Rebase to main fork

.gitignore

@@ -1,10 +1,21 @@
 .DS_Store
+/.vscode/
+/dist/
+/es5/
 /.idea/
 /igv.js.iml
 /node_modules/.bin/cake
 /node_modules
-/dist/
 /tmp/
 /cBio/
 /miRNA/
 *.iml
+/npm-debug.log
+/css/.sass-cache/ab483755b4a226863a81d799c4857b21ee6820d0/_igv_trackgear_popup.scssc
+/css/.sass-cache/ab483755b4a226863a81d799c4857b21ee6820d0/_igv-colorpicker.scssc
+/css/.sass-cache/ab483755b4a226863a81d799c4857b21ee6820d0/_igv-generic-container.scssc
+/css/.sass-cache/ab483755b4a226863a81d799c4857b21ee6820d0/igv.scssc
+/css/.sass-cache/ab483755b4a226863a81d799c4857b21ee6820d0/_igv-trackgear-popup.scssc
+/css/.sass-cache/ab483755b4a226863a81d799c4857b21ee6820d0/_igv-user-feedback.scssc
+/css/.sass-cache/ab483755b4a226863a81d799c4857b21ee6820d0/_igv-generic-dialog-container.scssc
+/css/.sass-cache

.travis.yml

@@ -0,0 +1,9 @@
+language: node_js
+dist: trusty
+sudo: required
+node_js:
+  - "8.11.1"
+addons:
+  chrome: stable
+before_script: npm install -g grunt-cli; npm ls; grunt
+script: npm test

Gruntfile.js

@@ -1,13 +1,54 @@
+const webpackConfig = require('./webpack.config.js');
+
 module.exports = function (grunt) {
+    require("load-grunt-tasks")(grunt);
 
     // 1. All configuration goes here
     grunt.initConfig({
+
         pkg: grunt.file.readJSON('package.json'),
 
+        qunit_puppeteer: {
+            test: {
+                options: {
+                    headless: true,
+                    traceSettings: {
+                        outputConsole: false,
+                        outputAllAssertions: false
+                    },
+                    qunitPage: 'http://0.0.0.0:8000/test/runTests.html'
+                }
+            }
+        },
+
+        connect: {
+            server: {
+                options: {
+                    port: 8000,
+                    base: '.'
+                }
+            }
+        },
+
+        webpack: {
+            options: {
+                stats: !process.env.NODE_ENV || process.env.NODE_ENV === 'development'
+            },
+            prod: webpackConfig,
+            dev: Object.assign({ watch: true }, webpackConfig)
+        },
+
+        copy: {
+            igvjs: {
+                src: 'dist/igv.min.js',
+                dest: 'dist/igv.js',
+            },
+        },
+
         concat: {
             igv: {
                 src: [
-                    'wrapper/header.js',
+                    'wrapper/header-cjs.js',
                     'tmp/embedCss.js',
                     'vendor/jquery-3.3.1.slim.js',
                     'vendor/underscore.js',
@@ -16,12 +57,13 @@ module.exports = function (grunt) {
                     'vendor/jquery.mousewheel.js',
                     'vendor/rbtree.js',
                     'vendor/tdigest.js',
+                    'vendor/cram-bundle.js',
                     'js/**/*.js',
-                    'wrapper/footer.js'
+                    'wrapper/footer-cjs.js'
                 ],
-                dest: 'dist/igv.js'
+                dest: 'tmp/igv-cjs.js'
             },
-            igv_es6: {
+            igv_esm: {
                 src: [
                     'wrapper/header-esm.js',
                     'tmp/embedCss.js',
@@ -32,6 +74,7 @@ module.exports = function (grunt) {
                     'vendor/jquery.mousewheel.js',
                     'vendor/rbtree.js',
                     'vendor/tdigest.js',
+                    'vendor/cram-bundle.js',
                     'js/**/*.js',
                     'wrapper/footer-esm.js'
                 ],
@@ -83,30 +126,55 @@ module.exports = function (grunt) {
                 dest: 'dist/igv.esm.min.js'
             }
         },
+        babel: {
+            options: {
+                sourceMap: true,
+                presets: ['es2015']
+            },
+            dist: {
+                files: {
+                    'dist/igv.esm.js': 'dist/igv.esm.js',
+                    'dist/igv.js': 'dist/igv.js',
+                }
+            }
+        }
+
+        clean: {
+            dist: ['dist'],
+            tmp: ['tmp']
+        }
 
     });
 
     // 3. Where we tell Grunt we plan to use this plug-in.
     grunt.loadNpmTasks('grunt-contrib-concat');
     grunt.loadNpmTasks('grunt-contrib-uglify-es');
+    grunt.loadNpmTasks('grunt-qunit-puppeteer');
+    grunt.loadNpmTasks('grunt-contrib-connect');
+    grunt.loadNpmTasks('grunt-contrib-clean');
+    grunt.loadNpmTasks('grunt-contrib-copy');
+    grunt.loadNpmTasks('grunt-webpack');
 
     // 4. Where we tell Grunt what to do when we type "grunt" into the terminal.
-    grunt.registerTask('default', [ 'concat:css', 'embed-css', 'concat:igv', 'concat:igv_es6', 'uglify:igv', 'uglify:igv_esm']);
+    grunt.registerTask('default', ['clean:dist', 'concat:css', 'embed-css', 'concat:igv', 'webpack:prod', 'concat:igv_esm', 'babel', 'uglify:igv_esm', 'copy:igvjs', 'clean:tmp']);
 
     grunt.registerTask('doc', ['md2html']);
 
