I submitted a pull request with patches that allowed me to compile SeqPrep under OS X 10.10. If you want to try this out locally, you could do something like:
$ mkdir /tmp/SeqPrep_test
$ cd /tmp/SeqPrep_test
$ git clone https://github.com/alexpreynolds/SeqPrep.git
$ cd SeqPrep
$ git checkout clang-patch
I don't use this tool, so I don't know if my patches yield a binary that generates correct results, but the code compiles.