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
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
Merge branch 'master' into rna_seq

Conflicts:
	lib/perl/Genome/VariantReporting/Framework/Component/Adaptor.pm
catch the correct type of error
clean up if-else block
Merge branch 'master' into rna_seq
ensure that if-else block covers all cases
test coverage for resolve_plan_attributes subroutine
add test for get_attribute subroutine
Use status_msg instead of debug_msg in (un)archive

Maybe now it will be clear why some allocations silently fail to
archive...
make sure that we can call rethrow
pull error handling logic into separate subroutine
enhance error checking around sam-dump