Changed the main class EQtlPermutationTranscriptionFactorAnalysis and created a default test class for the main class. (The test class is not modified yet and thus quite useless at this moment) The changes to the main class include using the EQtlTextFile class to read the eQTL results file, using the TextFile class to write results to a file and other code cleaning and modification thingies :)
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Changed the readEQtlResultsData method to use the EQTL and EQtlTextFile classes. Removed the methods performAnalysisStep, getNearbyVariants, and getEQtlsAsGenotypeSnps. Added the method: findSnpsInRegulomeDb and calculateLd.
Merge pull request #96 from MatthieuBeukers/master

Code change for eqtl functional enrichment