Convert Biostrings2classes.Rnw to .Rmd #83
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@villafup Please remove .Rnw file. I don't think you need to modify the DESCRIPTION because there are other PRs that add BiocStyle |
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We are waiting on some changes from @villafup. I'll slack him :) |
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| external pointers to store the string data, (2) use bit patterns to | ||
| encode the string data, (3) provide the user with a convenient class of | ||
| objects where each instance can store a set of views *on the same* big | ||
| string (these views being typicallythe matches returned by a search |
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space between typicallythe
| However, there is a flaw in the `r Biocpkg('Biostring')` class design that prevents | ||
| the search algorithms to return correct information about the matches | ||
| (i.e. the views) that they found. The new classes address this issue by | ||
| replacing the `r Biocpkg('Biostrings')` class (implemented in `r Biocpkg('Biostrings')` 1) by 2 new |
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I think lines 37 and 40 (the first reference only) reference an old BioString class, so replace
`r Biocpkg('Biostrings')`
with
BioString
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@villafup Just 3 small changes.
I noticed that it doesn't currently generate the Rmd via R CMD build because VignetteBuild: knitr isn't in this version of the DESCRIPTION file; however, when it's merged, it should create the .Rmd.
It'll be ready for Herve after these changes.
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I'm surprised this vignette made it to the sweave2rmd list. It's very old and outdated and doesn't have much value anymore. It was written to document the classes that I introduced when I took over the package and transitioned it from Biostrings 1 to Biostrings 2 about 18 years ago! The only reason it's still around is that Biostrings doesn't have a good general vignette, so I guess having the "Biostrings 2 classes" vignette was better than nothing. However we should start thinking about addressing that @ahl27. In the mean time I think it's ok to close this unless @jwokaty or @villafup oppose. Thanks! |
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Sounds good, I'll wait for either of them to chime in to confirm and then we can consider closing it. Is the other PR still something we need to merge? I can ping you on that PR so the conversation stays localized to the PR |
@Bioconductor/sweave2rmd for review