pileup

pileup.js

pileup.js is an interactive in-browser track viewer. Try a demo!

It is built from the ground up to take advantage of the modern JavaScript ecosystem, e.g. ES2015, static type analysis, React.js and Promises. Read more about the motivations behind pileup.js in our paper.

Showing a structural variant (large deletion):

Usage

To use pileup.js in a project, install it via NPM:

npm install --save pileup

And then source either node_modules/pileup/dist/pileup.min.js or pileup.js.

To create a pileup, use pileup.create(). You specify a container DOM element, an initial range and a list of tracks:

var div = document.getElementById('your-id');
var p = pileup.create(div, {
  range: {contig: 'chr17', start: 7512384, stop: 7512544},
  tracks: [
    {
      viz: pileup.viz.genome(),
      isReference: true,
      data: pileup.formats.twoBit({
        url: 'http://www.biodalliance.org/datasets/hg19.2bit'
      }),
      name: 'Reference'
    },
    {
      viz: pileup.viz.pileup(),
      data: pileup.formats.bam({
        url: '/test-data/synth3.normal.17.7500000-7515000.bam',
        indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai'
      }),
      cssClass: 'normal',
      name: 'Alignments'
    }
    // ...
  ]
});

Each track has a name, a data source and a visualization. See /examples/playground.js for a complete set of track types.

To style the track viewer, use CSS! pileup.js uses flexbox for track layout. You can view this codepen for a simple demo of the skeleton. For example, to allocate 1/3 of the space to a variant track and 2/3 to a pileup track, you could use this CSS:

.track.variants { flex: 1; }
.track.pileup   { flex: 2; }

To style multiple tracks of the same type, you can use the cssClass property.

API

The pileup object returned by pileup.create has these methods:

• setRange: Update the visible range in the pileup. This takes a GenomeRange object, e.g. {contig: "chr17", start: 123, stop: 456}. The coordinates are 1-based and the range is inclusive on both ends.
• getRange: Returns the currently-visible range. This is a GenomeRange object (see description in setRange).
• zoomIn: Zooms current range in by a factor of 2.
• zoomOut: Zooms current range out by a factor of 2.
• toSvg: Converts pileup object to SVG data URL.
• destroy: Tears down the pileup and releases references to allow proper garbage collection.

If you want to change the set of tracks in a pileup, tear it down and create a new one. The caches are stored on the individual source and visualization objects so, as long as you reuse these, the destroy / create cycle is relatively cheap and will not incur extra trips to the network.

Development

Basic Setup

git clone https://github.com/hammerlab/pileup.js.git
cd pileup.js
npm install
npm run build

To play with the demo, start an http-server:

npm run http-server

Then open http://localhost:8080/examples/index.html in your browser of choice.

To view integration with GA4GH schemas, view http://localhost:8080/examples/ga4gh-example.html.

Testing

Run the tests from the command line:

npm run test

Run the tests in a real browser:

npm run http-server
open http://localhost:8080/src/test/runner.html

To continuously regenerate the combined pileup and test JS, run:

npm run watch

To run a single test from the command line, use:

npm run test -- --grep=pileuputils

To do the same in the web UI, pass in a ?grep= URL parameter.

To typecheck the code, run

npm run flow

For best results, use one of the flowtype editor integrations.

Design

See DESIGN.md.

If you're looking for ideas, see ROADMAP.md

Releases

To cut a new release:

• Update version in both package.json and pileup.js. Commit this change.
• Run scripts/publish.sh
• Run npm publish
• Push to github and tag a release there. Add release notes.

License

pileup.js is Apache v2 licensed.