jannovar should be updated

[jvlasblom]

Jannovar has had several updates posted on the git repository https://github.com/charite/jannovar.git

(This is Peter Robinson's repository, we don't have/want write access to it).

We've absorbed the Jannovar source code as a subproject of medsavant (in subdir medsavant/jannovar) as of late-march. The changes posted to https://github.com/charite/jannovar.git since then should be merged in with our own changes.

[meatcar]

What really should be done, is Jannovar should be forked under the compbio-UofT organization, and that fork should be used either as a git submodule, or a maven dependency when building medsavant. That way, any changes we make to Jannovar could be potentially pushed upstream (i.e. logging) via pull requests, while updates upstream can be easily merged into our version.

[meatcar]

Jannovar has forked to https://github.com/compbio-UofT/jannovar, Changes in the jannovar folder have been added to the fork as individual commits.

Next Steps:

• Fix Jenkins build ()
• Remove jannovar folder from MedSavant source
• Add compbio-UofT/jannovar as a maven dependency.