update script to write out command lines
change overflow from error to warning
typo in last commit
add script valSTats
remove totalSq now that weve switched to 2 pass solution for no good reason
Add logscale and scale options to valStats
extend --transProbs option to work with supervised mode
overhaul trianing options.  can now force specific transition and emission probabilities at end of training
dont make unknown symbol fatal error
convert sequence to lower case
fix bug where variance incorrect if transform applied
add foreceEmProbs option to bencmark
add chopper script
fix bug in ordering of right slices
jack up default iter from 10 to 100
Add fasta track support