Removed the writing of data in the calculateLd method.
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Made changes to the pom.xml file (done by Patrick) and changed the code of the main class to correctly display the regulomeDB support data and accept commandline parameters.
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Made the code functional and to perform the correct analysis, that is select the transcription factors per eQTL and count how many times each TF is found
Made changes to include the permutation data in the analysis. Added methods to filter top eQTL effects and top permutation effects on shared probes. the findSnpsInRegulomeDb methods now returns a HashMap with counts per transcription factor. Added the method getFisherPValues.
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Fix by Patrick to allow windows linebreaks in haps reader
Reads and filters eQTL and Permutation data. Changed the findSnpsInRegulomeDb method to just count the amount of hits on transcription factors and return a hasmpa with counts. Also added a method to calculate the fisher exact pvalue test (note: Please check if this method uses the correct values as the correct parameter; ty in advance).

P.S.: Sorry for this late commit
Merge pull request #124 from MatthieuBeukers/master

eQTL Functional Enrichment