Added some extra data to the output of the analyzes such as the direction of the enrichment and a header. Also added classes that will be further used to centralize the analysis code. The EnrichmentDataReader class will be responsible for reading the data (for most analysis the read data will be returned as a GenomicBoundaries object). The eQtlDataParser reads and filters eQTL results on top and non top effects.
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Made changes to the EnrichmentDataReader and modified the tools such as SplitWigTextDataOnChromosome and WriteWigToText. Also added a histone enrichment test method to see what's wrong
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Made final changes to analysis code for the Transcription Factor Enrichment (fixed enrichment direction), added some more methods to the EnrichmentReader and HistoneSiteEnrichment. Added new class to perform Enrichment on output for regressing out results.
fixed error message
First step multipart paths
fix import
editable genotype data
Use trove to improve memory footprint of binary plink
fix comparator metatrait4. Should only be 0 is equals is true.
made members private
improved textfile reader
use text file iterable that split using new object to save memory and give clean code
use updated textfile reader
added metaTrait4 treeset
First version of trityper writer
Added test for trityper writer + bug fix writer
fixed test clean up
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