Merge pull request #2 from igvteam/2.6.x

Update igv.js to 2.6.x branch

README.md

@@ -15,13 +15,13 @@ See the [Wiki](https://github.com/igvteam/igv.js/wiki) for more documentation.
 
 # Examples
 
-***[Alignments](https://igv.org/web/release/2.5.5/examples/cram.html)***
+***[Alignments](https://igv.org/web/release/2.6.8/examples/cram.html)***
 
-***[Copy number](https://igv.org/web/release/2.5.5/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.6.8/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.5.5/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.6.8/examples/multi-locus.html)***
 
-***[More](https://igv.org/web/release/2.5.5/examples/)***
+***[More](https://igv.org/web/release/2.6.8/examples/)***
 
 
 # Quickstart
@@ -30,11 +30,11 @@ See the [Wiki](https://github.com/igvteam/igv.js/wiki) for more documentation.
 igv.js consists of a single javascript file with no external dependencies.  To link directly to the current release copy this snippet
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.5.5/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.6.8/dist/igv.min.js"></script>
 ``` 
 
 Pre-built files for ES5 (igv.min.js) and ES6 (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.5.5/dist/](https://cdn.jsdelivr.net/npm/igv@2.5.5/dist/).   
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.6.8/dist/](https://cdn.jsdelivr.net/npm/igv@2.6.8/dist/).   
 
 Alternatively you can install with npm  
 
@@ -48,11 +48,11 @@ To use igv.js include it with a script tag
 
 ***or*** import it as a requirejs module 
 
-```requirejs(['igv.min'], function (igv) {...}```   *(see [examples/igv-require.html](https://igv.org/web/release/2.5.5/examples/igv-require.html))*
+```requirejs(['igv.min'], function (igv) {...}```   *(see [examples/igv-require.html](https://igv.org/web/release/2.6.8/examples/igv-require.html))*
 
 ***or*** import it as an es6 module 
 
-```import igv from 'igv.esm.min.js'```  *(see [examples/igv-esm.html](https://igv.org/web/release/2.5.5/examples/igv-esm.html))*
+```import igv from 'igv.esm.min.js'```  *(see [examples/igv-esm.html](https://igv.org/web/release/2.6.8/examples/igv-esm.html))*
 
 
 
@@ -117,19 +117,6 @@ This creates a dist folder with the following files
 * igv.esm.js --  ES6 module 
 * igv.esm.min.js --  minified version of igv.esm.js
 
-### Tests
-
-To run the tests from the command line
-
-```
-npm run test
-```
-
-To run the tests in a browser start an [http-server](https://www.npmjs.com/package/http-server)
-
-    npm run http-server
-
-Then open [http://localhost:8080/test/runTests.html](http://localhost:8080/test/runTests.html).
 
 
 ### Examples
@@ -141,14 +128,14 @@ To run the examples start an [http-server](https://www.npmjs.com/package/http-se
 Then open [http://localhost:8080/examples](http://localhost:8080/examples).
 
 
-# Supported Browsers
+### Supported Browsers
 
-igv.js require a modern web browser with support for Javascript ECMAScript 2015. 
+igv.js require a modern web browser with support for Javascript ECMAScript 2015.
 
-# License
+### License
 
 igv.js is [MIT](/LICENSE) licensed.
 
-# [_Release Notes_](https://github.com/igvteam/igv.js/releases)
+### [_Release Notes_](https://github.com/igvteam/igv.js/releases)
 
 

css/igv.scss

@@ -52,7 +52,7 @@ $igv-trackgear-popover-border-radius: 4px;
 $igv-trackgear-font-color: #4b4b4b;
 $igv-trackgear-default-font-face: 'Open Sans', sans-serif;
 
-$igv-track-components-margin: 5px;
+$igv-track-components-margin: 0px;
 
 @mixin generic-input {
 
@@ -189,16 +189,16 @@ $igv-track-components-margin: 5px;
 
   // igv logo
   .igv-logo {
+    all: initial;
     width: 34px;
     height: $igv-navbar-height;
-    margin-top:6px;
+    //margin-top:6px;
     //margin-left: 8px;
     margin-right: 8px;
   }
 
   .igv-current-genome {
     height: $igv-navbar-height;
-    width: 40px;
     margin-left: 4px;
     margin-right: 4px;
     user-select: none;
@@ -558,9 +558,14 @@ $igv-track-components-margin: 5px;
     font-weight: 700;
     color: #141414;
   }
+}
 
+.igv-canvas {
+  all: initial;
 }
 
+
+
 // root container
 .igv-root-div {
 
@@ -592,6 +597,8 @@ $igv-track-components-margin: 5px;
 .igv-track-div {
   position: relative;
   width: 100%;
+  margin-top: 5px;
+  margin-bottom: 5px;
 }
 
 .igv-viewport-container {
@@ -822,8 +829,6 @@ $igv-track-components-margin: 5px;
   left: 0;
   width: 50px;
   height: 100%;
-  margin-top: $igv-track-components-margin;
-  margin-bottom: $igv-track-components-margin;
 
   canvas {
     position: absolute;
@@ -868,8 +873,6 @@ $igv-track-components-margin: 5px;
   width: 12px;
 
   margin-left: 2px;
-  margin-top: $igv-track-components-margin;
-  margin-bottom: $igv-track-components-margin;
 
   height: 100%;
 
@@ -904,7 +907,7 @@ $igv-track-components-margin: 5px;
   position: absolute;
 
   left: 8px;
-  top: 4px;
+  top: 8px;
 
   width: auto;
   height:auto;
@@ -952,9 +955,6 @@ $igv-track-components-margin: 5px;
   right: 0;
   width: 14px;
   height: 100%;
-  margin-top: $igv-track-components-margin;
-  margin-bottom: $igv-track-components-margin;
-
   background-color: white;
 
   div {

dev/2contig.html

@@ -0,0 +1,57 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8">
+    <meta content="IE=edge" http-equiv="X-UA-Compatible">
+    <meta content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no" name="viewport">
+    <meta content="" name="description">
+    <meta content="" name="author">
+    <link href=img/favicon.ico rel="shortcut icon">
+    <title>IGV - Dev</title>
+    <link href="css/dev.css" rel="stylesheet" type="text/css"/>
+
+</head>
+
+<body>
+
+<h1>single contig fasta</h1>
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../js/index.js";
+
+    var options =
+        {
+            reference: {
+                fastaURL: 'https://s3.amazonaws.com/igv.org.test/data/1contig/fasta.fasta',
+                indexURL: 'https://s3.amazonaws.com/igv.org.test/data/1contig/fasta.fai',
+                //wholeGenomeView: false
+            },
+            tracks: [
+                {
+                    type: 'variant',
+                    format: 'vcf',
+                    url: 'https://s3.amazonaws.com/igv.org.test/data/1contig/snp.vcf',
+                    indexed: false,
+                    name: 'snps'
+                }
+
+            ]
+        };
+
+    var igvDiv = document.getElementById("igvDiv");
+
+    igv.createBrowser(igvDiv, options)
+        .then(function (browser) {
+            console.log("Created IGV browser");
+            window.igvBrowser = browser;
+        })
+
+
+</script>
+
+</body>
+
+</html>