TLDR: Biostrings removed pairwiseAlignment method and the method is moved to pwalign
pwalign contains the pairwiseAlignment-related stuff taken from Biostrings. The plan is to deprecate this stuff in Biostrings (in BioC 3.19), and to redirect the user to the stuff that is now in pwalign. Then to defunct it in Biostrings (in BioC 3.20), and to finally remove it from Biostrings (in BioC 3.21).
The motivations for this split are:
Biostrings is too big and hard to maintain. In particular, the pairwiseAlignments-related stuff in it adds a lot of complexity to the package (via additional specialized classes, generics, and methods, and a lot of complex C code to support them). This split will make Biostrings about 20% smaller. This in turn will make its maintenance easier and will also make R CMD check slightly faster.
About 500 Bioconductor packages depend on Biostrings. However, very few of them need the pairwiseAlignment functionality. So this split won't affect most of Biostrings revdeps. However they will now depend on a lighter Biostrings that will be slightly faster to install (faster to download, compile, and load).
Separation of responsibilities: The plan is for Aidan Lakshman (@ahl27) to take over maintenance of Biostrings in the near future while I'll remain the maintainer of pwalign. This split will remove the burden of maintaining the pairwiseAlignment-related stuff from Aidan's plate.
kankenny
commented
3 months ago
TLDR: Biostrings removed pairwiseAlignment method and the method is moved to pwalign