Added GA4GHAlignments to be accessible through raw json

[akmorrow13]

This is primarily to allow pileup.js to be used in platforms other than the browser. For example, a user can load data into a pandas data frame in python, and pipe the dataframe using the to_json() function into pileup. Since python notebook supports html and JS, one can immediately view their in the same environment.

I think I will eventually add similar functionality for variants, features, etc. but thought this is a good starting point for discussion.

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This change is 

[coveralls]

Coverage decreased (-0.08%) to 90.93% when pulling c09531b on akmorrow13:json-python into 8b7ef01 on hammerlab:master.

[coveralls]

Coverage decreased (-0.07%) to 90.94% when pulling bfa734f on akmorrow13:json-python into 8b7ef01 on hammerlab:master.

[armish]

Thanks, @akmorrow13! This is great — notebook integration has been something on our todo list since early days (#297)

If you get it to work fully, would love to test it out and put an example on the repo.

[akmorrow13]

Hi @armish ! Tagging @jpdna for interest. The reads visualization already works in a widget (with my personal pileup branch with these JSON changes). The widget repo can be found here: https://github.com/akmorrow13/genomicviz

This is more of a wrapper, with pileup.js being the main focus. However, we will be adding in some other exciting visualizations, such as heat maps and stuff. Any useful viz recommendations would be welcome.

I am working to add variants and features next. First though, I will be adding GA4GH formats for these types into pileup.js. PR is coming soon!

[armish]

@akmorrow13 @jpdna - that is amazing news! I will keep an eye on the project in case you need beta testers :)