DRAFT Collator merge PR 3 of 3

Draft with extensive refactoring of the Collation.pm module, which collates raw QC results:

Includes changes from identity and gencall pull requests
Converted Collation.pm to a Moose class Collator.pm; enables better code structure and use of Loggable Role
Replace single collate() method with individual methods to write output files, update pipeline database, etc.
Supply only one JSON config file, which determines all thresholds (instead of allowing a filter file to override the config thresholds for the pipeline database update)
Use Text::CSV instead of split() to read metric results
Update collate_qc_results.pl and run_qc.pl to use new Collator class

After review (and additional changes, if any), draft can be squashed into a single commit before merging.

wtsi-npg / genotyping