As pysam is compiled C, i've never been able to run pysam under pypy.
This is a shame, since for most Bioinformatical operations (string manipulation, typical data structures, etc) pypy is considerably faster than python2.x
I think its probably worth getting pysam to run over pypy if possible - but before I start down that road, has anyone ever figured out how to get it to work already? :)
Thanks so much!