Remaining variant changes for adam2vcf, unit tests, and CLI modifications

[nealsid]

FYI, this PR is against vcf-work, but includes vcf-work-vcf-conversion. The most recent commit is the only commit necessary to review in this PR.
Thanks,
Neal

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/172/

[tdanford]

As with #151, I'm still unclear as to how the commits in this PR relate to #147 ?

[fnothaft]

Looks good here! Excited to see #150 and #151, can't wait to get them and the topic branch merged in.

[nealsid]

Great. 150 & 151 are ready to go unless you have more comments.
Thanks, Frank.

On Thu, Feb 27, 2014 at 12:25 PM, Frank Austin Nothaft <
notifications@github.com> wrote:

Looks good here! Excited to see #150https://github.com/bigdatagenomics/adam/pull/150and
#151 #151, can't wait to
get them and the topic branch merged in.

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/150#issuecomment-36267195
.

[fnothaft]

Thanks @nealsid! Merged.