Testing implememntation of viterbi

Testing different things to decrease memory and time
In particular, using sparse trellis and bitset instead of
std::set container to keep track of possible transitions
Finished testing low memory implementation of trellis in mem_trellis

Working on implementing the necessary changes througout the library.

Trellis (only keep applicable data)
Sequences ( Ambiguous characters are calculated before hand (positive numbers that
correlate with lexical table indices)
Lexical Table ( Emissions ) ( Use deep table instead of calculating indices)
Middle of adapting ambiguous characters to positive indices
Ambiguous characters changed to positive values
Evaluate pre-calculation of ambiguous emissions and low memory trellis

Transferring and adapting code to for other algorithms to the new trellis
class.
Finished newStochHMM  & Fix Transitions error and Initial transition bug in viterbi

When first state isn't the state directly following the Init, it was producing an error.
Stochastic Viterbi added.
Added beginning of explicit duration code to viterbi
Started adding explicit duration.  Split explicit duration decoding algorithms
off to complex decoding algorithms that keep track of values for other calculations
Added checking of model Topology.
Fix Model finalize calling checks on NULL transitions
Add Continuous PDF emission for Real track
Remove CSV from SeqTracks and make Fasta Default format
Update README.md
Update README.md
Update README.md
Update usage statement and add ability to print posterior table
Merge branch 'master' of github.com:KorfLab/StochHMM

Conflicts:
	README.md
Fix example sequences

Example sequence 3_16Eddy.fa had a copy of the model copied into the file
so it wouldn't work.
Update README.md
Merge branch 'master' of github.com:KorfLab/StochHMM
Testing and updating development branch