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.
`error_message()` will, by default, print the message to the screen every time it's called.  So as is you get to see the `error_message()` three times.  Even as one line you still see it twice.  Which makes me wonder if the `*_message()` should only print when called in void context...