Refactoring of VCF converter

- Move logic specific to Fluidigm or Sequenom into the respective AssayResult classes
- VCF converter class takes a SNPSet object instead of a manifest path as argument; move SNPSet creation into the command line script
- Other tidying up to make code more clear and maintainable
- 2014-08-27: Additional commits incorporate PL release 1.5.11, plus fixes/improvements to test data, better use of the snp_assayed() function, and bugfix to handling of 'No Call' in converter.