Add initial paired read tracks

src/JBrowse/Store/SeqFeature/BAM.js

@@ -71,6 +71,7 @@ define( [
             'JBrowse/Store/DeferredFeaturesMixin',
             'JBrowse/Store/SeqFeature/IndexedStatsEstimationMixin',
             'JBrowse/Model/XHRBlob',
+            'JBrowse/Model/SimpleFeature',
         ],
         function(
             declare,
@@ -80,6 +81,7 @@ define( [
             DeferredFeaturesMixin,
             IndexedStatsEstimationMixin,
             XHRBlob,
+            SimpleFeature
         ) {
 
 return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, IndexedStatsEstimationMixin ], {
@@ -207,11 +209,33 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
         let seqName = query.ref || this.refSeq.name
         seqName = this.browser.regularizeReferenceName( seqName );
 
-        this.bam.getRecordsForRange(seqName, query.start, query.end)
+        this.bam.getRecordsForRange(seqName, query.start, query.end, {viewAsPairs: true})
             .then(records => {
-                for (let i = 0; i < records.length; i += 1) {
-                    featCallback(this._bamRecordToFeature(records[i]))
+                records.sort((a, b) => a.get('name').localeCompare(b.get('name')))
+                let recs = records.map(r => r.get('name'))
+                for(let i = 0; i < records.length-1; i++) {
+                    const r1 = records[i]
+                    const r2 = records[i+1]
+                    if(r1.get('name') == r2.get('name')) {
+                        featCallback(new SimpleFeature({
+                            id: r1.get('name'),
+                            data: {
+                                start: Math.min(r1.get('start'), r2.get('start')),
+                                end: Math.max(r1.get('end'), r2.get('end')),
+                                insert_size: r1.get('template_length'),
+                                type: 'match',
+                                subfeatures: [
+                                    { start: r1.get('start'), end: r1.get('end') },
+                                    { start: r2.get('start'), end: r2.get('end') }
+                                ]
+                            }
+                        }))
+                        i++;
+                    }
                 }
+                // for (let i = 0; i < records.length; i += 1) {
+                //     featCallback(this._bamRecordToFeature(records[i]))
+                // }
 
                 endCallback()
             })

src/JBrowse/View/FeatureGlyph/PairedRead.js

@@ -0,0 +1,40 @@
+define([
+    'dojo/_base/declare',
+    'dojo/_base/array',
+    'dojo/_base/lang',
+    'JBrowse/View/FeatureGlyph/Segments'
+],
+function(
+    declare,
+    array,
+    lang,
+    FeatureGlyph
+) {
+    return declare(FeatureGlyph, {
+
+
+        //same as parent but without clearRect
+        renderFeature: function( context, fRect ) {
+            this.renderConnector( context,  fRect );
+            this.renderSegments( context, fRect );
+            this.renderLabel( context, fRect );
+            this.renderDescription( context, fRect );
+            this.renderArrowhead( context, fRect );
+        },
+
+        layoutFeature: function(viewArgs, layout, feature) {
+            var rect = this.inherited(arguments);
+            if (!rect) {
+                return rect;
+            }
+            var t = Math.abs(feature.get('insert_size'))
+
+            // need to set the top of the inner rect
+            rect.rect.t = t / (this.config.scaleFactor||1);
+            rect.t = t / (this.config.scaleFactor||1);
+
+            return rect;
+        }
+    });
+});
+

src/JBrowse/View/Track/PairedReads.js

@@ -0,0 +1,34 @@
+define( [
+            'dojo/_base/declare',
+            'dojo/_base/lang',
+            'JBrowse/View/Track/CanvasFeatures',
+            'JBrowse/Util'
+        ],
+        function(
+            declare,
+            lang,
+            CanvasFeatures,
+            Util,
+        ) {
+
+return declare(CanvasFeatures, {
+	_defaultConfig: function() {
+		return Util.deepUpdate(lang.clone(this.inherited(arguments)), {
+			glyph: 'JBrowse/View/FeatureGlyph/PairedRead',
+			maxFeatureScreenDensity: 60,
+			showLabels: false
+		});
+	},
+
+	// override getLayout to access addRect method
+	_getLayout: function() {
+		var layout = this.inherited(arguments);
+		return declare.safeMixin(layout, {
+			addRect: function() {
+				this.pTotalHeight = this.maxHeight;
+				return 0;
+			}
+		});
+	}
+});
+});