Picard genotype concordance

A new command is available as of Picard 1.122 to compare two VCF files for the purpose of genotype concordance.

This PR includes the gmt wrapper with tests to run GenotypeConcordance using Picard 1.123.  @iferguson90 is currently working on the packaging of the latest version of PIcard.

This PR also contains a new RefAlign command intended to replace CompareSnpsSummary for new models that use mpileup.  Currently those CompareSnp results are all zeros since it doesn't handle the new file format.  The new command is entirely VCF based.
The printing of messages isn't controlled by the context, it's controlled by a setting. ```$obj->dump_error_messages(0)``` will turn off printing to the terminal.  errors and warnings are turned on by default, the others (status, debug) are off.

Maybe there should be a fatal_message() throws an exception, prints the message only once, and can still get trapped and sent to logstash.