Added switches to spark context creation code

[fnothaft]

Adds the following switches to the spark context creation code:

• A switch to allow for configuring the size of the Spark Kryo buffer. This is necessary for indel realignment on larger datasets.
• A switch to add a logger that prints debug text after every stage. This debug text contains information about data movement inside of the command that is being run, and is useful for performance analysis/profiling.

This addresses #149.

[tdanford]

Jenkins, test this please.

[tdanford]

Awww, Jenkins doesn't like me :-(

[fnothaft]

Jenkins, test this please.

@tdanford I think there is a list of Jenkins admins who Jenkins will look for comments from. I'm not sure about this though; @jey/@massie?

[tdanford]

I thought matt had added us to that list? Maybe I'm hallucinating, or am
mis-remembering an old email.

On Mon, Mar 3, 2014 at 1:20 PM, Frank Austin Nothaft <
notifications@github.com> wrote:

Jenkins, test this please.

@tdanford https://github.com/tdanford I think there is a list of
Jenkins admins who Jenkins will look for comments from. I'm not sure about
this though; @jey/@massie https://github.com/massie?

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/161#issuecomment-36540174
.

[carlyeks]

Yeah, I think this may be some deeper issue; Jenkins should have tested this anyway since it was from someone who should be whitelisted...

[fnothaft]

@tdanford if it's any consolation, @AmplabJenkins doesn't seem to be listening to me either. I think our faithful butler has shown up to work drunk today.

[tdanford]

Noooo, don't do it Jenkins! :-)

[tdanford]

Frank, can you add a comment about this in the CHANGES file(s)?

[fnothaft]

I'm holding on that, pending the resolution of the current email thread. If we stick with the CHANGES.md file, that file shouldn't be hand edited anyways.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/193/

[carlyeks]

Can you include an update to the changes document? Otherwise, this looks ready to merge.

[fnothaft]

@carlyeks CHANGES files are updated.

[tdanford]

Thanks, Frank!