Changed all colt dependecies in systemsgenetics to parallelcolt

Colt 1.2.0 and Colt1.0.3 are dependencies of dependecies of other
libraries so are still in after downloading. Try to use the parallelcolt
functions when possible.
SNP necessary for PCopt
introduction of matrix.DoubleMatrixDataset

Moved DoubleMatrixDataset2 to legacy. Before definitive removal.
Merge pull request #30 from Bonder-MJ/master

SNP lists necessary for PCopt, Changed to parallelcolt, new double matrix