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.
Added gene information.

And fixed a few typos per feedback from @doll.
Updated genomic coordinate conversion information.

per feedback from @doll

Also regenerated docs.
Reverted formating changes.

Per feedback from @siddharthab
Updates per feedback from @siddharthab
Merge pull request #11 from deflaux/master

An initial vignette for Variant Annotation.