Enable insert size coloring on normal alignments track

GMOD · Nov 9, 2018 · d19cf20 · d19cf20
1 parent 703d4f7
commit d19cf20
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -222,6 +222,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
             .then(records => {
                 if(query.viewAsPairs) {
                     const recs = records.map(f => this._bamRecordToFeature(f))
+                    recs.forEach(r => this.insertSizeCache.insertFeat(r))
                     this.pairFeatures(query, recs, featCallback, endCallback, errorCallback)
                 } else {
                     for(let i = 0; i < records.length; i++) {

diff --git a/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js b/src/JBrowse/Store/SeqFeature/_InsertSizeCache.js
@@ -24,14 +24,14 @@ return declare(null, {
     },
 
     insertFeat(feat) {
-        this.featureCache[feat.get('name')] = feat
+        this.featureCache[feat.get('name')] = Math.abs(feat.get('template_length'))
     },
 
     getInsertSizeStats() {
         if(Object.keys(this.featureCache).length > this.insertStatsCacheMin) {
             var total = Object.keys(this.featureCache).length
             var tlens = Object.entries(this.featureCache)
-                .map(([k, v]) => Math.abs(v.get('template_length')))
+                .map(([k, v]) => Math.abs(v))
                 .filter(tlen => tlen < this.insertMaxSize)
                 .sort((a, b) => a - b)
             var sum = tlens.reduce((a, b) => a + b, 0)

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -61,12 +61,12 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
 
         var m = {
             type: 'dijit/Menu',
-            label: 'Pair options',
+            label: 'Track visualization options',
             children: []
         }
         var c = {
             type: 'dijit/Menu',
-            label: 'Color options',
+            label: 'Coloring options',
             children: []
         }