igv-rails 1.0.9.3 → 1.0.9.4

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 67e4aa36df01edd7e27bf9a30a2b636d430c8eff
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+  data.tar.gz: 81c8923667cd449fdec6c7cf0168c949b6dc1129
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data/lib/igv/rails/version.rb

@@ -1,5 +1,5 @@
 module Igv
   module Rails
-    VERSION = "1.0.9.3"
+    VERSION = "1.0.9.4"
   end
 end

data/vendor/assets/javascripts/igv.js

@@ -11611,10 +11611,14 @@ var igv = (function (igv) {
             this.render = renderFusionJuncSpan;
             this.height = config.height || 50;
             this.autoHeight = false;
-        } else if ("snp" === config.type) {
-            // TODO -- snp specific render function
-            this.render = renderFeature;
-        } else {
+        }
+        else if ('snp' === config.type) {
+            this.render = renderSnp;
+            // colors ordered based on priority least to greatest
+            this.snpColors = ['rgb(0,0,0)', 'rgb(0,0,255)', 'rgb(0,255,0)', 'rgb(255,0,0)'];
+            this.colorBy = 'function';
+        }
+        else {
             this.render = renderFeature;
             this.arrowSpacing = 30;
 
@@ -12216,6 +12220,104 @@ var igv = (function (igv) {
 
     }
 
+    /**
+     *
+     * @param snp
+     * @param bpStart  genomic location of the left edge of the current canvas
+     * @param xScale  scale in base-pairs per pixel
+     * @param pixelHeight  pixel height of the current canvas
+     * @param ctx  the canvas 2d context
+     */
+    function renderSnp(snp, bpStart, xScale, pixelHeight, ctx) {
+
+        var coord = calculateFeatureCoordinates(snp, bpStart, xScale),
+            py = 20,
+            h = 10,
+            colorArrLength = this.snpColors.length,
+            colorPriority;
+
+            switch(this.colorBy) {
+                case 'function':
+                    colorPriority = colorByFunc(snp.func);
+                    break;
+                case 'class':
+                    colorPriority = colorByClass(snp['class']);
+            }
+
+        ctx.fillStyle = this.snpColors[colorPriority];
+        ctx.fillRect(coord.px, py, coord.pw, h);
+
+        // Coloring functions, convert a value to a priority
+
+        function colorByFunc(theFunc) {
+            var funcArray = theFunc.split(',');
+            // possible func values
+            var codingNonSynonSet = new Set(['nonsense', 'missense', 'stop-loss', 'frameshift', 'cds-indel']),
+                codingSynonSet = new Set(['coding-synon']),
+                spliceSiteSet = new Set(['splice-3', 'splice-5']),
+                untranslatedSet = new Set(['untranslated-5', 'untranslated-3']),
+                priorities;
+            // locusSet = new Set(['near-gene-3', 'near-gene-5']);
+            // intronSet = new Set(['intron']);
+
+            priorities = funcArray.map(function(func) {
+                if (codingNonSynonSet.has(func) || spliceSiteSet.has(func)) {
+                    return colorArrLength - 1;
+                } else if (codingSynonSet.has(func)) {
+                    return colorArrLength - 2;
+                } else if (untranslatedSet.has(func)) {
+                    return colorArrLength - 3;
+                } else { // locusSet.has(func) || intronSet.has(func)
+                    return 0;
+                }
+            });
+
+            return priorities.reduce(function(a,b) {
+                return Math.max(a,b);
+            });
+        }
+
+        function colorByClass(cls) {
+            if (cls === 'deletion') {
+                return colorArrLength - 1;
+            } else if (cls === 'mnp') {
+                return colorArrLength - 2;
+            } else if (cls === 'microsatellite' || cls === 'named') {
+                return colorArrLength - 3;
+            } else { // cls === 'single' || cls === 'in-del' || cls === 'insertion'
+                return 0;
+            }
+        }
+    }
+
+    igv.FeatureTrack.prototype.popupMenuItemList = function(config) {
+        if (this.render === renderSnp) {
+
+            var menuItems = [], self = this;
+
+            menuItems.push({
+                name: 'Color by function',
+                click: function() {
+                    setColorBy('function');
+                }
+            });
+            menuItems.push({
+                name: 'Color by class',
+                click: function() {
+                    setColorBy('class');
+                }
+            });
+
+            return menuItems;
+
+            function setColorBy(value) {
+                self.colorBy = value;
+                self.trackView.update();
+                config.popover.hide();
+            }
+        }
+    };
+
 
     return igv;
 
@@ -13403,9 +13505,6 @@ var igv = (function (igv) {
             igv.xhr.loadJson(url, self.config)
                 .then(function (data) {
                     if (data) {
-                        data.forEach(function (json) {
-                            decodeJson(json);
-                        });
                         fulfill(data);
                     } else {
                         fulfill(null);
@@ -13417,11 +13516,6 @@ var igv = (function (igv) {
         });
     };
 
-    // TODO -- generalize
-    function decodeJson(feature) {
-        if(feature.start) feature.start = Number.parseInt(feature.start);
-        if(feature.end)  feature.end = Number.parseInt(feature.end);
-    }
 
     return igv;
 })(igv || {});
@@ -14818,12 +14912,12 @@ var igv = (function (igv) {
                         },
                         decode: function (json) {
                             // If specific callSetIds are specified filter to those
-                            if (self.callSetIds) {
+                             if (self.callSetIds) {
                                 var filteredCallSets = [],
                                     csIdSet = new Set();
 
                                 self.callSetIds.forEach(function (csid) {
-                                    csIdSet.add(m);
+                                    csIdSet.add(csid);
                                 })
                                 json.callSets.forEach(function (cs) {
                                     if (csIdSet.has(cs.id)) {
@@ -23460,6 +23554,7 @@ var igv = (function (igv) {
             case "snp":
             case "genes":
             case "fusionjuncspan":
+            case "snp":
                 return new igv.FeatureTrack(conf);
                 break;
 
@@ -27031,11 +27126,11 @@ var igv = (function (igv) {
 
         function calcHeterozygosity(ac, an) {
             var sum = 0,
-                altFreqs = ac.split(','),
+                altFreqs = Array.isArray(ac) ? ac : ac.split(','),
                 altCount = 0,
                 refFrac;
 
-            an = parseInt(an);
+            an = Array.isArray(an) ? parseInt(an[0]) : parseInt(an);
             altFreqs.forEach(function (altFreq) {
                 var a = parseInt(altFreq),
                     altFrac = a / an;

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: igv-rails
 version: !ruby/object:Gem::Version
-  version: 1.0.9.3
+  version: 1.0.9.4
 platform: ruby
 authors:
 - William Van Etten, PhD
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-09-26 00:00:00.000000000 Z
+date: 2017-09-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: railties