First (incomplete) series of API docs for genotype.py

**Note**: This work is **incomplete**!

This patch is a stab at documenting part of the functions in genotype.py. It is mostly done so that in future it would be easier for (possibly) external contributors to add new capabilities. It will also highlight where parameter clarififcation is needed (empty descriptions). 

I'm also doing this so I can understand better how to integrate muTect in the pipeline.

I'm using the Python style docstrings with reST. Feel free to comment if this is OK.

In case this is the way forward, I'll continue adding docstrings in genotype.py.