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
Merge pull request #236 from PatrickDeelen/vcfReaderUpdate

ASE
fixes in repo
fixes after last merge
fix
Merge pull request #237 from Bonder-MJ/master

Fix after fail to pull normaly