Based on suggested conflicts with PR #68
Merge branch 'trio_with_homopolymer' of https://github.com/jasonwalker80/genome into jasonwalker80-trio_with_homopolymer
Merge branch 'jasonwalker80-trio_with_homopolymer'
Merge branch 'master' of https://github.com/genome/genome
Merge branch 'master' of https://github.com/genome/genome
Merge branch 'master' of https://github.com/genome/genome
Add the GenotypeConcordance command in Picard 1.122.  Also a basic RefAlign command to generate genotype concordance from VCF files.
Add test case and all native picard options.
Whitespace.
Correct doc line.
Update to v1.123 including filename and sensitivity calculation changes.
Remove unused include.
New command to manually staple models to analysis projects.
Clarify wording: It's assigned to "another" project.
Consistently get the AnalysisProject from $self.
Use (s) consistently.
Rename the command to include microarray.  take a single build as input instead of many models.  This command is inteded to replace CompareSnpsSummary for operations use on new VCF based microarray and refalign builds ex. PCGP
Remove unused v1.122 test data files and the reference to v1.122 install location
Remove debugger breakpoint
Add strand specificity to the Picard RNA-seq metrics including a PP param for RNA-seq models.
Initial revision of gmt BedToIntervalList wrapper for Picard tool.