* Added a parser for the CopyNumberSpecification format, version .5.
* No longer using opencv.
* Removed some unneccessary imports.
* Added the indexer object for the CNPair object.
Make some HMC methods public for reuse in the rejfree sampling project
Bump version
Add javadocs and source to artifacts
Make some fields public for rejfree experiment
Fix javadoc
Bump version
Add control over number of HMC cycle per aux var update

Also, print out selected HMC hyper params
Add ESS of evolutionary statistics
Bump version, fix coda printing interfering with tests
Fix version of java in travis
Added a clause to fix JavaDoc problem.