@candig/igv

This is a CanDIG fork of the igv.js, which adds support for Reads and Variants API of candig-server.

igv.js

igv.js is an embeddable interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team.

Below are examples and a quickstart guide. See the Wiki for more documentation.

Examples

Alignments

Interactions

Copy number

Multiple regions

Mutation Annotation Format (MAF)

Variant color options

More

Quickstart

Installation

igv.js consists of a single javascript file with no external dependencies.

Pre-built files for ES5 (igv.min.js) and ES6 (igv.esm.min.js) can be downloaded from https://cdn.jsdelivr.net/npm/[email protected]/dist/.

To import igv as an ES6 module

import igv from "https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.esm.min.js"

Or as a script include (defines the "igv" global)

<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.min.js"></script>

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)

or import it as an es6 module

import igv from 'igv.esm.min.js' (see 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. For example, to open a browser on a single alignment track opened at a specific locus:

      var igvDiv = document.getElementById("igv-div");
      var options =
        {
            genome: "hg38",
            locus: "chr8:127,736,588-127,739,371",
            tracks: [
                {
                    "name": "HG00103",
                    "url": "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram",
                    "indexURL": "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram.crai",
                    "format": "cram"
                }
            ]
        };

        igv.createBrowser(igvDiv, options)
                .then(function (browser) {
                    console.log("Created IGV browser");
                })

For more details see the 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.

Building

Building igv.js and running the examples requires node.js.

git clone https://github.com/igvteam/igv.js.git
cd igv.js
npm install
npm run build

This creates a dist folder with the following files

• igv.js - ES5 compatible UMDS file for script include, AMD, or CJS modules. A script include will define an "igv" global.
• igv.min.js - minified version of igv.js
• 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

Examples

To run the examples install http-server.

Start http-server from the project root directory

npx http-server 

Then open http://localhost:8080/examples in a web browser.

Supported Browsers

igv.js require a modern web browser with support for Javascript ECMAScript 2015.

License

igv.js is MIT licensed.

Release Notes