initial commit of porting VCF implementation from GWAS branch, note: only CohortMAF is working
VCFs AF should always contain additional info
if QD isn't defined in VCF's info field, return the quality column
fixed acgh chromosome region
Merge remote-tracking branch 'upstream/master'

Conflicts:
	application.properties
removed deprecated and wrong version of import
whitespace
made VcfValues implementation transient
whitespace
saner handling of position constraints for VCF
removed useless override
removed unused class
removed foreigners from vcf domain model
removed VcfValues from model, use ALIAS_TO_ENTITY_MAP
renamed column
removed useless comment
removed VcfPositionFactory, injecting with prototype scope
use projection instead of creating objects directly
collecting positions for all samples was broken
test data for variants support