igv 2.12.1 → 2.12.2

package/README.md

@@ -12,19 +12,19 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/2.12.1/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.12.2/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.12.1/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.12.2/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.12.1/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.12.2/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.12.1/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.12.2/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.12.1/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.12.2/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.12.1/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.12.2/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.12.1/examples/)***
+***[More](https://igv.org/web/release/2.12.2/examples/)***
 
  
 # Quickstart
@@ -33,18 +33,18 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for ES5 (igv.min.js) and ES6 (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.12.1/dist/](https://cdn.jsdelivr.net/npm/igv@2.12.1/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.12.2/dist/](https://cdn.jsdelivr.net/npm/igv@2.12.2/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.12.1/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.12.2/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.12.1/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.12.2/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -22796,7 +22796,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.12.1";
+const _version = "2.12.2";
 function version() {
     return _version
 }
@@ -24397,6 +24397,10 @@ class PairedAlignment {
             return this.firstAlignment.mate.strand    // Assumption is mate is first-of-pair
         }
     }
+
+    hasTag(str) {
+        return this.firstAlignment.hasTag(str) || (this.secondAlignment &&  this.secondAlignment.hasTag(str))
+    }
 }
 
 /*
@@ -31566,27 +31570,45 @@ const makePairedAlignmentChords = (alignments) => {
 
     const chords = [];
     for (let a of alignments) {
-        const mate = a.mate;
-        if (mate && mate.chr && mate.position) {
-            chords.push({
-                uniqueId: a.readName,
-                refName: shortChrName(a.chr),
-                start: a.start,
-                end: a.end,
-                mate: {
-                    refName: shortChrName(mate.chr),
-                    start: mate.position - 1,
-                    end: mate.position,
-                }
-            });
+
+        if(a.paired) {
+            if(a.firstAlignment && a.secondAlignment) {
+                chords.push({
+                    uniqueId: a.readName,
+                    refName: shortChrName(a.firstAlignment.chr),
+                    start: a.firstAlignment.start,
+                    end: a.firstAlignment.end,
+                    mate: {
+                        refName: shortChrName(a.secondAlignment.chr),
+                        start: a.secondAlignment.start,
+                        end: a.secondAlignment.end,
+                    }
+                });
+            }
+        }
+        else {
+            const mate = a.mate;
+            if (mate && mate.chr && mate.position) {
+                chords.push({
+                    uniqueId: a.readName,
+                    refName: shortChrName(a.chr),
+                    start: a.start,
+                    end: a.end,
+                    mate: {
+                        refName: shortChrName(mate.chr),
+                        start: mate.position - 1,
+                        end: mate.position,
+                    }
+                });
+            }
         }
     }
     return chords
 };
 
 const makeSupplementalAlignmentChords = (alignments) => {
-    const chords = [];
-    for (let a of alignments) {
+
+    const makeChords = (a) => {
         const sa = a.tags()['SA'];
         const supAl = createSupplementaryAlignments(sa);
         let n = 0;
@@ -31605,6 +31627,18 @@ const makeSupplementalAlignmentChords = (alignments) => {
                 });
             }
         }
+    };
+
+    const chords = [];
+    for (let a of alignments) {
+        if(a.paired) {
+            makeChords(a.firstAlignment);
+            if(a.secondAlignment) {
+                makeChords(a.secondAlignment);
+            }
+        } else {
+            makeChords(a);
+        }
     }
     return chords
 };
@@ -32326,11 +32360,18 @@ class BAMTrack extends TrackBase {
         const refFrame = viewport.referenceFrame;
         for (let a of viewport.cachedFeatures.allAlignments()) {
             if (a.end >= refFrame.start
-                && a.start <= refFrame.end
-                && a.mate
-                && a.mate.chr
-                && (a.mate.chr !== a.chr || Math.max(a.fragmentLength) > maxTemplateLength)) {
-                inView.push(a);
+                && a.start <= refFrame.end) {
+                if (a.paired) {
+                    if (a.end - a.start > maxTemplateLength) {
+                        inView.push(a);
+                    }
+                } else {
+                    if (a.mate
+                        && a.mate.chr
+                        && (a.mate.chr !== a.chr || Math.max(a.fragmentLength) > maxTemplateLength)) {
+                        inView.push(a);
+                    }
+                }
             }
         }
         const chords = makePairedAlignmentChords(inView);
@@ -33909,7 +33950,7 @@ class SampleNameViewport {
                         for (let {sampleNameViewport} of this.browser.trackViews) {
                             sampleNameViewport.setWidth(this.browser.sampleNameViewportWidth);
                         }
-                        this.browser.resize();
+                        this.browser.layoutChange();
                     }
                 };
 
@@ -48642,7 +48683,7 @@ class SampleNameControl {
                 }
             }
 
-            browser.resize();
+            browser.layoutChange();
 
 
         });
@@ -50312,7 +50353,16 @@ class Browser {
 
     }
 
+    /**
+     * API function to signal that this browser visibility has changed, e.g. from hiding/showing in a tab interface.
+     *
+     * @returns {Promise<void>}
+     */
     async visibilityChange() {
+        this.layoutChange();
+    }
+
+    async layoutChange() {
 
         const status = this.referenceFrameList.find(referenceFrame => referenceFrame.bpPerPixel < 0);