Made GenotypeIO indipendent of GeneticaLib

Allows usage of genotypeIO in GenaticaLib
Minor memory optimization
Made MAF calculator faster
Minor
Merge pull request #232 from PatrickDeelen/betterLoadingGenotypeIO

Made GenotypeIO indipendent of GeneticaLib
Attempt to fix jenkins
Merge branch 'master' of github.com:molgenis/systemsgenetics into betterLoadingGenotypeIO
Merge pull request #233 from PatrickDeelen/betterLoadingGenotypeIO

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
Merge pull request #234 from PatrickDeelen/betterLoadingGenotypeIO

Some performance optimizations FDR calculation + first steps ASE
make methods and inner class accesible
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Introduce GeneticVariantMeta and VCF implementation