Initial check in of c++ short read programming library. These classes give functional...

Initial check in of c++ short read programming library. These classes give functionality to store and to basic processing on short read data and gneomic coordinates. Functions include loading in a list of reads, mapping them to selected windows, identifying variants and heterozygosities in the regions, and outputting the sequences and variants. The goal is to start to consolidate the various versions of these classes scattered amongst the existing code in order to create a more robust and easy to improve code base.