igv 3.2.5 → 3.2.6

package/README.md

@@ -18,19 +18,19 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/3.2.4/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.2.6/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.2.4/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.2.6/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.2.4/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.2.6/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.2.4/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.2.6/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.2.4/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.2.6/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.2.4/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.2.6/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.2.4/examples/)***
+***[More](https://igv.org/web/release/3.2.6/examples/)***
 
  
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.2.4/dist/](https://cdn.jsdelivr.net/npm/igv@3.2.4/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.2.6/dist/](https://cdn.jsdelivr.net/npm/igv@3.2.6/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@3.2.4/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.2.6/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@3.2.4/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@3.2.6/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -10946,7 +10946,7 @@ function createMenuElements$1(itemList, popover) {
     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,
@@ -11006,6 +11006,9 @@ const typeErrorCreate = unconstruct(TypeError);
  */
 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];
     }
@@ -11244,7 +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 = '3.2.4';
+  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
@@ -11849,7 +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 (currentNode.hasChildNodes() && !_isNode(currentNode.firstElementChild) && regExpTest(/<[/\w!]/g, currentNode.innerHTML) && regExpTest(/<[/\w!]/g, currentNode.textContent)) {
       _forceRemove(currentNode);
       return true;
     }
@@ -16343,7 +16346,10 @@ class FeatureParser {
                 }
             } 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");
@@ -30852,7 +30858,7 @@ function indentLevel(str) {
 }
 
 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 = {
 
@@ -30860,7 +30866,7 @@ const GenomeUtils = {
 
         if (!GenomeUtils.KNOWN_GENOMES) {
 
-            GenomeUtils.KNOWN_GENOMES = {};
+            let table = {};
 
             const processJson = (jsonArray, table) => {
                 jsonArray.forEach(function (json) {
@@ -30873,12 +30879,12 @@ const GenomeUtils = {
             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);
                     }
@@ -30890,11 +30896,12 @@ const GenomeUtils = {
             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;
         }
     },
 
@@ -47621,7 +47628,7 @@ class AlignmentTrack extends TrackBase {
         if (!this.colorBy) {
             this.colorBy = this.hasPairs ? "unexpectedPair" : "none";
         }
-        
+
         let pixelTop = options.pixelTop - BAMTrack.coverageTrackHeight;
         if (this.top) {
             ctx.translate(0, this.top);
@@ -48328,7 +48335,12 @@ class AlignmentTrack extends TrackBase {
             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
+        }
     }
 
 
@@ -48375,7 +48387,12 @@ class AlignmentTrack extends TrackBase {
             }
         }
 
-        return {name: undefined, element: createCheckbox(menuItem.label, showCheck), dialog: clickHandler, init: undefined}
+        return {
+            name: undefined,
+            element: createCheckbox(menuItem.label, showCheck),
+            dialog: clickHandler,
+            init: undefined
+        }
 
     }
 
@@ -48497,38 +48514,88 @@ class AlignmentTrack extends TrackBase {
                     });
                 }
 
+                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$1) {
                         list.push({
                             label: 'BLAT read sequence',
@@ -48546,7 +48613,7 @@ class AlignmentTrack extends TrackBase {
                         list.push({
                             label: 'BLAT left soft-clipped sequence',
                             click: () => {
-                                const clippedSequence = seqstring.substr(softClips.left.seqOffset, softClips.left.len);
+                                const clippedSequence = seqstring.substring(softClips.left.seqOffset, softClips.left.seqOffset + softClips.left.len);
                                 const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(clippedSequence) : clippedSequence;
                                 const name = `${clickedAlignment.readName} - blat left clip`;
                                 const title = `${this.name} - ${name}`;
@@ -48558,7 +48625,7 @@ class AlignmentTrack extends TrackBase {
                         list.push({
                             label: 'BLAT right soft-clipped sequence',
                             click: () => {
-                                const clippedSequence = seqstring.substr(softClips.right.seqOffset, softClips.right.len);
+                                const clippedSequence = seqstring.substring(softClips.right.seqOffset, softClips.right.seqOffset + softClips.right.len);
                                 const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(clippedSequence) : clippedSequence;
                                 const name = `${clickedAlignment.readName} - blat right clip`;
                                 const title = `${this.name} - ${name}`;
@@ -48607,7 +48674,7 @@ class AlignmentTrack extends TrackBase {
         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);
@@ -69446,7 +69513,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.2.5";
+const _version = "3.2.6";
 function version() {
     return _version
 }