Added database class for Sequenom LIMS
Reduce chunk size for faster zcall test
Updated the fragile SNP set count test
Merge branch 'devel' into sequenom_irods
Merge branch 'release-0.8.2' into devel
Added Graphviz dot graphs of the Illuminus and GenoSNP workflows
Use study_id obtained by joining to current_aliquot table in the warehouse
Renamed method to be more descriptive

Formatted SQL query for maintenance

Formatted code to match style of surrounding code
Added first draft of method to filter multiple metrics
Check for existence of manifest file
Added merge script and method for QC JSON output, with test
Fixed syntax errors
Correctly report name of test on completion
Added move_object and replace_object functions.

Switched to using patched imeta that delivers its data object result
paths on a single line, rather than split up. Previously the query was
performed with iquest. However, iquest queries did not permit multiple
clauses (they are accepted, but return unexpected results).
Added functions to create metadata fingerprints.
Added a general purpose function for finding plates by name.
Refactored file/data object publication to decouple the initial push
with immutable metadata (e.g. from LIMS) from later updates with
mutable metadata (e.g. organisational metadata) and from setting of
iRODS access permissions.

Introduced metadata fingerprints for object identification.

Added Sequenom genotyping data publication.

Improved logging options.
Separate methods to parse QC thresholds, and read from file
Major rewrite to allow more flexible QC filtering
Initial commit