Merge pull request #302 from PatrickDeelen/master

Fix tests
Fix test
Merge pull request #303 from PatrickDeelen/master

eQTL and ASE
Added special fdr
skipped first variance calc
added special fdr
Merge branch 'master' of https://github.com/molgenis/systemsgenetics

Conflicts:

	genetica-libraries/src/main/java/umcg/genetica/io/trityper/TriTyperExpressionData.java
Merge branch 'master' of https://github.com/Bonder-MJ/systemsgenetics
removed un-necessary calculation
fixes to special fdr
Fixes special fdr
fixes meta main and noldsnplistcreator
Bump
Fix in NoLdSnpProbeListCreator
Updated metaQTL

Warning: this gices a slightly different use case than normal in the
trityperexpressiondata set.
Small change in ussage to be sure that the ussage is more as expected.
Revert "Small change in ussage to be sure that the ussage is more as expected."

This reverts commit 09dd574a9a26b28ab741bf2c04e88f268689c20c.
Small change to get more similar to old handeling.
Merge pull request #305 from Bonder-MJ/master

Alot of small stuff and fix for issue raised by Lude
Fixed incompatible options in defaults.

Incompatible defaults fixed and in-compatible FDR/plotting settings
fixed.