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
Testing and updating development branch
Finish univariate PDF functions, Add initial default PDFs
Completed coding of the PDF functions and created default loading
of those function using void StateFuncs::loadUnivariatePdf()
Added loadUnivariatePdf() function call to StateFuncs constructor
Fix coding syntax mistakes in PDF functions
Updated documentation. Changed parameters as ref to pointers

Updated the doxygen documentation on the PDF functions.

Also, changed the parameters passed as pointer to std::vector
instead of reference to std::vector.  Thus, if no parameters are
given for some functions we don't have to create any parameter vector.
Standardize stateFuncs to output value in log space

Changed the PDF functions used with StateFuncs so that they
output log'd probabilities.
Add preliminary support for Multivariate Emissions

//TODO: Need to still test the code
Found Floating point precision error using Lettuce
Fix Viterbi/Forward/Backward next state on initialization

Previously assigning only the state which had score, but should have
been initialized as the bitset vector of states to that state.

Changed to getFrom() or getTo();

Also created naive_backward and naive_forward();  Will use to benchmark
banding code.