added a showBaseMismatches conf var to alignment tracks

GMOD · Nov 26, 2012 · 8b9db7d · 8b9db7d
1 parent 74cc42a
commit 8b9db7d
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/release-notes.txt b/release-notes.txt
@@ -1,5 +1,9 @@
 {{$NEXT}}
 
+ * Added a `showBaseMismatches` configuration variable for Alignment
+   tracks that, when set to false, disables display of per-base
+   mismatches parsed from a SAM/BAM MD field.
+
  * Fixed a bug with the BAM data backend in which some BAM files were
    parsed as if they held no data.
 

diff --git a/src/JBrowse/View/Track/Alignments.js b/src/JBrowse/View/Track/Alignments.js
@@ -17,6 +17,7 @@ return declare( HTMLFeatures,
             {
                 maxFeatureScreenDensity: 1.5,
                 layoutPitchY: 4,
+                showBaseMismatches: true,
                 style: {
                     _defaultLabelScale: 50,
                     className: 'alignment',
@@ -28,7 +29,9 @@ return declare( HTMLFeatures,
 
     renderFeature: function(feature, uniqueId, block, scale, containerStart, containerEnd, destBlock ) {
         var featDiv = this.inherited( arguments );
-        this._drawMismatches( feature, featDiv, scale );
+
+        if( this.config.showBaseMismatches )
+            this._drawMismatches( feature, featDiv, scale );
 
         // if this feature is part of a multi-segment read, and not
         // all of its segments are aligned, add missing_mate to its