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 don't think there is a way to just feed it an extension - if you need the extension then you just need to specify the file name - it seems you have taken reasonable precautions to get a unique name in most situations.  I just ran into this recently when fixing a fireteam bug where the file name was not necessary and was causing problems, which is why I thought of it.