+    grunt.registerTask('test', ['connect', 'qunit_puppeteer:test']);
+
     grunt.task.registerTask('embed-css', 'One line-ify igv.css.', function () {
 
         var ping,
             pong,
             foo;
 
         ping = grunt.file.read('tmp/igv-all.css');
+        ping = ping.replace(/\r\n/g, '\\n');
         pong = ping.replace(/\n/g, '\\n');
         ping = pong.replace(/"/g, '\\"');
 
         foo = grunt.file.read('wrapper/embedCss.js');
-        foo = foo.replace('_CSS_', ping)
+        foo = foo.replace('_CSS_', ping);
 
         grunt.file.write('tmp/embedCss.js', foo);
     });

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2018 The Regents of the University of California
+Copyright (c) 2018 Regents of the University of California and Broad Institute
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,7 +1,150 @@
-igv.js
-=======
+# igv.js
+[![Build Status](https://travis-ci.org/igvteam/igv.js.svg?branch=master)](https://travis-ci.org/igvteam/igv.js)
 
+igv.js is an embeddable interactive genome visualization component developed by the 
+ [Integrative Genomics Viewer (IGV)](https://igv.org) team. 
+
+Below are examples and a quickstart guide.  
+See the [Wiki](https://github.com/igvteam/igv.js/wiki) for more documentation.  
 
-igv.js is an embeddable interactive genome visualization component.  It is based on the desktop [Integrative Genomics Viewer (IGV)](http://www.broadinstitute.org/igv), and developed by the same team.
+
+# Examples
+
+***[Alignments](https://igv.org/web/release/2.2.0/examples/bam.html)***
 
-See the [Wiki](https://github.com/igvteam/igv.js/wiki) for more information.
+***[GA4GH](https://igv.org/web/release/2.2.0/examples/ga4gh.html)***
+
+***[Copy number](https://igv.org/web/release/2.2.0/examples/copyNumber.html)***
+
+***[Multiple regions](http://igv.org/release/2.2.0/test/examples/multi-locus.html)***
+
+***[More](http://igv.org/web/release/2.2.0/examples)***
+
+
+# Quickstart
+
+## Installation
+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@2.2.0/dist/igv.min.js"></script>
+``` 
+
+Pre-built expanded and minified js files for ES5 (igv.js, igv.min.js) and ES6 (igv.esm.js, igv.esm.min.js)
+can be downloaded from [https://igv.org/web/release/2.2.0/dist/](https://igv.org/web/release/2.2.0/dist/).   
+
+Alternatively you can install with npm  
+
+ ```npm install igv```
+
+and source the appropriate file for your module system (igv.min.js or igv.esm.min.js)  in node_modules/igv/dist.
+
+To use igv.js include it with a script tag
+
+````<script src="igv.min.js/>````
+
+***or*** import it as a requirejs module 
+
+```requirejs(['igv.min'], function (igv) {...}```   *(see [examples/igv-require.html](http://igv.org/web/release/2.2.0/examples/igv-require.html))*
+
+***or*** import it as an es6 module 
+
+```import igv from 'igv.esm.min.js'```  *(see [examples/igv-esm.html](http://igv.org/web/release/2.2.0/examples/igv-esm.html))*
+
+
+
+## Usage
+
+To create an igv.js ***browser*** supply a container div 
+and an initial configuration defining the reference genome, initial tracks, and other state to the 
+function ```igv.createBrowser(div, config)```.  
+
+This function returns a promise for an igv.Browser object which can used to control the browser.  An 
+[example](http://igv.org/web/release/2.0.0-rc5/examples/bam.html) of
+a browser on a single alignment track opened at a specific locus:
+
+```
+      var igvDiv = document.getElementById("igv-div");
+      var options =
+        {
+            genome: "hg19",
+            locus: "chr8:128,747,267-128,754,546",
+            tracks: [
+                {
+                    type: 'alignment',
+                    format: 'bam',
+                    url: 'https://data.broadinstitute.org/igvdata/1KG/b37/data/HG02450/alignment/HG02450.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam',
+                    name: 'HG02450'
+                }
+            ]
+        };
+
+        igv.createBrowser(igvDiv, options)
+                .then(function (browser) {
+                    console.log("Created IGV browser");
+                })
+```
+
+For more details see the [Wiki](https://github.com/igvteam/igv.js/wiki) for full documentation of the API.
+
+## Development
+
+### Requirements
+
+Building igv.js and running the examples require Linux or MacOS.  Other Unix environments will probably
+work but have not been tested.  
+
+Windows users can use [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10).
+
+### Building
+
+Building igv.js and running the examples requires [node.js](https://nodejs.org/).
+
+
+```  
+git clone https://github.com/igvteam/igv.js.git
+cd igv.js
+npm install
+npm run grunt
+```
+
+This creates a dist folder with the following files
+
+* igv.js, igv.min.js - ES5 compatible files for script or requirejs imports
+* igv.esm.js,  igv.esm.min.js --  ES6 module 
+
+
+### Tests
+
+To run the tests from the command line
+
+```
+    grunt 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
+
+To run the examples start an [http-server](https://www.npmjs.com/package/http-server)
+
+    npm run http-server
+
+Then open [http://localhost:8080/index.html](http://localhost:8080/index.html).
+
+
+# Supported Browsers
+
+igv-webapp and igv.js require a modern web browser with support for Javascript ECMAScript 2015. We test on the latest versions of Chrome, Safari, Firefox, and Edge. Internet Explorer (IE) is not supported.
+
+# License
+
+igv.js is [MIT](/LICENSE) licensed.
+
+[documentation]: https://github.com/igvteam/igv.js/wiki
+[examples]: http://igv.org/web/test/examples