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.
As noted in the PR description this command is intended to be a functional replacement for CompareSnpsSummary.  This command is intended for users to run from the command-line to generate QC results for models that are missing them (like samtools r982 or newer). 

 For somatic validation you would want a different command, one that took somatic validation builds or models as input.