Cleanup of adapter code

GMOD · Oct 31, 2018 · b109d0d · b109d0d
1 parent a379c39
commit b109d0d
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Showing 5 changed files with 84 additions and 17 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -21,13 +21,10 @@ class PairedBamRead {
             return Math.max(this.read1._get('end'), this.read2._get('end'))
         } else if(field === 'name') {
             return this.read1._get('name')
+        } else if(field === 'pair_orientation') {
+            return this.read1._get('pair_orientation')
         }
     }
-	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() {}
 }

diff --git a/src/JBrowse/View/FeatureGlyph/Alignment.js b/src/JBrowse/View/FeatureGlyph/Alignment.js
@@ -11,7 +11,6 @@ define([
            MismatchesMixin
        ) {
 
-// adapted from igv.js, illumina standard --> <-- pairs are fr https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
 var orientationTypes = {
     "fr": {
 
@@ -82,9 +81,15 @@ return declare( [BoxGlyph,MismatchesMixin], {
                         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];
+                        const type = orientationTypes[track.config.orientationType]
+                        const orientation = type[feature.get('pair_orientation')]
+                        const map = {
+                            'LR': 'color_pair_lr',
+                            'RR': 'color_pair_rr',
+                            'RL': 'color_pair_rl',
+                            'LL': 'color_pair_ll'
+                        };
+                        return glyph.getStyle( feature, map[orientation] || 'color_nostrand' );
                       }
                       else if(track.config.useXS) {
                         var xs = feature.get('xs')
@@ -144,17 +149,20 @@ return declare( [BoxGlyph,MismatchesMixin], {
                     color_rev_missing_mate: '#1919D1',
                     color_fwd_diff_chr: '#000000',
                     color_rev_diff_chr: '#969696',
+                    color_pair_lr: 'grey',
+                    color_pair_rr: 'navy',
+                    color_pair_rl: 'teal',
+                    color_pair_ll: 'green',
                     color_nostrand: '#999999',
                     border_color: null,
 
                     strandArrow: false,
                     strandInlay: true,
-
                     height: 7,
                     marginBottom: 1,
                     showMismatches: true,
                     mismatchFont: 'bold 10px Courier New,monospace',
-                    orientationType: 'fr'
+                    orientationType: 'fr' // default illumina adapter sequence --> <--
                 }
             }
         );

diff --git a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
@@ -10,6 +10,8 @@ function(
     lang,
     Alignment
 ) {
+
+
 return declare(Alignment, {
 
 renderFeature( context, fRect ) {

diff --git a/src/JBrowse/View/FeatureGlyph/PairedArc.js b/src/JBrowse/View/FeatureGlyph/PairedArc.js
@@ -10,16 +10,79 @@ function(
     lang,
     FeatureGlyph
 ) {
+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(FeatureGlyph, {
 
         _defaultConfig: function() {
             return this._mergeConfigs(lang.clone(this.inherited(arguments)), {
                 style: {
-                    color: function(feature, score) {
+                    color: function( feature, score, glyph, track ) {
+                        if(track.config.colorByOrientation) {
+                            const type = orientationTypes[track.config.orientationType]
+                            const orientation = type[feature.get('pair_orientation')]
+                            const map = {
+                                'LR': 'color_pair_lr',
+                                'RR': 'color_pair_rr',
+                                'RL': 'color_pair_rl',
+                                'LL': 'color_pair_ll'
+                            };
+                            return glyph.getStyle( feature, map[orientation] || 'color_nostrand' );
+                        }
                         return 'hsl(' + Math.abs(score / 10) + ',50%,50%)';
                     },
+                    color_pair_lr: 'grey',
+                    color_pair_rr: 'navy',
+                    color_pair_rl: 'teal',
+                    color_pair_ll: 'green',
+                    color_nostrand: '#999999',
                     mouseovercolor: 'rgba(0,0,0,0)',
-                    strandArrow: false
+                    strandArrow: false,
+                    orientationType: 'fr' // default illumina adapter sequence --> <--
                 }
             });
         },
@@ -30,7 +93,7 @@ function(
                 return;
             }
             context.beginPath();
-            context.strokeStyle = this.getConf('style.color', [fRect.f, r.span]);
+            context.strokeStyle = this.getConf('style.color', [fRect.f, r.span, this, this.track]);
             context.arc(r.drawTo + r.r, 0, Math.abs(r.r), 0, Math.PI);
             context.stroke();
         },

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -93,7 +93,6 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
             }
         });
 
-        console.log(this.config.viewAsPairs == false && this.config.readCloud == false)
         displayOptions.push({
             label: 'View normal',
             onClick: function(event) {
@@ -104,8 +103,6 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
             }
         });
 
-
-            console.log('t1',this.config.viewAsPairs == true && this.config.readCloud == false)
         displayOptions.push({
             label: 'View as pairs',
             onClick: function(event) {