igv 3.2.5 → 3.2.6

package/dist/igv.js

@@ -10952,7 +10952,7 @@
        return list;
    }
 
-   /*! @license DOMPurify 3.2.4 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.2.4/LICENSE */
+   /*! @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 */
 
    const {
      entries,
@@ -11012,6 +11012,9 @@
     */
    function unapply(func) {
      return function (thisArg) {
+       if (thisArg instanceof RegExp) {
+         thisArg.lastIndex = 0;
+       }
        for (var _len = arguments.length, args = new Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) {
          args[_key - 1] = arguments[_key];
        }
@@ -11250,7 +11253,7 @@
    function createDOMPurify() {
      let window = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : getGlobal();
      const DOMPurify = root => createDOMPurify(root);
-     DOMPurify.version = '3.2.4';
+     DOMPurify.version = '3.2.5';
      DOMPurify.removed = [];
      if (!window || !window.document || window.document.nodeType !== NODE_TYPE.document || !window.Element) {
        // Not running in a browser, provide a factory function
@@ -11855,7 +11858,7 @@
          allowedTags: ALLOWED_TAGS
        });
        /* Detect mXSS attempts abusing namespace confusion */
-       if (currentNode.hasChildNodes() && !_isNode(currentNode.firstElementChild) && regExpTest(/<[/\w]/g, currentNode.innerHTML) && regExpTest(/<[/\w]/g, currentNode.textContent)) {
+       if (currentNode.hasChildNodes() && !_isNode(currentNode.firstElementChild) && regExpTest(/<[/\w!]/g, currentNode.innerHTML) && regExpTest(/<[/\w!]/g, currentNode.textContent)) {
          _forceRemove(currentNode);
          return true;
        }
@@ -16349,7 +16352,10 @@
                    }
                } else {
                    // All directives that could change the format, and thus decoder, should have been read by now.
-                   this.setDecoder(header.format);
+                   // Set the decoder, unless it is explicitly set in the track configuration (not common)
+                   if(!this.config.decode) {
+                       this.setDecoder(header.format);
+                   }
 
                    // If the line can be parsed as a feature assume we are beyond the header, if any
                    const tokens = line.split(this.delimiter || "\t");
@@ -30858,7 +30864,7 @@
    }
 
    const DEFAULT_GENOMES_URL = "https://igv.org/genomes/genomes.json";
-   const BACKUP_GENOMES_URL = "https://raw.githubusercontent.com/igvteam/igv.js/main/packages/igv/src/genomes/genomes.json";
+   const BACKUP_GENOMES_URL = "https://raw.githubusercontent.com/igvteam/igv-genomes/refs/heads/main/dist/genomes.json";
 
    const GenomeUtils = {
 
@@ -30866,7 +30872,7 @@
 
            if (!GenomeUtils.KNOWN_GENOMES) {
 
-               GenomeUtils.KNOWN_GENOMES = {};
+               let table = {};
 
                const processJson = (jsonArray, table) => {
                    jsonArray.forEach(function (json) {
@@ -30879,12 +30885,12 @@
                if (config.loadDefaultGenomes !== false) {
                    try {
                        const jsonArray = await igvxhr.loadJson(DEFAULT_GENOMES_URL, {timeout: 2000});
-                       processJson(jsonArray, GenomeUtils.KNOWN_GENOMES);
+                       processJson(jsonArray, table);
                    } catch (error) {
                        try {
                            console.error("Error initializing default genomes:", error);
                            const jsonArray = await igvxhr.loadJson(BACKUP_GENOMES_URL, {timeout: 2000});
-                           processJson(jsonArray, GenomeUtils.KNOWN_GENOMES);
+                           processJson(jsonArray, table);
                        } catch (e) {
                            console.error("Error initializing backup genomes:", error);
                        }
@@ -30896,11 +30902,12 @@
                if (genomeList) {
                    if (typeof genomeList === 'string') {
                        const jsonArray = await igvxhr.loadJson(genomeList, {});
-                        processJson(jsonArray, GenomeUtils.KNOWN_GENOMES);
+                        processJson(jsonArray, table);
                    } else {
-                        processJson(genomeList, GenomeUtils.KNOWN_GENOMES);
+                        processJson(genomeList, table);
                    }
                }
+               GenomeUtils.KNOWN_GENOMES = table;
            }
        },
 
@@ -47627,7 +47634,7 @@
            if (!this.colorBy) {
                this.colorBy = this.hasPairs ? "unexpectedPair" : "none";
            }
-           
+
            let pixelTop = options.pixelTop - BAMTrack.coverageTrackHeight;
            if (this.top) {
                ctx.translate(0, this.top);
@@ -48334,7 +48341,12 @@
                this.trackView.repaintViews();
            }
 
-           return {name: undefined, element: createCheckbox(menuItem.label, showCheck), click: clickHandler, init: undefined}
+           return {
+               name: undefined,
+               element: createCheckbox(menuItem.label, showCheck),
+               click: clickHandler,
+               init: undefined
+           }
        }
 
 
@@ -48381,7 +48393,12 @@
                }
            }
 
-           return {name: undefined, element: createCheckbox(menuItem.label, showCheck), dialog: clickHandler, init: undefined}
+           return {
+               name: undefined,
+               element: createCheckbox(menuItem.label, showCheck),
+               dialog: clickHandler,
+               init: undefined
+           }
 
