Explore IGV.js and pileup.js integration options

[scottx611x]

We are migrating away from our current implementation of IGV in favor of a version embedded within Refinery due to the current imp. being not so user-friendly.

Some potential options are:

• IGV | http://igv.org/doc/doc.html
• Pileup | http://www.hammerlab.org/2015/06/19/introducing-pileup-js-a-browser-based-genome-viewer/

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TO-DO:

• Weigh pros and cons of both options
• Provide some proof of concept that this can be achieved with one (or both) of the above
• Work on a more thorough integration

[mccalluc]

Glancing at both:

• IGV has some active development; Pileup has been very quiet in 2016.
• Both produce similar html: nested divs, with canvas elements for the tracks.
• Data sources:
  • Pileup: "This can be achieved by running a GA4GH server. pileup.js supports v0.5 of the
    GA4GH protocol (Terry et al., 2014). Support for other data loading schemes can be added via user-defined sources."
  • IGV: I'm not confident whether it uses the same format as IGV java for high level indexes, but expect so. I can see it making byte range requests at the lowest level.
• IGV: 11 examples; Pileup: 2.
• Documentation: IGV has five detailed pages in the wiki. Pileup: "See /examples/playground.js for a complete set of track types.", and that file isn't very useful.

IGV.js looks much more mature. Close?