Add inversions to our simulated volvox bam file

GMOD · Oct 31, 2018 · 410e090 · 410e090
1 parent 7e8b162
commit 410e090
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Showing 5 changed files with 63 additions and 22 deletions.
diff --git a/docs/tutorial/data_files/volvox-sv.bam b/docs/tutorial/data_files/volvox-sv.bam
diff --git a/docs/tutorial/data_files/volvox-sv.bam.bai b/docs/tutorial/data_files/volvox-sv.bam.bai
diff --git a/src/JBrowse/View/FeatureGlyph/Alignment.js b/src/JBrowse/View/FeatureGlyph/Alignment.js
@@ -11,6 +11,54 @@ define([
            MismatchesMixin
        ) {
 
+// adapted from igv.js, illumina standard --> <-- pairs are fr https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
+var orientationTypes = {
+    "fr": {
+
+        "F1R2": "LR",
+        "F2R1": "LR",
+
+        "F1F2": "LL",
+        "F2F1": "LL",
+
+        "R1R2": "RR",
+        "R2R1": "RR",
+
+        "R1F2": "RL",
+        "R2F1": "RL"
+    },
+
+    "rf": {
+
+        "R1F2": "LR",
+        "R2F1": "LR",
+
+        "R1R2": "LL",
+        "R2R1": "LL",
+
+        "F1F2": "RR",
+        "F2F1": "RR",
+
+        "F1R2": "RL",
+        "F2R1": "RL"
+    },
+
+    "ff": {
+
+        "F2F1": "LR",
+        "R1R2": "LR",
+
+        "F2R1": "LL",
+        "R1F2": "LL",
+
+        "R2F1": "RR",
+        "F1R2": "RR",
+
+        "R2R1": "RL",
+        "F1F2": "RL"
+    }
+};
+
 return declare( [BoxGlyph,MismatchesMixin], {
 
     constructor: function() {
@@ -30,8 +78,14 @@ return declare( [BoxGlyph,MismatchesMixin], {
                 style: {
                     color: function( feature, path, glyph, track ) {
                       var strand = feature.get('strand');
-                      if(Math.abs(strand) != 1 && strand != '+' && strand != '-')
+                      if(Math.abs(strand) != 1 && strand != '+' && strand != '-') {
                         return track.colorForBase('reference');
+                      }
+                      else if(track.config.colorByOrientation) {
+                          const type = orientationTypes[track.config.orientationType]
+                          const orientation = type[feature.get('pair_orientation')]
+                          return {"LR": "grey", "RR": "navy", "RL": "teal", "LL": "green" }[orientation];
+                      }
                       else if(track.config.useXS) {
                         var xs = feature.get('xs')
                         var strand={'-':'color_rev_strand','+':'color_fwd_strand'}[xs];
@@ -99,7 +153,8 @@ return declare( [BoxGlyph,MismatchesMixin], {
                     height: 7,
                     marginBottom: 1,
                     showMismatches: true,
-                    mismatchFont: 'bold 10px Courier New,monospace'
+                    mismatchFont: 'bold 10px Courier New,monospace',
+                    orientationType: 'fr'
                 }
             }
         );

diff --git a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
@@ -59,7 +59,7 @@ renderConnector( context, fRect ) {
 _defaultConfig() {
     return this._mergeConfigs(dojo.clone( this.inherited(arguments) ), {
         readCloudLog: true,
-        readCloudStretch: 50,
+        readCloudStretch: 20,
         style: {
             connectorColor: '#333',
             connectorThickness: 1,

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -23,6 +23,8 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
                 glyph: 'JBrowse/View/FeatureGlyph/Alignment',
                 maxFeatureGlyphExpansion: 0,
                 maxFeatureScreenDensity: 15,
+                colorByOrientation: true,
+                orientationType: 'fr',
 
                 hideDuplicateReads: true,
                 hideQCFailingReads: true,
@@ -141,26 +143,10 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
         });
         displayOptions.push({
             label: 'Color by pair orientation',
-            type: 'dijit/RadioMenuItem',
-            group: 'g2',
+            type: 'dijit/CheckedMenuItem',
+            checked: this.config.colorByOrientation,
             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.config.colorByOrientation = this.get('checked');
                 thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
             }
         });