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.
Update to v1.123 including filename and sensitivity calculation changes.
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.
Add valid values for strand sensitivity.
A few changes based on PR feedback. Remove unsorted test data and remove unintentional exit at the end of the test.
Changes to the command class inherited from.  Remove exit from .t. Suggeted changes based on code-review.
Get picard_strand_specificity from the model via PP instead of build.
Get picard_strand_specificity from the model via PP instead of build.
Allow default vcf_description and vcf_id

It should be obvious when you are writing a report that something
needs to be filled in, otherwise, if you don't care it doesn't crash
Remove Framework::EntryProcessor

Now that Reporters are created with their Interpreters and Filters
already attached, the EntryProcessor logic can be moved onto the
Reporter.