Start migrating scripts to App:Cmd. Start with genome_coverage.
Start using MooseX::App::Cmd which marries Moose with App::Cmd

* Can now define command line options as Moose attributes
* Use roles to encapsulate options and methods
Create role for GTF command line option. Reads gene/transcript collection
Create role for reads collection command line option. Reads the collection
Migrate script count_reads_on_genic_elements.pl to MooseX::App::Cmd
Create role for transcript GTF command line option. Reads transcript collection
Use new roles in genome_coverage.pm
Delete legacy command line option roles
Rename Help role to HelpOption. Update pod
Rename OutputPrefix role to OutputPrefixOption. Update pod
Update pod in HelpOption role
Rename Verbose role to VerbosityOption. Update pod
Update pod
Delete legacy role OutputFile
Update pod in app commands
Migrate script distribution_on_genic_elements to MooseX::App::Cmd
Merge branch 'develop' into make_app
Migrate script distribution_on_introns_exons to MooseX::App::Cmd
Migrate script genomic_distribution to MooseX::App::Cmd
Fix deep recursion bug in ReadsCollectionInput when filters where used