Rearrange some files

src/JBrowse/Store/SeqFeature/BAM.js

@@ -7,6 +7,21 @@ const bamIndexedFilesCache = LRU(5)
 
 const BlobFilehandleWrapper = cjsRequire('../../Model/BlobFilehandleWrapper')
 
+class PairedBamRead {
+    id() {
+        return Math.min(+this.f1.id(), +this.f2.id())
+    }
+    children() {
+    }
+    get(field) {
+        if(field == 'start') {
+			return Math.min(this.f1.get('start'), this.f2.get('start'))
+        } else if(field == 'end') {
+			return Math.max(this.f1.get('end'), this.f2.get('end'))
+        }
+    }
+}
+
 class BamSlightlyLazyFeature {
 
     _get_name() { return this.record._get('name') }
@@ -66,8 +81,8 @@ class BamSlightlyLazyFeature {
 
 function canBePaired(alignment) {
     return alignment.isPaired() &&
-        alignment.isMateMapped() &&
-        alignment.chr === alignment.mate.chr &&
+        !alignment.isMateUnmapped() &&
+        alignment._refID === alignment._next_refid() &&
         (alignment.isRead1() || alignment.isRead2()) &&
         !(alignment.isSecondary() || alignment.isSupplementary());
 }
@@ -212,7 +227,6 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
         .then(() => this.bam.hasRefSeq(this._refNameToId(seqName)))
         .then(callback, errorCallback)
     },
-    ,
 
     // called by getFeatures from the DeferredFeaturesMixin
     _getFeatures( query, featCallback, endCallback, errorCallback ) {
@@ -235,40 +249,18 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                         if (feat) {
                             feat.f2 = records[i]
                             pairCache[records[i]._get('name')] = undefined
+                            featCallback(feat)
                         }
                         else {
-                            feat = { f1: records[i] }
-                            pairCache[alignment._get('name')] = feat
-                            featCallback(feat)
+                            feat = new PairedBamRead()
+                            feat.f1 = records[i]
+                            pairCache[records[i]._get('name')] = feat
                         }
                     }
                     else {
-                        featCallback(feat)
+                        featCallback(records[i])
                     }
-                    // const r1 = records[i]
-                    // const r2 = records[i+1]
-                    // if(r1.get('name') == r2.get('name')) {
-                    //     featCallback({ r1, r2 })
-                        // 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()
             })
             .catch(err => {

src/JBrowse/View/FeatureGlyph/PairedAlignment.js

@@ -0,0 +1,46 @@
+define([
+    'dojo/_base/declare',
+    'dojo/_base/array',
+    'dojo/_base/lang',
+    'JBrowse/View/FeatureGlyph/Alignment'
+],
+function(
+    declare,
+    array,
+    lang,
+    Alignment
+) {
+return declare(Alignment, {
+
+renderFeature( context, fRect ) {
+    this.renderConnector( context,  fRect );
+    this.renderSegments( context, fRect );
+},
+
+renderSegments( context, fRect ) {
+    const f1 = dojo.clone(fRect);
+    const f2 = dojo.clone(fRect);
+    f1.f = fRect.f.f1
+    f2.f = fRect.f.f2
+    this.inherited(arguments, [context, f1])
+    this.inherited(arguments, [context, f2])
+},
+
+renderConnector( context, fRect ) {
+    // connector
+    var connectorColor = this.getStyle( fRect.f, 'connectorColor' );
+    if( connectorColor ) {
+        context.fillStyle = connectorColor;
+        var connectorThickness = this.getStyle( fRect.f, 'connectorThickness' );
+        context.fillRect(
+            fRect.rect.l, // left
+            Math.round(fRect.rect.t+(fRect.rect.h-connectorThickness)/2), // top
+            fRect.rect.w, // width
+            connectorThickness
+        );
+    }
+}
+
+});
+});
+

src/JBrowse/View/Track/FloatingAlignment.js

@@ -0,0 +1,50 @@
+define([
+    'dojo/_base/declare',
+    'dojo/_base/array',
+    'dojo/_base/lang',
+    'JBrowse/View/FeatureGlyph/Alignment'
+],
+function(
+    declare,
+    array,
+    lang,
+    Alignment
+) {
+return declare([Segments, Alignment], {
+
+renderFeature( context, fRect ) {
+    this.renderConnector( context,  fRect );
+    this.renderSegments( context, fRect );
+},
+
+layoutFeature(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;
+},
+renderConnector( context, fRect ) {
+    // connector
+    var connectorColor = this.getStyle( fRect.f, 'connectorColor' );
+    if( connectorColor ) {
+        context.fillStyle = connectorColor;
+        var connectorThickness = this.getStyle( fRect.f, 'connectorThickness' );
+        context.fillRect(
+            fRect.rect.l, // left
+            Math.round(fRect.rect.t+(fRect.rect.h-connectorThickness)/2), // top
+            fRect.rect.w, // width
+            connectorThickness
+        );
+    }
+}
+
+});
+});
+

src/JBrowse/View/Track/PairedReads.js

@@ -14,7 +14,7 @@ define( [
 return declare(CanvasFeatures, {
 	_defaultConfig: function() {
 		return Util.deepUpdate(lang.clone(this.inherited(arguments)), {
-			glyph: 'JBrowse/View/FeatureGlyph/PairedRead',
+			glyph: 'JBrowse/View/FeatureGlyph/PairedAlignment',
 			maxFeatureScreenDensity: 60,
 			showLabels: false
 		});