Check R code from BioConductor variant annotation vignette.

This code was extracted via:
```
Sweave2knitr('~/VCF_projects/VariantAnnotation/inst/doc/VariantAnnotation.Rnw') purl('~/VCF_projects/VariantAnnotation/inst/doc/VariantAnnotation-knitr.Rnw')
```
Now also returning a value from the getReadData method and whitespace cleanup.
Refactored variants code to allow for various converters.
Added variantsToGRanges converter.

This was needed for the VariantAnnotation vignette.

Also updated roxygen and regenerated docs.
Initial version of the VariantAnnotation vignette.

There is much room for improvement, but this is a start.