You're going to want to use the Biostrings C API. You can see TwoBitFile_read() in src/twoBit.c in rtracklayer for an example. It's not trivial.
Michael On Tue, Jan 5, 2016 at 5:21 AM, Sean Davis <seand...@gmail.com> wrote: > Forgive the really naive questions, but my C/C++ and Biostrings skills are > pretty rough. I have been playing with Rcpp to interface to an external > library for reading sequence formats. I am reading DNA sequences > one-at-a-time and would like to package a set of those up as a DNAStringSet. > I have at least two options: > > 1) Return a character vector back to R and then create a DNAStringSet in R. > This works now and works fine. > 2) Create the DNAStringSet in the cpp code. > > Are there advantages to using choice #2? If so, where would I start to get > the necessary Rcpp/Biostrings glue in place? I know how to make new S4 > objects in Rcpp, so it is really a question of knowing what class hierarchy > I need to instantiate and, roughly, how. Any pointers or code examples? > > Thanks, > Sean > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
