Color alignmet insert sizes only if they are paired

GMOD · Nov 19, 2018 · 3dbb199 · 3dbb199
1 parent 71b6358
commit 3dbb199
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 8 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -27,6 +27,7 @@ class BamSlightlyLazyFeature {
     _get_pair_orientation() { return this.record.getPairOrientation()}
     _get_unmapped() { return this.record.isSegmentUnmapped()}
     _get_next_seq_id() { return this.record.isPaired() ? this._store._refIdToName(this.record._next_refid()) : undefined }
+    _get_is_paired() { return this.record.isPaired() }
     _get_next_pos() { return this.record.isPaired() ? this.record._next_pos() : undefined }
     _get_next_segment_position() { return this.record.isPaired()
         ? ( this._store._refIdToName(this.record._next_refid())+':'+(this.record._next_pos()+1)) : undefined}

diff --git a/src/JBrowse/Store/SeqFeature/CRAM.js b/src/JBrowse/Store/SeqFeature/CRAM.js
@@ -32,6 +32,7 @@ class CramSlightlyLazyFeature {
     _get_multi_segment_first() { return this.record.isRead1()}
     _get_multi_segment_last() { return this.record.isRead2()}
     _get_multi_segment_next_segment_reversed() { return this.record.isMateReverseComplemented()}
+    _get_is_paired() { return !!this.record.mate }
     _get_unmapped() { return this.record.isSegmentUnmapped()}
     _get_template_length() { return this.record.templateLength || this.record.templateSize}
     _get_next_seq_id() { return this.record.mate ? this._store._refIdToName(this.record.mate.sequenceId) : undefined }

diff --git a/src/JBrowse/View/FeatureGlyph/AlignmentColoring.js b/src/JBrowse/View/FeatureGlyph/AlignmentColoring.js
@@ -80,13 +80,16 @@ var AlignmentColoring = {
     },
 
     colorByOrientation(feature, score, glyph, track)  {
-        if (feature.get('seq_id') != feature.get('next_seq_id')) {
-            return 'orange'
-        } else if (track.upperPercentile < Math.abs(feature.get('template_length'))) {
-            return 'red'
-        } else if (track.lowerPercentile > Math.abs(feature.get('template_length'))) {
-            return 'pink'
+        if (feature.get('is_paired')) {
+            if(feature.get('seq_id') != feature.get('next_seq_id')) {
+                return 'orange'
+            } else if (track.upperPercentile < Math.abs(feature.get('template_length'))) {
+                return 'red'
+            } else if (track.lowerPercentile > Math.abs(feature.get('template_length'))) {
+                return 'pink'
+            }
         }
+
         const type = Util.orientationTypes[track.config.orientationType]
         const orientation = type[feature.get('pair_orientation')]
         const map = {
@@ -100,7 +103,7 @@ var AlignmentColoring = {
     },
 
     colorByInsertDistance(feature, score, glyph, track) {
-        if (feature.get('seq_id') != feature.get('next_seq_id')) {
+        if (feature.get('is_paired') && feature.get('seq_id') != feature.get('next_seq_id')) {
             return 'orange'
         }
 

diff --git a/src/JBrowse/View/Track/BlockBased.js b/src/JBrowse/View/Track/BlockBased.js
@@ -958,7 +958,7 @@ return declare( [Component,DetailsMixin,FeatureFiltererMixin,Destroyable],
                   new TrackConfigEditor( that.config )
                       .show( function( result ) {
                           // replace this track's configuration
-                          that.browser.cookie('track-' + that.name, JSON.stringify(result.config));
+                          that.browser.cookie('track-' + that.name, JSON.stringify(result.conf));
                           that.browser.publish( '/jbrowse/v1/v/tracks/replace', [result.conf] );
                       });
               }