Refactoring:
    New Runner/Task schema.
All uses of VcfRecord converted to Variant
Writers use Variant instead of VcfRecord
Added includestats/effect/samples attributes to writers
getEffectsWithPolyPhenAndSift calculates Effect with polyphen and sift
Removed 'JsonProperty' tags and changed HashMap -> Map
Changed PedDataReader/Writer to PedigreeReader/Writer
Renamed files. Replaced Vcf with Variant
Added test data (vcf & ped)
Moved annots/filters/effect/stats to parent folder
Removed unused or useless code
size() == 0 converted to isEmpty()
Merge branch 'feature/newRunners' of github.com:opencb/java-libs into feature/newRunners
Merge branch 'feature/newRunners' into develop