Cleaning up mpileup command

[arahuja]

This just cleans up the mpileup command to separate out the context handling

A few questions:

1. Does this command still have utility? Also is its only utility in local spark?
2. If so, should we combine PileupTraversable and the other pileup processing since both seem to implement the same read to pileup parsing

[massie]

The original idea around this command was to allow ADAM to rapidly pre-process aligned reads and them pipe them to mpileup-based variant callers. I'm not sure who, if anyone, is using this functionality. There was interest from UCSC months ago but I haven't been tracking that work since.

The PileupTraversable does "on the fly" pileup creation assuming sorted input which is a bit different than the other pileup approaches.

[AmplabJenkins]

One or more automated tests failed
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/211/

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/212/

[fnothaft]

@arahuja I believe this is ready to be merged but needs to be squashed first. Can you squash this?

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/225/

[fnothaft]

Merged! Thanks @arahuja!