Use log scale by default

GMOD · Nov 18, 2018 · 1672f73 · 1672f73
1 parent 31c6bd3
commit 1672f73
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -294,7 +294,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                     }
                     console.log(Object.keys(this.featureCache).length)
                     Object.entries(this.featureCache).forEach(([k, v]) => {
-                        if(v._get('end') - v._get('start') < 10000 && (v._get('end') > query.start && v._get('start') < query.end)) {
+                        if(v._get('end') - v._get('start') < 1000000 && (v._get('end') > query.start && v._get('start') < query.end)) {
                             featCallback(v)
                         }
                     })

diff --git a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
@@ -58,6 +58,8 @@ renderConnector( context, fRect ) {
 
 _defaultConfig() {
     return this._mergeConfigs(dojo.clone( this.inherited(arguments) ), {
+        readCloudLog: true,
+        readCloudStretch: 50,
         style: {
             connectorColor: '#333',
             connectorThickness: 1,
@@ -73,10 +75,11 @@ layoutFeature(viewArgs, layout, feature) {
         if(feature.pairedFeature()) {
             var tlen = feature.read1.get('template_length')
             var t = Math.abs(tlen)
+            var k = this.config.readCloudLog ? Math.log(t+1) : t
+            k *= this.config.readCloudStretch
 
-            // need to set the top of the inner rect
-            rect.rect.t = t / (this.config.scaleFactor||1);
-            rect.t = t / (this.config.scaleFactor||1);
+            rect.rect.t = k
+            rect.t = k
         } else {
             rect.t = 0
             rect.rect.t = 0