Begin paired orientation grabber

GMOD · Nov 6, 2018 · d381bc5 · d381bc5
1 parent 7e0a9e2
commit d381bc5
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Showing 3 changed files with 33 additions and 1 deletion.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -23,6 +23,11 @@ class PairedBamRead {
             return this.read1._get('name')
         }
     }
+	getPairOrientation() {
+		const s1 = this.read1._get('strand') === 1 ? 'F1' : 'R1';
+		const s2 = this.read2._get('strand') === 1 ? 'F2' : 'R2';
+		return s1 + s2;
+	}
     pairedFeature() { return true }
     children() {}
 }
@@ -287,6 +292,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                             featCallback(feat)
                         }
                     }
+                    console.log(Object.keys(this.featureCache).length)
                     Object.entries(this.featureCache).forEach(([k, v]) => {
                         if(v._get('end') - v._get('start') < 10000 && (v._get('end') > query.start && v._get('start') < query.end)) {
                             featCallback(v)

diff --git a/src/JBrowse/Store/SeqFeature/CRAM.js b/src/JBrowse/Store/SeqFeature/CRAM.js
@@ -66,6 +66,8 @@ class CramSlightlyLazyFeature {
     parent() {}
 
     children() {}
+
+    pairedFeature() { return false }
 }
 
 define( [

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -139,7 +139,31 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
                 thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
             }
         });
-
+        displayOptions.push({
+            label: 'Color by pair orientation',
+            type: 'dijit/RadioMenuItem',
+            group: 'g2',
+            onClick: function(event) {
+                thisB.config.viewAsPairs = true
+                thisB.config.style.color = feat => {
+                    if(feat.pairedFeature()) {
+                        const ret = feat.getPairOrientation()
+                        if(ret == 'F1R2') {
+                            return 'green'
+                        } else if(ret == 'R1R2') {
+                            return 'red'
+                        } else if(ret == 'F1F2') {
+                            return 'purple'
+                        } else if(ret == 'R1F2') {
+                            return 'orange'
+                        }
+                    }
+                    return 'grey'
+                }
+                thisB.config.glyph = 'JBrowse/View/FeatureGlyph/PairedAlignment'
+                thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+            }
+        });
         return all([ this.inherited(arguments), this._alignmentsFilterTrackMenuOptions(), displayOptions ])
             .then( function( options ) {
                        var o = options.shift();