ASE stuff
Bug fix calculating maf and filtering samples
Minor
Merge pull request #263 from harmjanwestra/master

Some minor edits
ASE output samples supporting ASE
added sample support to tests
Added test for sample support ASE
Fixed bug VCF phasing
Improved intergration of new VCF reader

Including automapping of of probs, dosage and genotypes depending on
avalible fields
Fix VCF
eQTL building process
Merge pull request #264 from PatrickDeelen/master

eQTL building, ASE, Genotype IO
update eQTL readme
Merge pull request #265 from PatrickDeelen/master

update eQTL readme
- DoubleMatrixDataset: use more generic List instead of ArrayList
- Some other minor edits
- Some initial binarymeta code
- This should fix the trans-QTL meta-analysis part
- write type of analysis in binary matrix
- This fixes writing to the text file
- Dirty POM.xml hack to get back the all in one jar file (please keep it in by the way)
- Some binary meta-analysis code tweaks
- Reads ZScores from matrix