Move away from visibleRegion dependency

src/JBrowse/GenomeView.js

@@ -1098,6 +1098,7 @@ slide: function(distance) {
 },
 
 setLocation: function(refseq, startbp, endbp) {
+    console.log('setLocation', refseq, startbp, endbp)
     if (startbp === undefined) startbp = this.minVisible();
     if (endbp === undefined) endbp = this.maxVisible();
     if( typeof refseq == 'string' ) {

src/JBrowse/Store/SeqFeature/BAM.js

@@ -257,6 +257,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
 
     // called by getFeatures from the DeferredFeaturesMixin
     _getFeatures( query, featCallback, endCallback, errorCallback ) {
+        console.log(query)
         let seqName = query.ref || this.refSeq.name
         seqName = this.browser.regularizeReferenceName( seqName );
         const pairCache = {};

src/JBrowse/View/Track/Alignments2.js

@@ -163,7 +163,6 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
     },
 
     fillBlock: function( args ) {
-
         // workaround for the fact that initial load of JBrowse invokes fillBlock on nonsense regions
         // and then the cache cleanup can be invoked in ways that destroys visible features
         this.removeFeaturesFromCacheAfterDelay = this.removeFeaturesFromCacheAfterDelay || false
@@ -174,12 +173,13 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
         }
         if(this.config.viewAsPairs) {
             let supermethod = this.getInherited(arguments)
-            var reg = this.browser.view.visibleRegion()
-            var len = Math.max(reg.end - reg.start, 4000)
+            var min = args.leftBase
+            var max = args.rightBase
+            var len = Math.max(min - max, 4000)
             const region = {
                 ref: this.refSeq.name,
-                start: Math.max( 0, reg.start ),
-                end: reg.end,
+                start: Math.max( 0, min ),
+                end: max,
                 viewAsPairs: true
             }