Modified CalculateDepth to get coverage on whole alignment adam files

[akmorrow13]

No description provided.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1175/

Build result: FAILURE

GitHub pull request #1010 of commit 4d0510d automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/1010/merge^{commit} # timeout=10 > git branch -a --contains 31569d7f0f819af91bf84f92e278e563c9fc5944 # timeout=10 > git rev-parse remotes/origin/pr/1010/merge^{commit} # timeout=10Checking out Revision 31569d7f0f819af91bf84f92e278e563c9fc5944 (origin/pr/1010/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 31569d7f0f819af91bf84f92e278e563c9fc5944First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[fnothaft]

Delete here.

[fnothaft]

Since this is a major modification of CalculateDepth, perhaps we should move this/calculate depth into two separate commands? That would be my preference.

[akmorrow13]

let's save this as a feature

[fnothaft]

@akmorrow13 I'm going to close this in favor of bigdatagenomics/quinine#14. LMK if you object.