igv 2.12.1 → 2.12.2

package/dist/igv.js

@@ -23093,7 +23093,7 @@
       }
     };
 
-    const _version = "2.12.1";
+    const _version = "2.12.2";
 
     function version$1() {
       return _version;
@@ -25481,6 +25481,10 @@
         }
       }
 
+      hasTag(str) {
+        return this.firstAlignment.hasTag(str) || this.secondAlignment && this.secondAlignment.hasTag(str);
+      }
+
     }
 
     /*
@@ -48271,20 +48275,36 @@
       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
+              }
+            });
+          }
         }
       }
 
@@ -48292,9 +48312,7 @@
     };
 
     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;
@@ -48314,6 +48332,20 @@
             });
           }
         }
+      };
+
+      const chords = [];
+
+      for (let a of alignments) {
+        if (a.paired) {
+          makeChords(a.firstAlignment);
+
+          if (a.secondAlignment) {
+            makeChords(a.secondAlignment);
+          }
+        } else {
+          makeChords(a);
+        }
       }
 
       return chords;
@@ -49040,8 +49072,16 @@
         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);
+          if (a.end >= refFrame.start && 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);
+              }
+            }
           }
         }
 
@@ -50566,7 +50606,7 @@
                 sampleNameViewport.setWidth(this.browser.sampleNameViewportWidth);
               }
 
-              this.browser.resize();
+              this.browser.layoutChange();
             }
           };
           this.browser.inputDialog.present(config, event);
@@ -65409,7 +65449,7 @@
             }
           }
 
-          browser.resize();
+          browser.layoutChange();
         });
       }
 
@@ -67032,8 +67072,18 @@
           trackView.setTrackHeight(newHeight);
         });
       }
+      /**
+       * 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);
 
         if (status) {