Merge pull request #34 from wtsi-npg/master

Changes from wtsi-npg:master up to release 1.5.3
Merge pull request #35 from wtsi-npg/release-1.5.4

Merge changes to release 1.5.4
Merge branch 'master' into devel
Added tests on updating manual QC metadata for Sequenom results.
Added some comments on metadata cache behaviour.
Added support for Infinium methylation chips.
Added support for the new inline metadata updates to the publishing
scripts. I missed these in the last commits.

Added a new --reference-zone command line argument to
publish_fluidigm_genotypes.pl
Merge pull request #254 from keithj/devel

Methylation chip support
Replace the default value for the reference_zone attribute.
Changed find_project_chip_design to return a reference to play better
with the cache and be more consistent with other methods.
Merge remote-tracking branch 'wtsi-npg/devel' into devel
Merge pull request #255 from keithj/devel

Fixes for mistakes made by working too late on Friday night
Use a reference path in Fluidigm publishing rather than a reference
zone because it enables a more specific query for references.
Refactored file (re-)publishing so that the logic for handling
exisiting data is clearer.
Merge pull request #256 from keithj/devel

Refactored iRODS file (re-)publishing to be clearer
Merge branch 'release-1.5.6'
Merge pull request #36 from wtsi-npg/devel

Bring up to date with recent wtsi-npg changes
Prevent Genome Studio Control Probe Profile files being mistaken for
annotation files.

Simplified file format guessing.
Merge pull request #257 from keithj/devel

Improvements to gene expression publication
Improved the reliability with which Sequenom data are found for
publishing to iRODS. This method works around the problem that the
LIMS does not update its plate timestamp when a plate is finished.