[Bioc-devel] Creating Biostrings DNAStringSet from Rcpp/C++

[Sean Davis]

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