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'm not as worried about BEDTools as I am Picard.  I removed all the VCF temp file names and it complains:
Exception in thread "main" java.lang.IllegalArgumentException: Must specify file or stream output type.

Picard is usually pretty picky about file extensions.  They are used to explicitly type the expected input/output.  Many times the file extension determines the output file type or compressed vs. uncompressed output.