Removed proportionOutlier. The 'temper' parameter has the same purpose.
Set default of temper variable in EmissionParam to 100
Fix bug in emission updates (remove d/d+dens_unif)
Move NA_filter() inside .hmm function
Bug fix for tempering variable.  Had 1/temper * dnorm + (1-1/temper) * dunif

Should have been (1-1/tmper) * dnorm + 1/temper*dunif
passes unit tests
Add code for computing a posterior probability for a given segment
emission probabilities for BAFs are weighted by Pr(HOM)*unif + Pr(Het)*emission

Simplified transition probability matrix in viterbi2
Added documentation.  Remove unnecessary exports
update document of methods and functions
Defined HMM class and several accessors. This class contains the GRanges object, as well as the emission probabilities.

Will need something more efficient when looping over samples...
Add methods for FilterParam class
commit all man files.  Add cnvFilter family of methods
Updates to documentation / man pages
Add HMMList class. hmm2 does not store the emission matrix when
processing multiple samples
Update grangesData to subset SummarizedExperiment columns according to
the id labels in the granges object
Updates to documentation, ArrayViews methods, and vignette.
Update documentation.  Parameter class for plotting trellis.  Methods
for plotting idiograms.