Merge pull request #60 from PatrickDeelen/master

Examples and documentation. small bug fix and improvements
Merge pull request #61 from PatrickDeelen/master

Bug fix filtered trityper genotype reader and better testing.
Merge pull request #62 from PatrickDeelen/master

Refactoring, testing and fixing variant filter
Fixes in new DoubleMatrixDataset

Casting fixes
Changed output of normalizer during PCA step.
Updated pom

Now there is no need anymore for installing local jars.
Added a readme.md for the eQTL mapping software
Removed install-local-jars and changed main README.md
Merge pull request #64 from Bonder-MJ/master

Updates in new Matrix, additions in PCA output, updated pom and changes in Readme's
Merge pull request #65 from PatrickDeelen/master

Genotype aligner readme + fixes aligner
Merge pull request #66 from PatrickDeelen/master

Full test of genotype aligner using hapmap3 and 1000G as test + some minor bug fixes and improvements
Update README.md
Genotype reader readme update
Updates in matrix unified loading from text files
Addition of MatrixTools
Merge pull request #68 from Bonder-MJ/master

DoubleMatrixDataset2 update
minor updates in text output
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
bug fixes in binary plink reader