Merge pull request #33 from wtsi-npg/devel

Merge recent changes from wtsi-npg:devel
Moved identity check functions from script into module
Added --plink and --manifest arguments to check_identity_bed.pl and moved QC test data into pipeline test directory
Added resultset/result classes for Sequenom.
Merge pull request #226 from keithj/devel

Added resultset/result classes for Sequenom.
Working first draft of flexible identity threshold
Refactor of metadata management utilities as Moose Roles.
Changed Infinium plate barcode -> plate name for consistency
Sequenom publisher to annotate the SNP set name as iRODS metadata on each CSV file exported to iRODS.

Added some basic methods to read back Sequenom CSV results (the SNP
set name is contained with in the result file).
Merge pull request #227 from keithj/metadata_roles

Refactor of metadata management utilities as Moose Roles
Revert from using TAP::Harness because it broke "./Build testcover"
Merge pull request #228 from keithj/sequenom_metadata

Sequenom publisher to annotate the SNP set name
Merge pull request #229 from keithj/devel

Revert from using TAP::Harness because it broke "./Build testcover"
Added t (test) directory to lib path of generated Build script
Merge pull request #230 from keithj/devel

Added t (test) directory to lib path of generated Build script
Major refactoring to implement flexible identity threshold and improved swap check
Remove --manifest argument and add --swap
Removed --manifest argument
Changed identity input file
Write dummy JSON output if insufficient SNPs found