Merge pull request #37 from wtsi-npg/master

Merge of wtsi-npg/master with iainrb/master
Merge pull request #38 from iainrb/master

Merge master into devel
Create VCF from Fluidigm/Sequenom CSV and run consistency check
Merge updates from plex_consistency and resolve conflicts
Make SNPSet name read-only
Removed incorrect 'use' statement referrring to a deleted package.

This passed tests unexpectedly because the ./Build clean step was
omitted.
Merge pull request #267 from keithj/devel

Removed incorrect 'use' statement referring to a deleted package.
Two further incorrect 'use' statements. Removing these completes the cleanup.
Merge pull request #268 from keithj/devel

Two further incorrect 'use' statements.
Added miget utiliuty script.

Added get_object and get_collection methods to iRODS.pm.
Reinstated Moose type checks on publishers
Remove code to read files from iRODS or local filesystem; instead take AssayResultSet objects as arguments
Modified for new input syntax
Include code to create AssayResultSet objects from iRODS or local filesystem (formerly in VCFConverter.pm)
Rename *_plex_dir to *_plex_coll
Rename arguments to converter and scripts
Rename plex_dir to plex_coll, additional sanity checking, update to help text
Merge pull request #269 from keithj/devel

Added miget utility script.
Merge pull request #39 from wtsi-npg/devel

Merge recent changes from wtsi-npg:devel
Updated pipeline states to remove deprecated states and add new ones.

Fixed some latent bugs in DBIC classes where a missing log methos was called.

Fixed a latent bug where Fluidigm SNP sets could be classed as
Infinium SNP sets