Add a skips and deletions mode for the rendering to avoid cluttered z…

…oomed out view
GMOD · Oct 19, 2018 · b1042ad · b1042ad
1 parent e78bae3
commit b1042ad
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -267,7 +267,6 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                         featCallback(this._bamRecordToFeature(records[i]))
                     }
                 }
-                console.log(query, Object.keys(pairCache).sort())
                 endCallback()
             })
             .catch(err => {

diff --git a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
@@ -20,8 +20,17 @@ renderFeature( context, fRect ) {
     if(fRect.f.pairedFeature()) {
         this.renderConnector( context, fRect );
         this.renderSegments( context, fRect );
-        this._drawMismatches( context, fRect, fRect.f.f1, this._getMismatches( fRect.f.f1 ) );
-        this._drawMismatches( context, fRect, fRect.f.f2, this._getMismatches( fRect.f.f2 ) );
+        if( fRect.w > 2 ) {
+            if( fRect.viewInfo.scale > 0.2 ) {
+                this._drawMismatches( context, fRect, fRect.f.f1, this._getMismatches( fRect.f.f1 ) );
+                this._drawMismatches( context, fRect, fRect.f.f2, this._getMismatches( fRect.f.f2 ) );
+            }
+            else {
+                this._drawMismatches( context, fRect, fRect.f.f1, this._getSkipsAndDeletions( fRect.f.f1 ));
+                this._drawMismatches( context, fRect, fRect.f.f2, this._getSkipsAndDeletions( fRect.f.f2 ));
+            }
+        }
+
     } else {
         this.inherited(arguments)
     }