Convert VariantAnnotation.Rnw, filterVcf.Rnw to VariantAnnotation.Rmd, filterVcf.Rmd

[villafup]

@Bioconductor/sweave2rmd

for review

[mcarlsn]

FYI I'm reviewing this PR. Will follow-up w more soon

[jwokaty]

• [x] the .Rmd file knits to HTML

• [x] R CMD build runs without errors or timeouts

• [x] the tarball from R CMD build contains the HTML (check with the following by substituting the package name and vignette name tar ztf package_name.tar.gz | grep 'doc/vignette_name')

• [x] the .Rnw file has been removed

• In the DESCRIPTION file

  • [x] BiocStyle and knitr are listed in Suggests
  • [x] the line VignetteBuilder: knitr exists
  • [ ] any added lines use the same spacing and indents as the existing document

• If agreed with the Maintainer

  • [ ] the contributor is in the author list in the DESCRIPTION file*.
  • [ ] the contributor is in the author list in the vignette's YAML*.

• If this pull request involves converting from separate Author and Maintainer lines to the Authors@R vector, please ensure that

  • [x] the Authors@R vector includes the maintainer as specified with role='cre'.
  • [ ] the Maintainer line is completely removed.

• [x] HTML document is representative of the PDF in content and in general the presentation

• [x] Where the contributor was not able to preserve the content and presentation of the PDF is noted as a comment in the pull request

• [x] the R Markdown file is representative of the Sweave document and follows best practices, such as replacing links to Bioconductor packages with calls to BiocStyle's Biocpkg()

• [x] Only files necessary for the conversion are included in the pull request.

• [x] Long lines have been broken up and reformatted, you can achieve this by selecting the text in your script and then clicking on Code > Reflow Comment in R Studio.

• [x] Code blocks are surrounded by a blank line, and there are no blank lines before the start or after the end of the code within the code block.

• Refer to the contribution guide for acceptable formats