Add BAQ computation to index reader

[berndbohmeier]

This is a WIP PR to start discussion on how to get BAQ computation in this library (#482).
BAQ can greatly improve follow up variant calls as it will remove bias from wrong alignments by down weighting ambiguous alignments.

I followed the implementation in samtools https://github.com/samtools/samtools/blob/3952c89e5552a44ee926446627272fab0b305131/cut_target.c#L149

I know that this might be not be how we want it, but I wanted to first create a (for me) working example and then go from there.

I think questions to answer are:

• Is it okay to extent IndexReader or do we want a new e.g BAQIndexReader or similar?
• To spend less compute time on computations of BAQ which is pretty compute heavy, it is better to filter before doing BAQ. Is it okay to extend IndexReader by filtering, or do you not want this here?
• Do you think it is okay to give the necessary setting directly to the indexedReader via a setter function, or should it go as parameters into .pileup, or a new function .pileup_with_baq or similar (I tried this but failed so far as I was not able to pass the data around)?
• Do think this should be done completely different?