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igvteam · Jul 30, 2024 · 0114afb · 0114afb
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diff --git a/README.md b/README.md
@@ -14,23 +14,23 @@ James T Robinson, Helga Thorvaldsdottir, Douglass Turner, Jill P Mesirov, igv.js
 implementation of the Integrative Genomics Viewer (IGV), Bioinformatics, Volume 39, Issue 1, January 2023, 
 btac830, https://doi.org/10.1093/bioinformatics/btac830
 
-Below are examples and a quickstart guide.  See the [Wiki](https://github.com/igvteam/igv.js/wiki) for more documentation.  
+Below are examples and a quickstart guide.  See the [developer documentation](https://igv.org/doc/igvjs) for more documentation.  
 
 # Examples
 
-***[Alignments](https://igv.org/web/release/2.15.13/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/3.0.0/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.15.13/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/3.0.0/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.15.13/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/3.0.0/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.15.13/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/3.0.0/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.13/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.0/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.15.13/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/3.0.0/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.15.13/examples/)***
+***[More](https://igv.org/web/release/3.0.0/examples/)***
 
 
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 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/igv@2.15.13/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/](https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/igv.min.js"></script>
 ```   
 
 Alternatively you can install with npm  

diff --git a/dev/alignment/basemods/6mA_pacbio.json b/dev/alignment/basemods/6mA_pacbio.json
@@ -8,7 +8,7 @@
       "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
       "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
       "height": 400,
-      "name": "PacBio - 6mA 2 Color",
+      "name": "5mC and 6mA - 2 color mode",
       "colorBy": "basemod2",
       "groupBy": "strand",
       "baseModificationThreshold": 0
@@ -19,7 +19,7 @@
       "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
       "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
       "height": 400,
-      "name": "PacBio - 6mA",
+      "name": "5mC and 6mA - mono color mode",
       "colorBy": "basemod",
       "groupBy": "strand"
     }

diff --git a/examples/base-modifications.html b/examples/base-modifications.html
@@ -0,0 +1,57 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+
+    <title>igv.js</title>
+</head>
+
+<body>
+
+<h1>Base Modifications</h1>
+
+<div id="igvDiv" style="padding-top: 10px;padding-bottom: 10px; border:1px solid lightgray"></div>
+
+<script type="module">
+
+    import igv from "../dist/igv.esm.min.js"
+
+    const options = {
+        "genome": "hg38",
+        "locus": "chr11:119094729-119094804",
+        "tracks": [
+            {
+                "type": "alignment",
+                "format": "bam",
+                "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
+                "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
+                "height": 400,
+                "name": "5mC and 6mA - 2 color mode",
+                "colorBy": "basemod2",
+                "groupBy": "strand",
+                "baseModificationThreshold": 0
+            },
+            {
+                "type": "alignment",
+                "format": "bam",
+                "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
+                "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
+                "height": 400,
+                "name": "5mC and 6mA - mono color mode",
+                "colorBy": "basemod",
+                "groupBy": "strand"
+            }
+        ]
+    }
+
+    var igvDiv = document.getElementById("igvDiv")
+
+    igv.createBrowser(igvDiv, options)
+        .then(function (browser) {
+            console.log("Created IGV browser")
+        })
+
+</script>
+
+</body>
+
+</html>
diff --git a/js/bam/alignmentContainer.js b/js/bam/alignmentContainer.js
@@ -764,7 +764,6 @@ function getGroupValue(al, groupBy, expectedPairOrientation) {
         // Add cases for other options as needed
         case 'base':
 
-            // Use a string prefix to enforce grouping rules:
             //    1: alignments with a base at the position
             //    2: alignments with a gap at the position
             //    3: alignment that do not overlap the position (or are on a different chromosome)

diff --git a/js/version.js b/js/version.js
@@ -1,4 +1,4 @@
-const _version = "2.16.0"
+const _version = "3.0.0"
 function version() {
     return _version
 }

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "igv",
-  "version": "2.16.0",
+  "version": "3.0.0",
   "main": "dist/igv.esm.js",
   "browser": "dist/igv.js",
   "module": "dist/igv.esm.js",