Added if statement to test for exome or WGS data. Works with WGS but not exome yet
Added exome only option to MakeCircosPlot. Will use WGS if available. If not, will use exome data. Will use WGS if both are available.
corrects regex in MakeCircosPlot.pm to work with the snv and indel files from exome, WGS, or exome and WGS
Corrects column used for sort command on top 100 gene names used for the outside circle of Circos plots
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.
whitespace
add Genome::Command::Copy
integrate Genome::Command::Copy into Genome::Command::Crud
enable copy for Genome::Library
bugfix of the error checking logic
remove object_with_translations as first step to refactoring
overwrite object subroutine for ReporterPlan so that filters and interpreters are attached there
implement object_with_translations subroutine directly on the plan objects
improved error message
Add test case and all native picard options.