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.
I can separate the create from the execute.  I prefer that style to be honest, but sometimes it's a bit verbose to check that the object was created and it executed with a result.  

I don't think this has ALWAYS been this way.  If I'm reading that commit correctly the change was made in 2009.