Updated examples. Version bump.

igvteam · Oct 11, 2024 · b962c35 · b962c35
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Showing 7 changed files with 63 additions and 59 deletions.
diff --git a/README.md b/README.md
@@ -18,19 +18,19 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 
 # Examples
 
-***[Alignments](https://igv.org/web/release/3.0.7/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.0.8/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/3.0.7/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.0.8/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/3.0.7/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.0.8/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/3.0.7/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.0.8/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.7/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.8/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/3.0.7/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.0.8/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/3.0.7/examples/)***
+***[More](https://igv.org/web/release/3.0.8/examples/)***
 
 
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [developer documentation](ht
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/[email protected].7/dist/](https://cdn.jsdelivr.net/npm/[email protected].7/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/[email protected].8/dist/](https://cdn.jsdelivr.net/npm/[email protected].8/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/[email protected].7/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/[email protected].8/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/[email protected].7/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/[email protected].8/dist/igv.min.js"></script>
 ```   
 
 Alternatively you can install with npm  

diff --git a/dev/encode/bigwig.html b/dev/encode/bigwig.html
@@ -1,46 +1,24 @@
 <head>
 
-    <link rel="stylesheet" href="https://unpkg.com/@reservoirgenomics/[email protected]/dist/hglib.css">
-    <script crossorigin src="https://unpkg.com/[email protected]/dist/higlass-plugins.min.js">
-
-    </script>
-    <script crossorigin src="https://unpkg.com/@reservoirgenomics/[email protected]/dist/hglib.js">
-
-    </script>
-
     <meta charset="UTF-8"/>
     <meta http-equiv="X-UA-Compatible" content="IE=edge"/>
-    <title>Juicebox</title>
+    <title>IGV</title>
     <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
 
-    <!-- IGV JS -->
-    <script src="../../dist/igv.min.js"></script>
-
-
-
 </head>
 <body>
 
 <div id="igv-container" style="width: auto; margin-left: 10px; border: 1px solid black;">
 </div>
 
-<script>
+<script type="module">
+
+    import igv from "../../js/index.js"
+
     const igvConfig ={
-        "reference": {
-            "id": "hg19",
-            "name": "Human (CRCh37/hg19)",
-            "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta",
-            "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai",
-            "cytobandURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt"
-        },
-        "locus": [
-            "chr8:128,746,315-128,755,680"
-        ],
+        "genome": "hg19",
+        "locus": "chr8:128,746,315-128,755,680",
         "tracks": [
-            {
-                "type": "sequence",
-                "order": -1.7976931348623157e+308
-            },
             {
                 "url": "https://www.encodeproject.org/files/ENCFF000ATR/@@download/ENCFF000ATR.bigWig",
                 "color": "#018448",
@@ -76,23 +54,6 @@
                 "height": 50,
                 "autoscale": true,
                 "order": 5
-            },
-            {
-                "name": "Refseq Genes",
-                "format": "refgene",
-                "url": "https://s3.amazonaws.com/igv.org.genomes/hg19/refGene.sorted.txt.gz",
-                "indexURL": "https://s3.amazonaws.com/igv.org.genomes/hg19/refGene.sorted.txt.gz.tbi",
-                "visibilityWindow": -1,
-                "removable": false,
-                "order": 1000000,
-                "filename": "refGene.sorted.txt.gz",
-                "sourceType": "file",
-                "type": "annotation",
-                "maxRows": 500,
-                "filterTypes": [
-                    "chromosome",
-                    "gene"
-                ]
             }
         ]
     }

diff --git a/dev/ucsc/simpleGenark.html b/dev/ucsc/simpleGenark.html
@@ -0,0 +1,17 @@
+<html>
+
+<body>
+
+<div id="igvDiv"></div>
+
+<script type="module">
+
+    import igv from "https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.esm.min.js"
+
+   igv.createBrowser(document.getElementById('igvDiv'), {genome: "GCA_000002305.1"})
+
+</script>
+
+</body>
+
+</html>
diff --git a/examples/genark.html b/examples/genark.html
@@ -0,0 +1,26 @@
+<html>
+
+<body>
+
+<h1>UCSC Genark Example</h1>
+
+<p>Example of specifying a genome hosted at the <a href="https://hgdownload.soe.ucsc.edu/hubs/" target="_blank">UCSC
+    Genark</a> assembly hub. For a complete list of available assemblies see the
+    <a href="https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt" target="_blank">hub assembly list.</a>
+</p>
+
+<div id="igvDiv"></div>
+
+<script type="module">
+
+    import igv from "../dist/igv.esm.min.js"
+
+    const config = {genome: "GCA_000002305.1"}
+
+    igv.createBrowser(document.getElementById('igvDiv'), config)
+
+</script>
+
+</body>
+
+</html>
diff --git a/js/embedCss.js b/js/embedCss.js
diff --git a/js/version.js b/js/version.js
@@ -1,4 +1,4 @@
-const _version = "3.0.7"
+const _version = "3.0.8"
 function version() {
     return _version
 }

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "igv",
-  "version": "3.0.7",
+  "version": "3.0.8",
   "main": "dist/igv.esm.js",
   "browser": "dist/igv.js",
   "module": "dist/igv.esm.js",