Added new VariantFactory interface. The code from old VariantFactory now is in VariantVcfFactory. VariantVcfFactory implements VariantFactory. Added some tests #3
Properly assign genotype count when that genotype was not previously registered in a VariantStats object
Genotype can be constructed using the Integer encoding as argument
Mean quality added as VariantGlobalStats attribute
Variant HGVS converted from List to Set, and VariantStats default constructor initializes with impossible values (such as null and -1)
Properly decoding genotypes represented as an int
Add VariantVcfReaderTest. pre() adds sampleNames to source. #3
Add new VariantVcfEVSFactory for EVS File. (EVS contains MAF and genotype count in the INFO field) #3
Minor changes. #3
Added some test to VariantVcfEVSFactory. Close #3
Added new tests to VariantVcfEVSFactory
Removed wrong code from Genotype
Fixed regular expression for replacing chromosome prefix
VariantVcfEVSReader class deleted, and associated test moved to VariantVcfReaderTest
Some automatic reformatting on the code
Merge branch 'aaleman-develop' into develop