Extracting reader API
The first commit of the New Illumina report reader
Adding generated java code and xml schemas...

... used to generate the code using xjc
Move tests from old to new implementation
New implementation of xml reader
Updating test resources to match
First version of new setup files
Almost at a working state after refactoring
Work in progress...
Working NewSetupXMLReader
Adding switch for which setup to use
Changed from running packages to classes

This makes it easier to choose what to run when time is of the essence.
Intergration tests and fix of reference bug
Adding requirements on only one ref. per sample
Unit tests for new Sample class
First commit of new SetupFileCreator
Generalized some methods
Finished setup file creator