Ensure iRODS path strings are absolute
Add optional debug mode to logging
Added find_sample_by_plate method

Added documentation
Added Infinium plate barcode and well to Infinium metadata fingerprint

Removed setting access levels from initial publication into the
metadata update phase (where data from the Sequencescape warehouse are
updated).
Switched from genotype-call to g2i for format-shifting GTC to Plink BED.

Removed genotype-call conversion methods

Added g2i conversion method, shimmed to give it the same signature as
the genotype-call method (g2i has different argument conventions from
genotype-call)

Fixed incorrectly named test class (TestSimtoolsTasks was called
TestGenotypeCallTasks)
Use mysql_auto_reconnect for connections to the Sequencescape warehouse
Added a script to export Sequenom data to a directory instead of to iRODS
Merge pull request #144 from keithj/devel

New features plus change from genotype-call to g2i