Convert Rsamtools-Overview.Rnw to Rsamtools-Overview.Rmd

[bellatrick]

Rsamtools-Overview.pdf HTML

@Bioconductor/sweave2rmd @jwokaty Hello, could you review my PR for the sweave2rmd conversion. I was assigned this task on the Outreachy project board

[bellatrick]

Great work @bellatrick. Once you've resolved the comments I left in the script, you'll be able to check mark the following items in the list below. Please let me know if you have any questions!

• [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
• [x] in the DESCRIPTION, BiocStyle and knitr are listed in Suggests
• [x] in the DESCRIPITON, the line VignetteBuilder: knitr exists
• [ ] any added lines use the same spacing and indents as the existing document
• [x] if agreed with the Maintainer, the contributor is in the author list in the DESCRIPTION file; refer to the contribution guide for acceptable formats
• [x] if agreed with the Maintainer, the contributor is in the author list in the vignette's YAML; refer to the contribution guide for acceptable formats
• [x] if this pull request includes a conversion from using the separate Author and Maintainer lines into the Authors@R vector, check that the Authors@R vector includes the maintainer as specified with role='cre'.
• [x] if this pull request includes a conversion from using the separate Author and Maintainer lines into the Authors@R vector, the Maintainer line is completely removed.
• [ ] HTML document is representative of the PDF in content and in general the presentation
• [ ] Where the contributor was not able to preserve the content and presentation of the PDF is noted as a comment in the pull request
• [ ] 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()

Thanks for the review, I will make the necessary changes.

[bellatrick]

@mcarlsn I have made the requested changes. Also, I noticed that the URL in line 167 doesn't reflow and goes past the margin in both RStudio and in the HTML file, do you have any suggestions to correct that?

[mcarlsn]

Amazing, thank you @bellatrick! It is okay that the URL extends past the margin. Doing a final pass on the vignette, I noticed that the following text chunks extend past the vertical line:

• lines 180-203
• 219-220
• 229
• 231
• 235
• 245
• 433
• 492

Please fix those chunks. Lastly, edit line 57 to say, "Those desiring more functionality are encouraged to explore samtools and related software efforts." Right now, there is no mention of "samtools" in that passage. Once those edits are made, you're good to go!

[bellatrick]

Amazing, thank you @bellatrick! It is okay that the URL extends past the margin. Doing a final pass on the vignette, I noticed that the following text chunks extend past the vertical line:

• lines 180-203
• 219-220
• 229
• 231
• 235
• 245
• 433
• 492

Please fix those chunks. Lastly, edit line 57 to say, "Those desiring more functionality are encouraged to explore samtools and related software efforts." Right now, there is no mention of "samtools" in that passage. Once those edits are made, you're good to go!

@mcarlsn Thanks for pointing out all the problematic paragraphs and for your patience. I initially used VScode's terminal to push my changes and I am only now realizing that its editor makes RMD files lose their formatting. I have pushed my update.

[mcarlsn]

Amazing, thank you @bellatrick! It is okay that the URL extends past the margin. Doing a final pass on the vignette, I noticed that the following text chunks extend past the vertical line:

• lines 180-203
• 219-220
• 229
• 231
• 235
• 245
• 433
• 492

Please fix those chunks. Lastly, edit line 57 to say, "Those desiring more functionality are encouraged to explore samtools and related software efforts." Right now, there is no mention of "samtools" in that passage. Once those edits are made, you're good to go!

@mcarlsn Thanks for pointing out all the problematic paragraphs and for your patience. I initially used VScode's terminal to push my changes and I am only now realizing that its editor makes RMD files lose their formatting. I have pushed my update.

Wonderful, it looks great! Thanks for all your work on this, @bellatrick.

[jwokaty]

Thanks for your contribution!