Merge pull request #157 from Bonder-MJ/master

Fixes
Fixed a major mistake in the transcription factor analysis. Added code for the dbrip analysis and repeat data analysis.
Changed the main class. The main class now needs a parameter that tells which analysis to perform
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge pull request #158 from Bonder-MJ/master

bug fix in eqtlcompare
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Added Patrick's GTF Reader (under the package umcg.genetica.io.gtf) which is useful for reading files such as encode annotation data files. This reader can also be useful in combination with the genomic boundaries.
Test classes for the GTF Reader.
Added two classes for two encode analyses.
Commented out the prototype tests for the GTF Reader so fails dont happen.
Removed the gtf dummy tests. The change in the RegulomeDbEntry is only the removal of one empty line.
Merge pull request #160 from MatthieuBeukers/master

Functional Enrichment and
Update README.md
eQTL compare split gene names
Merge branch 'master' of github.com:molgenis/systemsgenetics
Update readme genotype aligner
Update readme
Merge pull request #161 from PatrickDeelen/master

eQTL compare split gene names