added minimal test
made readme GH flavoured md
basic cmake build
updated README
start work on post-processor for 'putatoins'
basic post-procsoor (allele freq counter) in place
Start on using bamtools refernce index...

bamtools indexing doesn't allow acess by name, and actual index is
private memeber of the Fasta class. New plan is to add to bamtools
implimentation, and include our own header/implmentation for this
in distribution.
using pileup datas refID as reference
pass references by ref
cleaned out some commented code
removed reference to SeqAn in README
changed ModelInput struct
Started work on option parsing

NOTE: not compiling at this commit
Options parsing working

Compliles with clang... Cmake build still broken
updated README
further updated the README
Options parser works, VariantVisitor takes options
sensible argument names, cleaner formating an updated README
tweak to README mardkdown
more fussing with the README