[ADAM-589] Removed pileup code.

[fnothaft]

Resolves #589.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/610/
Test PASSed.

[tdanford]

This code has been a crufty thorn in our side for a long time. I'm ready to merge this right now.

Any objections? Going once... going twice...

(I'll give it a couple of hours.)

Ping @laserson @carlyeks @massie

[tdanford]

Alright, here we go.

[pkaleta]

@tdanford I'm trying to follow this tutorial: http://ampcamp.berkeley.edu/5/exercises/genome-analysis-with-adam.html

It's using adamRecords2Pileup method which was removed as part of this. Are there any examples/tutorial of how to achieve a similar functionality?

[fnothaft]

Hi @pkaleta! We've eliminated this code a long time back. What sort of computation are you trying to run? If you can give details, then we can point you in the direction of the current "best practice".