Fix some issues with memory management

GMOD · Oct 31, 2018 · 7c9988d · 7c9988d
1 parent bf8166b
commit 7c9988d
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Showing 2 changed files with 23 additions and 10 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -251,9 +251,8 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                             feat = pairCache[name]
                             if (feat && records[i].id() != feat.f1.id()) {
                                 feat.f2 = this._bamRecordToFeature(records[i])
-                                delete pairCache[name]
+                                pairCache[name] = undefined
                                 this.featureCache[name] = feat
-                                featCallback(feat)
                             }
                             else {
                                 feat = new PairedBamRead()
@@ -266,8 +265,11 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                             featCallback(feat)
                         }
                     }
-                    Object.keys(this.featureCache).forEach(k => {
-                        featCallback(this.featureCache[k])
+                    console.log(Object.keys(this.featureCache).length)
+                    Object.entries(this.featureCache).forEach(([k, v]) => {
+                        if(v.get('end') - v.get('start') < 10000) {
+                            featCallback(v)
+                        }
                     })
                 } else {
                     for(let i = 0; i < records.length; i++) {
@@ -287,6 +289,13 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                 .then(records => {
                     let min = Infinity;
                     let max = -Infinity;
+                    Object.entries(this.featureCache).forEach(([k, v]) => {
+                        if(v.get('start') > query.end) {
+                            delete this.featureCache[k]
+                        } else if(v.get('end') < query.start) {
+                            delete this.featureCache[k]
+                        }
+                    })
                     for(let i = 0; i < records.length; i++) {
                         if(records[i]._get('start') < min) {
                             min = records[i]._get('start')
@@ -295,6 +304,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                             max = records[i]._get('end')
                         }
                     }
+
                     featCallback({ min, max })
                 }).catch(errorCallback)
         }, errorCallback)

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -143,22 +143,25 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
 
     fillBlock: function( args ) {
         if(this.config.viewAsPairs) {
-            this.initial = new Promise((resolve, reject) => {
+            let supermethod = this.getInherited(arguments)
+            var initial = new Promise((resolve, reject) => {
                 var reg = this.browser.view.visibleRegion()
+                var len = reg.end - reg.start
                 const region = {
                     ref: this.refSeq.name,
                     start: Math.max( 0, reg.start ),
                     end: reg.end,
                     viewAsPairs: true
                 }
+                region.start = Math.max( 0, region.start )
+                region.end = region.end
+
                 this.store.getPairedRanges(region, range => {
-                    region.start = range.min
-                    region.end = range.max
+                    region.start = Math.max(0, Math.max(range.min, reg.start - len*4))
+                    region.end = Math.min(range.max, reg.end + len*4)
                     this.store.getFeatures(region, function() {}, resolve, reject)
                 }, reject)
-            })
-            let supermethod = this.getInherited(arguments)
-            this.initial.then(() => {
+            }).then(() => {
                 supermethod.apply(this, [args])
             })
         } else {