Updating to latest pysam

Latest pysam (0.8.1) ATM has renamed some of the Reference used by this software.

See this commit for example: https://github.com/pysam-developers/pysam/commit/cba80e909c3954214221bae4801701b31fe71321 or this one: 
https://github.com/mattions/pysam/blob/master/pysam/csamfile.pxd

This PR fix this

P.S.: I've also added `.pydevproject` and `.project` to the gitignore, you many need to re-create these and they won't be added to the repo.