Add an upper limit to fetch size

GMOD · Nov 15, 2018 · 8896f7f · 8896f7f
1 parent c4da153
commit 8896f7f
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Showing 2 changed files with 8 additions and 9 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js b/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js
@@ -12,7 +12,6 @@ return declare(null, {
         this.featureCache = {}
         this.insertStatsCacheMin = args.insertStatsCacheMin || 400
         this.insertMaxSize = args.insertMaxSize || 50000
-        this.orientationType = args.orientationType || 'fr'
     },
 
     cleanFeatureCache(query) {
@@ -28,8 +27,8 @@ return declare(null, {
     },
 
     getInsertSizeStats() {
-        if(Object.keys(this.featureCache).length > this.insertStatsCacheMin) {
-            var total = Object.keys(this.featureCache).length
+        const total = Object.keys(this.featureCache).length
+        if(total > this.insertStatsCacheMin) {
             var tlens = Object.entries(this.featureCache)
                 .map(([k, v]) => Math.abs(v))
                 .filter(tlen => tlen < this.insertMaxSize)
@@ -39,8 +38,8 @@ return declare(null, {
             var avg = sum / total;
             var sd = Math.sqrt((total * sum2 - sum*sum) / (total * total));
             return {
-                upper: avg + 3*sd,
-                lower: avg - 3*sd
+                upper: avg + 3 * sd,
+                lower: avg - 3 * sd
             }
         }
         return { upper: Infinity, lower: 0 }

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -217,16 +217,16 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
         }
         if(this.config.viewAsPairs || this.config.viewAsSpans || this.config.colorByOrientation) {
             let supermethod = this.getInherited(arguments)
-            const len = Math.max(args.rightBase - args.leftBase, 4000)
+            const len = Math.min(Math.max(args.rightBase - args.leftBase, 4000), 100000)
             const region = {
                 ref: this.refSeq.name,
                 start: Math.max(0, args.leftBase),
                 end: args.rightBase,
                 viewAsPairs: true
             }
-
-            const min = Math.max(0, region.start - len * 10)
-            const max = region.end + len * 10
+            const e = 30
+            const min = Math.max(0, region.start - len * e)
+            const max = region.end + len * e
             this.initialCachePromise = this.initialCachePromise || new Promise((resolve, reject) => {
                 this.store.getFeatures({
                     ref: this.refSeq.name,