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igvteam · Aug 7, 2024 · 63420c4 · 63420c4
1 parent 8abb2d6
commit 63420c4
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Showing 12 changed files with 217 additions and 134 deletions.
diff --git a/dev/wig/merged.html b/dev/wig/merged.html
@@ -6,6 +6,8 @@
 </head>
 
 <body>
+<button id="log-state">Log Session</button>
+<button id="bookmark">Bookmark</button>
 
 <h1>Merged track</h1>
 
@@ -22,25 +24,12 @@ <h1>Merged track</h1>
 
     var options =
         {
+            queryParametersSupported: true,
             genome: "hg19",
             locus: "chr4:40,174,668-40,221,204",
             tracks: [
-                // {
-                //     "type": "wig",
-                //     "format": "bigwig",
-                //     "url": "https://www.encodeproject.org/files/ENCFF000ASJ/@@download/ENCFF000ASJ.bigWig",
-                //     "color": "red",
-                //     "name": "ENCFF000ASJ"
-                // },
-                // {
-                //     "type": "wig",
-                //     "format": "bigwig",
-                //     "url": "https://www.encodeproject.org/files/ENCFF351WPV/@@download/ENCFF351WPV.bigWig",
-                //     "color": "green",
-                //     "name": "ENCFF351WPV"
-                // },
                 {
-                    name: "Merged - group autoscaled",
+                    name: "Merged - autoscaled",
                     type: "merged",
                     autoscale: true,
                     tracks: [
@@ -58,6 +47,26 @@ <h1>Merged track</h1>
                         }
                     ]
                 },
+                {
+                    name: "Merged - fixed scale",
+                    type: "merged",
+                    min: 0,
+                    max: 100,
+                    tracks: [
+                        {
+                            "type": "wig",
+                            "format": "bigwig",
+                            "url": "https://www.encodeproject.org/files/ENCFF000ASJ/@@download/ENCFF000ASJ.bigWig",
+                            "color": "red"
+                        },
+                        {
+                            "type": "wig",
+                            "format": "bigwig",
+                            "url": "https://www.encodeproject.org/files/ENCFF351WPV/@@download/ENCFF351WPV.bigWig",
+                            "color": "green"
+                        }
+                    ]
+                },
                 {
                     name: "Merged - individual autoscaled",
                     type: "merged",
@@ -77,15 +86,42 @@ <h1>Merged track</h1>
                             "autoscale": true
                         }
                     ]
-                }
+                },
+                {
+                    name: "Merged - individual fixed scale",
+                    type: "merged",
+                    tracks: [
+                        {
+                            "type": "wig",
+                            "format": "bigwig",
+                            "url": "https://www.encodeproject.org/files/ENCFF000ASJ/@@download/ENCFF000ASJ.bigWig",
+                            "color": "red",
+                            "max": 100
+                        },
+                        {
+                            "type": "wig",
+                            "format": "bigwig",
+                            "url": "https://www.encodeproject.org/files/ENCFF351WPV/@@download/ENCFF351WPV.bigWig",
+                            "color": "green",
+                            "max": 50
+                        }
+                    ]
+                },
             ]
         }
 
     var igvDiv = document.getElementById("igvDiv")
 
     igv.createBrowser(igvDiv, options)
         .then(function (browser) {
-            console.log("Created IGV browser")
+            document.getElementById("log-state").addEventListener("click", () => console.log(browser.toJSON()))
+
+            document.getElementById('bookmark').addEventListener('click', () => {
+                const path = window.location.href.slice()
+                const idx = path.indexOf("?")
+                const url = (idx > 0 ? path.substring(0, idx) : path) + "?sessionURL=blob:" + browser.compressedSession()
+                window.history.pushState({}, "IGV", url)
+            })
         })
 
 

diff --git a/examples/mergedWig.html b/examples/mergedWig.html
@@ -63,7 +63,27 @@ <h1>Merged track</h1>
                             "color": "green"
                         }
                     ]
-                }
+                },
+                {
+                    name: "Merged - individual autoscaled",
+                    type: "merged",
+                    tracks: [
+                        {
+                            "type": "wig",
+                            "format": "bigwig",
+                            "url": "https://www.encodeproject.org/files/ENCFF000ASJ/@@download/ENCFF000ASJ.bigWig",
+                            "color": "red",
+                            "autoscale": true
+                        },
+                        {
+                            "type": "wig",
+                            "format": "bigwig",
+                            "url": "https://www.encodeproject.org/files/ENCFF351WPV/@@download/ENCFF351WPV.bigWig",
+                            "color": "green",
+                            "autoscale": true
+                        }
+                    ]
+                },
             ]
         }
 

diff --git a/examples/spliceJunctions.html b/examples/spliceJunctions.html
@@ -13,7 +13,7 @@ <h1>Splice junctions</h1>
 
 <script type="module">
 
-    import igv from "../js/index.js";
+    import igv from "../dist/igv.esm.min.js"
 
     const tracks = [
         {
@@ -47,7 +47,7 @@ <h1>Splice junctions</h1>
         },
         {
             type: 'merged',
-            name: 'Splice Junctions',
+            name: 'Junctions + Coverage',
             height: 150,
             tracks: [
                 {

diff --git a/js/bam/coverageTrack.js b/js/bam/coverageTrack.js
@@ -9,6 +9,7 @@ class CoverageTrack  {
 
 
     constructor(config, parent) {
+        this.featureType = 'numeric'
         this.parent = parent
         this.featureSource = parent.featureSource
 

diff --git a/js/cnvpytor/cnvpytorTrack.js b/js/cnvpytor/cnvpytorTrack.js
@@ -141,12 +141,12 @@ class CNVPytorTrack extends TrackBase {
                 if (this.signals.includes(signal_name)) {
                     let tconf = {}
                     tconf.type = "wig"
-                    tconf.isMergedTrack = true
                     tconf.features = wig
                     tconf.name = signal_name
                     tconf.color = this.signal_colors.filter(x => x.singal_name === signal_name).map(x => x.color)
                     const t = await this.browser.createTrack(tconf)
                     if (t) {
+                        t.isMergedTrack = true
                         t.autoscale = false     // Scaling done from merged track
                         this.tracks.push(t)
                     } else {
@@ -328,12 +328,12 @@ class CNVPytorTrack extends TrackBase {
             if (this.signals.includes(signal_name)) {
                 let tconf = {}
                 tconf.type = "wig"
-                tconf.isMergedTrack = true
                 tconf.features = wig
                 tconf.name = signal_name
                 tconf.color = this.signal_colors.filter(x => x.singal_name === signal_name).map(x => x.color)
                 const t = await this.browser.createTrack(tconf)
                 if (t) {
+                    t.isMergedTrack = true
                     t.autoscale = false     // Scaling done from merged track
                     this.tracks.push(t)
                 } else {

diff --git a/js/feature/featureTrack.js b/js/feature/featureTrack.js
@@ -199,7 +199,7 @@ class FeatureTrack extends TrackBase {
         }
 
 
-        if (!this.config.isMergedTrack) {
+        if (!this.isMergedTrack) {
             IGVGraphics.fillRect(context, 0, options.pixelTop, pixelWidth, pixelHeight, {'fillStyle': "rgb(255, 255, 255)"})
         }