Converting OverlapEncodings Rnw file to Rmd #24
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Good work this vignette. It was quite long. There are a few issues to address within the document. Note that it's important to compare the HTML and the PDF to catch problems.
According to Marcel, the footnotes going to the bottom is related to a Pandoc issue, so we'll leave them as they are.
Please remove extra lines and format paragraphs with Code > Reflow comment.
| person("Martin", "Morgan", role="aut")) | ||
| person("Martin", "Morgan", role="aut"), | ||
| person("Beryl", "Kanali", role="ctb", | ||
| comment="Converted 'OverlapEncodings' vignette from Sweave to RMarkdown.")) |
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Please use the same indentation as line 18.
vignettes/OverlapEncodings.Rmd
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| Paired-end encodings `"2{-}{-}1:jm{-}{-}m:am{-}{-}m:af{-}{-}i:"` | ||
| (73 occurences in `U3.ovenc`), | ||
| `"1{-}{-}2:i{-}{-}jm:a{-}{-}am:a{-}{-}af:"` (53 occurences in | ||
| `U3.ovenc`), and | ||
| `"2{-}{-}2:jm{-}{-}mm:am{-}{-}mm:af{-}{-}jm:aa{-}{-}af:"` | ||
| (9 occurences in `U3.ovenc`), correspond to the following paired-end | ||
| overlaps: | ||
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| - `"2{-}{-}1:jm{-}{-}m:am{-}{-}m:af{-}{-}i:"` | ||
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| - paired-end read (1 skipped region on the first end, no skipped region | ||
| on the last end): ooo----------o oooo | ||
| - transcript: ... >>>>> >>>> >>>>>>>>> ... | ||
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| - `"1{-}{-}2:i{-}{-}jm:a{-}{-}am:a{-}{-}af:"` | ||
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| - paired-end read (no skipped region on the first end, 1 skipped region | ||
| on the last end): oooo oo---------oo | ||
| - transcript: ... >>>>>>>>>>> >>> >>>>>> ... | ||
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| - `"2{-}{-}2:jm{-}{-}mm:am{-}{-}mm:af{-}{-}jm:aa{-}{-}af:"` |
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Compare with original PDF. This section seems to have problems like the earlier section where braces surround hyphens.
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@BerylKanali @jwokaty Please make sure that things like this (from section 5.1.1):
or this (from section 5.2.1):
are rendered properly. I don't know how to do this, hopefully it's possible! 🤞 This is a tough vignette, but, AFAIK, not a very visited/popular one. I wonder if it's worth the effort of converting to Rmd 😞 Thanks, |
@hpages We had noticed some elements in the PDF did not render properly when we compared it to the code, This is how section 5.2.1 appears now in the HTML file. The paired-end encodings appear in full, in the PDF they were somehow slashed. Let me know if this is okay. |
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@BerylKanali |
Hi @LiNk-NY Do you mean these figures? |
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@BerylKanali Hi Beryl
Yes, the alignment should be maintained. |
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@jwokaty Is it ok to close this? |
Hi @jwokaty
HTML and PDF for comparison.
RMD BuildandRMD Checkpassed.Tried to do some self review. Hopefully it will have less issues.to be changed.