Merge pull request #161 from PatrickDeelen/master

eQTL compare split gene names
Changed the analysis to be performed on probes present in all datasets. Changed the top effect methods to get top effects for only the probes shared by all sets. Added code for the eQTLs in repeat data analysis. Disabled the dbrip analysis for now.
Merge pull request #164 from PatrickDeelen/master

Added oxford gen reader and writer, some updates to genotype harmonizer
Merge pull request #163 from MatthieuBeukers/master

Functional Enrichment Change
Merge pull request #165 from PatrickDeelen/master

fixed bug in allele determination of trityper data
More generalizations in the interaction model code.
This should fix a very old bug that causes the number of tests performed to be wrongly displayed.
This should fix the display of the number of tests performed (and adds the number of SNPs finally tested)
Change console output text
Merge pull request #166 from harmjanwestra/master

Fixes: number of tests performed
This should fix most of the high priority warnings in the code
Merge branch 'master' of https://github.com/molgenis/systemsgenetics.git
- ViolinBoxPlot now can handle values > 0 and < 1 for y-axis (still need to fix values < 0)
- Added option to save files after eQTLs have been regressed
Merge pull request #170 from harmjanwestra/master

Lots of minor fixes / changes
Merge branch 'master' of github.com:molgenis/systemsgenetics
bump in eqtl version to reflect recent updates