WIP: OpGen consensus sequence

This is work in progress. This will make a consensus sequence based on a mapping report from the opgen software and a renamed and filtered assembly.

* Decided to keep **all** ambiguous bases. This gave better in-silico cuts when mapping the consensus back to Opgen. And we get to keep more information
* Adjusted for 1-based indexing of opgen 

Merge when I'm happy with the results.
noooooo.. years of c++ programming trying to pileup "="