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
Merge pull request #1 from dennishendriksen/master

M2365 As genotypeIO user I want efficient VCF reader for streaming and random IO
Minor improvements error handeling
No settingsfile allowed fro pcaOptimum
Remove old file
Fix import
First part making old datatypes work with extented model