add new options to benchmark
add sequence
fix bugs
change log pass
Merge branch 'multitrack' of github.com:glennhickey/teHmm into multitrack
make supervized option
fix initbedtool
add score filter to cleanchaux
add initStartProbs
update tracks. replace termini with filtered. add back polny
ad start opts
update data tracks
add length filter
fix autoclean of termini to use forward strand
Merge branch 'multitrack' of github.com:glennhickey/teHmm into multitrack
splitstrand by default in launch of leantermini keeping only forward.  also dont call removeoverlaps
add correction to applyEmission prob for when a 1-probability gets downgraded
change to logger warning
add some information on training chaux params as well as initial distributions to git
update model