        }
 
@@ -48503,38 +48520,88 @@
                        });
                    }
 
+                   list.push('<hr/>');
+                   const softClips = clickedAlignment.softClippedBlocks();
                    list.push({
                        label: 'View read sequence',
                        click: () => {
-                           const seqstring = clickedAlignment.seq; //.map(b => String.fromCharCode(b)).join("");
-                           if (!seqstring || "*" === seqstring) {
-                               this.browser.alert.present("Read sequence: *");
-                           } else {
-                               this.browser.alert.present(seqstring);
-                           }
+                           const seqstring = clickedAlignment.seq;
+                           this.browser.alert.present(seqstring && seqstring !== "*" ? seqstring : "Read sequence: *");
                        }
                    });
 
+                   if (softClips.left && softClips.left.len > 0) {
+                       list.push({
+                           label: 'View left soft-clipped sequence',
+                           click: () => {
+                               const clippedSequence = clickedAlignment.seq.substring(softClips.left.seqOffset, softClips.left.seqOffset + softClips.left.len);
+                               this.browser.alert.present(clippedSequence);
+                           }
+                       });
+                   }
+
+                   if (softClips.right && softClips.right.len > 0) {
+                       list.push({
+                           label: 'View right soft-clipped sequence',
+                           click: () => {
+                               const clippedSequence = clickedAlignment.seq.substring(softClips.right.seqOffset, softClips.right.seqOffset + softClips.right.len);
+                               this.browser.alert.present(clippedSequence);
+                           }
+                       });
+                   }
+
+                   list.push('<hr/>');
+
                    if (isSecureContext()) {
                        list.push({
                            label: 'Copy read sequence',
                            click: async () => {
-                               const seq = clickedAlignment.seq; //.map(b => String.fromCharCode(b)).join("");
                                try {
-                                   await navigator.clipboard.writeText(seq);
+                                   await navigator.clipboard.writeText(clickedAlignment.seq);
                                } catch (e) {
                                    console.error(e);
                                    this.browser.alert.present(`error copying sequence to clipboard ${e}`);
                                }
-
                            }
                        });
+
+                       if (softClips.left && softClips.left.len > 0) {
+                           list.push({
+                               label: 'Copy left soft-clipped sequence',
+                               click: async () => {
+                                   try {
+                                       const clippedSequence = clickedAlignment.seq.substring(softClips.left.seqOffset, softClips.left.seqOffset + softClips.left.len);
+                                       await navigator.clipboard.writeText(clippedSequence);
+                                   } catch (e) {
+                                       console.error(e);
+                                       this.browser.alert.present(`error copying sequence to clipboard ${e}`);
+                                   }
+                               }
+                           });
+                       }
+
+                       if (softClips.right && softClips.right.len > 0) {
+                           list.push({
+                               label: 'Copy right soft-clipped sequence',
+                               click: async () => {
+                                   try {
+                                       const clippedSequence = clickedAlignment.seq.substring(softClips.right.seqOffset, softClips.right.seqOffset + softClips.right.len);
+                                       await navigator.clipboard.writeText(clippedSequence);
+                                   } catch (e) {
+                                       console.error(e);
+                                       this.browser.alert.present(`error copying sequence to clipboard ${e}`);
+                                   }
+                               }
+                           });
+                       }
                    }
 
-                   // TODO if genome supports blat
+                   // TODO test if genome supports blat
                    const seqstring = clickedAlignment.seq;
                    if (seqstring && "*" !== seqstring) {
 
+                       list.push('<hr/>');
+
                        if (seqstring.length < maxSequenceSize$1) {
                            list.push({
                                label: 'BLAT read sequence',
@@ -48552,7 +48619,7 @@
                            list.push({
                                label: 'BLAT left soft-clipped sequence',
                                click: () => {
-                                   const clippedSequence = seqstring.substr(softClips.left.seqOffset, softClips.left.len);
+                                   const clippedSequence = seqstring.substring(softClips.left.seqOffset, softClips.left.seqOffset + softClips.left.len);
                                    const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(clippedSequence) : clippedSequence;
                                    const name = `${clickedAlignment.readName} - blat left clip`;
                                    const title = `${this.name} - ${name}`;
@@ -48564,7 +48631,7 @@
                            list.push({
                                label: 'BLAT right soft-clipped sequence',
                                click: () => {
-                                   const clippedSequence = seqstring.substr(softClips.right.seqOffset, softClips.right.len);
+                                   const clippedSequence = seqstring.substring(softClips.right.seqOffset, softClips.right.seqOffset + softClips.right.len);
                                    const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(clippedSequence) : clippedSequence;
                                    const name = `${clickedAlignment.readName} - blat right clip`;
                                    const title = `${this.name} - ${name}`;
@@ -48613,7 +48680,7 @@
            const offsetY = y - this.top;
            const genomicLocation = clickState.genomicLocation;
 
-           if(features.packedGroups) {
+           if (features.packedGroups) {
                let minGroupY = Number.MAX_VALUE;
                for (let group of features.packedGroups.values()) {
                    minGroupY = Math.min(minGroupY, group.pixelTop);
@@ -69452,7 +69519,7 @@ ${indent}columns: ${matrix.columns}
        })
    }
 
-   const _version = "3.2.5";
+   const _version = "3.2.6";
    function version() {
        return _version
    }