Added functionality to skip cols and rows during read in.
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
Fixes and replacements
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge pull request #90 from PatrickDeelen/master

Update converte impute2 data to trityper + fix merge conflicts
Spelling fix
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge pull request #91 from PatrickDeelen/master

Update readme genotype reader
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge pull request #92 from Bonder-MJ/master

fixes
Introduction of reading GEO text tables

Extracting usefull information out of geo text tables.
Designed for HT12 v3 / v4 arrays
Updates in text reading
Merge pull request #93 from PatrickDeelen/master

Cleanup of unused legacy code
Merge pull request #94 from PatrickDeelen/master

Cleanup of unused legacy code, some minor stuff
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Fix in normalizationGUI
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
fix in merging old matrices
Changed the readEQtlResultsData method to use the EQTL and EQtlTextFile classes. Removed the methods performAnalysisStep, getNearbyVariants, and getEQtlsAsGenotypeSnps. Added the method: findSnpsInRegulomeDb and calculateLd.