Merge pull request #49 from wtsi-npg/master

Merge changes up to release 1.6.5
Merge pull request #50 from iainrb/master

Merge changes up to release 1.6.5
Ported to external iRODS library and DNAP Utilities library.
Merge pull request #299 from keithj/with-dnap-libs

Ported to external iRODS library and DNAP Utilities library.
Added Reference sequence class to indicate to which References a
SNPSet's coordinates apply.

Added a backref from SNP to SNPSet so that a SNP can find it's
context (SNPSet and Reference).

Added code to build References from iRODS metadata when a SNPSet is
loaded from an iRODS data object.

Updated the SNPSetPublisher to build References.
Merge pull request #51 from wtsi-npg/devel

Merge port to external iRODS library and DNAP Utilities library
Enable processing of multiple Fluidigm resultsets for a given sample and SNP
Remove unnecessary import of uniq function
Add test of get_calls for singular resultset, add _get_observed_calls method to avoid repetition of code
Improved testing, made logic of call merge more clear
Merge pull request #301 from iainrb/fluidigm_merge_2

Fluidigm merge multiple resultsets
Added improved model of gender markers.

Added validation via type contraints.

Made the test qc.csv SNP manifest identical to the production one.
Bugfix for RT#439785; correct divide by zero error
Merge pull request #302 from iainrb/fluidigm_merge_2

Bugfix for RT#439785; correct divide by zero error
Merged in recent changes on devel to complete work on adding Moose
constraints.
Correct binning of maximum x and y values
Merge pull request #303 from iainrb/fluidigm_merge_2

Correct binning of maximum x and y values
Added argument checks to WTSI::NPG::Genotyping::Call::merge.

WTSI::NPG::Genotyping::Fluidgim::AssayResult:

Added is_empty method.

Renamed npg_ to canonical_ in cases where the thing being created is a
canonical version.

Renamed assay_position to assay_address to be consistent with
sample_address.

WTSI::NPG::Genotyping::Fluidgim::AssayResultSet:

Added size method.
Added sample_name method.
Added assay_addresses method.
Added result_at method.
Removed get_calls method.

WTSI::NPG::Genotyping::Fluidgim::Subscriber:

Now both creates and merges calls so that the assay addresses can me
checked across all the resultsets involved.

Modified other code to propagate the API changes.
Merge pull request #304 from keithj/snpset-reference

Compilation of changes to add call merging
Added some tests where coverage was missing.

Removed some redundant comments.