Correct how GenOO becomes aware of a new db column in annotate_db_sample_with_deletions.pl

Previously DBIx::Class and GenOO were becoming aware of the new
database column "deletion" in an obscure way. The code now is much
cleaner. Also the updates are now done in batch in a single db
transaction. This should improve performance and stability.
Use cigar string to identify deletions -> huge performance improvement.

The script annotate_db_sample_with_deletions.pl was using GenOO methods
to identify deletions. Instead now it looks directly in the cigar
string which is a db column and therefore the update is extremely
faster
Start migrating scripts to App:Cmd. Start with genome_coverage.
gene to transcript file not needed
fixed pod
fixed genecollection / transcriptcollection bug
Merge branch 'develop' of /home/pan.alexiou/mylib/perl/GenOO-CLIP/v0.1 into develop
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