
-                                record["assembly"] = "Y";
-                                break
-                            case "chrX":
-                                record["ncbi"] = "21";
-                                record["assembly"] = "X";
-                                break
-                            case "chrY":
-                                record["ncbi"] = "22";
-                                record["assembly"] = "Y";
-                                break
-                            case "X":
-                                record["ucsc"] = "chrX";
-                                record["ncbi"] = "21";
-                                break
-                            case "Y":
-                                record["ucsc"] = "chrY";
-                                record["ncbi"] = "22";
-                                break
-
-                        }
-                    }
-                }
-            }
-
-            for (let rec of aliasRecords) {
-                for (let a of Object.values(rec)) {
-                    this.aliasRecordCache.set(a, rec);
-                }
-                this.aliasRecordCache.set(rec.chr.toLowerCase(), rec);
-                this.aliasRecordCache.set(rec.chr.toUpperCase(), rec);
-            }
-
-        }
-    }
-
-    search(alias) {
-        return this.aliasRecordCache.get(alias)
-
-    }
-
-    /**
-     * Extract the user friendly name from an NCBI accession
-     * example: gi|125745044|ref|NC_002229.3|  =>  NC_002229.3
-     */
-    static getNCBIName(name) {
-        const tokens = name.split("\\|");
-        return tokens[tokens.length - 1]
-    }
-
-}
-
 /**
  * The Genome class represents an assembly and consists of the following elements
  *   sequence - Object representing the DNA sequence
@@ -75848,6 +75869,21 @@ class Genome {
             if (!aliasRecord && chr !== chr.toLowerCase()) {
                 aliasRecord = await this.chromAlias.search(chr.toLowerCase());
             }
+            if(aliasRecord) {
+                // Add some aliases for case insensitivy
+                const upper = aliasRecord.chr.toUpperCase();
+                const lower = aliasRecord.chr.toLowerCase();
+                const cap = aliasRecord.chr.charAt(0).toUpperCase() + aliasRecord.chr.slice(1);
+                if(aliasRecord.chr !== upper) {
+                    aliasRecord["_uppercase"] = upper;
+                }
+                if(aliasRecord.chr !== lower) {
+                    aliasRecord["_lowercase"] = lower;
+                }
+                if(aliasRecord.chr !== cap) {
+                    aliasRecord["_cap"] = cap;
+                }
+            }
             this.#aliasRecordCache.set(chr, aliasRecord);  // Set even if undefined to prevent recurrent searches
             return aliasRecord
         }