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
Fixed indel color coding for MakeCircosPlot.pm
Improve Readcount test
remove version 0.2 exception which is no longer true
Make required parameters required.
Refactor out validate and command methods
Test expected command strings for all versions
Redirect error logs to /dev/null for versions previous to -w option
Made subroutine for RNA
Merge branch 'master' of github.com:kkrysiak/genome

Conflicts:
	lib/perl/Genome/Model/ClinSeq/Command/MakeCircosPlot.pm
Use keys of the expected hash
Use Genome::Sys for validation. use_version already has a default.
Merge pull request #140 from kkrysiak/master

MakeCircosPlot updates
Blessing clinseq build
Merge pull request #134 from gsanders/readcount_error_flood

Readcount error flood