Refactor VCF code to use NPG Genotyping classes and types

[iainrb]

• Major refactor of VCF module
• Use classes such as Genotyping::Call for methods and type checking
• Some modification of non-VCF classes, eg. adding quality scores to AssayResult classes
• Add GenderMarkerCall, a subclass of Call
• Use a '.' for quality scores in VCF output if none is available