Made GenotypeIO indipendent of GeneticaLib

Allows usage of genotypeIO in GenaticaLib
Minor memory optimization
Made MAF calculator faster
Minor
Attempt to fix jenkins
First part ASE
Fix error message that should not be displayed
Removed some non functional code
removed unused vars and edited comment
Minor improvement FDR
Replaced permutation 2d arrays with colt matrix
Update README.md
Working on ASE
Updates to DoubleMatrixDataset
No settingsfile allowed fro pcaOptimum
Attempt to speed up FDR
format QTL container
Merge branch 'master' of github.com:molgenis/systemsgenetics into eQTL_FDR
Merge branch 'master' of https://github.com/molgenis/systemsgenetics into FDR_Replacement
Merge pull request #1 from PatrickDeelen/eQTL_FDR

E qtl fdr