igv 3.1.1 → 3.1.3

package/dist/igv.js

@@ -19437,7 +19437,7 @@
        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,
@@ -19612,7 +19612,6 @@
    }
 
    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$1 = freeze(['svg', 'a', 'altglyph', 'altglyphdef', 'altglyphitem', 'animatecolor', 'animatemotion', 'animatetransform', 'circle', 'clippath', 'defs', 'desc', 'ellipse', 'filter', 'font', 'g', 'glyph', 'glyphref', 'hkern', 'image', 'line', 'lineargradient', 'marker', 'mask', 'metadata', 'mpath', 'path', 'pattern', 'polygon', 'polyline', 'radialgradient', 'rect', 'stop', 'style', 'switch', 'symbol', 'text', 'textpath', 'title', 'tref', 'tspan', 'view', 'vkern']);
    const svgFilters = freeze(['feBlend', 'feColorMatrix', 'feComponentTransfer', 'feComposite', 'feConvolveMatrix', 'feDiffuseLighting', 'feDisplacementMap', 'feDistantLight', 'feDropShadow', 'feFlood', 'feFuncA', 'feFuncB', 'feFuncG', 'feFuncR', 'feGaussianBlur', 'feImage', 'feMerge', 'feMergeNode', 'feMorphology', 'feOffset', 'fePointLight', 'feSpecularLighting', 'feSpotLight', 'feTile', 'feTurbulence']);
    // List of SVG elements that are disallowed by default.
@@ -19634,8 +19633,8 @@
    // eslint-disable-next-line unicorn/better-regex
    const MUSTACHE_EXPR = seal(/\{\{[\w\W]*|[\w\W]*\}\}/gm); // Specify template detection regex for SAFE_FOR_TEMPLATES mode
    const ERB_EXPR = seal(/<%[\w\W]*|[\w\W]*%>/gm);
-   const TMPLIT_EXPR = seal(/\${[\w\W]*}/gm);
-   const DATA_ATTR = seal(/^data-[\-\w.\u00B7-\uFFFF]/); // eslint-disable-line no-useless-escape
+   const TMPLIT_EXPR = seal(/\$\{[\w\W]*}/gm); // eslint-disable-line unicorn/better-regex
+   const DATA_ATTR = seal(/^data-[\-\w.\u00B7-\uFFFF]+$/); // 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
    );
@@ -19718,10 +19717,23 @@
        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
@@ -19774,7 +19786,7 @@
      const {
        importNode
      } = originalDocument;
-     let hooks = {};
+     let hooks = _createHooksMap();
      /**
       * Expose whether this browser supports running the full DOMPurify.
       */
@@ -20203,8 +20215,8 @@
          });
        }
        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);
@@ -20295,11 +20307,8 @@
      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);
        });
      }
@@ -20315,7 +20324,7 @@
      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);
@@ -20324,7 +20333,7 @@
        /* 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
        });
@@ -20395,7 +20404,7 @@
          }
        }
        /* Execute a hook if present */
-       _executeHook('afterSanitizeElements', currentNode, null);
+       _executeHooks(hooks.afterSanitizeElements, currentNode, null);
        return false;
      };
      /**
@@ -20456,12 +20465,12 @@
       */
      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 = {
@@ -20487,7 +20496,7 @@
          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-`
@@ -20562,7 +20571,7 @@
          } catch (_) {}
        }
        /* Execute a hook if present */
-       _executeHook('afterSanitizeAttributes', currentNode, null);
+       _executeHooks(hooks.afterSanitizeAttributes, currentNode, null);
      };
      /**
       * _sanitizeShadowDOM
@@ -20573,23 +20582,21 @@
        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) {
@@ -20675,15 +20682,13 @@
        /* 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) {
@@ -20747,21 +20752,16 @@
        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;
    }
@@ -28394,7 +28394,7 @@
            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
@@ -33163,7 +33163,7 @@
            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"
            }
        }
 
@@ -34853,7 +34853,7 @@
            // 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) {
@@ -40063,8 +40063,8 @@
        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 (
@@ -60028,7 +60028,7 @@
        }
 
        get supportsWholeGenome() {
-           return true
+           return typeof this.featureSource.supportsWholeGenome === 'function' ? this.featureSource.supportsWholeGenome() : true;
        }
 
        async getFeatures(chr, start, end) {
@@ -72574,7 +72574,7 @@
        })
    }
 
-   const _version = "3.1.1";
+   const _version = "3.1.3";
    function version() {
        return _version
    }
@@ -75192,6 +75192,188 @@
 
    }
 
+   /**
+    * 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
     *
@@ -75254,6 +75436,7 @@
            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);
@@ -75344,14 +75527,16 @@
                    }
 
                    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);
+                   }
+
                }
            }
        }
@@ -75509,170 +75694,6 @@
 
    }
 
-   /**
-    * 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
@@ -75854,6 +75875,21 @@
                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
            }