documentation updates

This contains a few updates to the AlignedRead documentation and should make it a bit clearer how the different possible lengths are related to each other (`alen`, `qlen`, `rlen`, `len(alignread.seq)`, and `len(alignedread.query)`). While working with soft- and hard-clipped reads, I found that quite confusing until I inspected the source code. 

It also fixes a problem in the documentation generation: The sys.path was modified such that an already installed version of pysam was picked up, not the one that is currently being built.