Added the second version of the EQtlPermutationTranscriptionFactorAnalysis and two executable files that will later be used to search for eQTLs and LD SNPs in repeat (LINES, SINES, etc) regions.
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Added method to check if conversion to Probabilities  is save
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Added methods so most old filetype can reviel probabilities. VCF and Trityper not yet
Merge remote-tracking branch 'origin/master' into prob_genotype_IO
More renaming
Merge pull request #149 from harmjanwestra/master

Zapped another gremlin
Changed DoubleMatrixDataset, it no longer extends DoubleMatrix2D

Removed the extention of DoubleMatrix2D. To be sure no DoubleMatrix2D
methods are useable on the DoubleMatrixDataset and no data is stored in
duplicate.
Merge pull request #151 from Bonder-MJ/master

Changed DoubleMatrixDataset, it no longer extends DoubleMatrix2D
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Renamed Genotype Aligner to Genotype Harmonizer
More renaming
removed old import
Added version 3 of the eqtl functional enrichment. This class speeds up the performance but uses more RAM memory. Also fixed a bug in the calculation of the Fisher exact pvalue by subtracting the amount of hits for one TF from the total hits.
Merge pull request #153 from MatthieuBeukers/master

Functional Enrichment update
Added option to match eQTL using snp pos instead of identifier
Minor fix bat files genotype harmonizer
Added probability support to genotype IO framework
Renamed some classes
increment of version