regenerate clean tracks
first stab at imporved confusion matrix state name mapping.  need more test
Merge branch 'development' of github.com:glennhickey/teHmm into development
Merge branch 'development' of github.com:glennhickey/teHmm into development
more logging
add maxprob and transmatepsilons options
Merge branch 'development' of github.com:glennhickey/teHmm into development
add fitopts options to benchmark
add new train options to benchmark
add maxprobcut option
littel speedup
oops
only do naive if wanted
Merge branch 'development' of github.com:glennhickey/teHmm into development
comment out tantan track
undo last commit
Add new segment opt and tack on orthology track to human
start dm3 tracks list
bump qualthresh default back up now that alg can be slow. . need to make more foolproof
Merge branch 'development' of github.com:glennhickey/teHmm into development