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).
Modified to use inline C; first draft
Extensively refactored and cleaned up
Now correctly working to write sample names and magnitude/xydiff
Move inline C from intensity_metrics.pl to SimFiles.pm; tidy up command line arguments
Use new SimFiles.pm with inline C
Corrected verbose on/off switch; made verbose output more informative
First draft of test updates
Add error checking on I/O operations
Force recompilation of inline C and added test on missing input
Redirect stdout from failure test
Remove unnecessary dependencies & variable
Remove unnecessary
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
Important bugfix, use calloc instead of malloc for magByProbe; various tidying up