fix --fixTrans and --initTrans options to be more precise
revise user specified parameters.  note need to work out why unit test fails all of the sudden
fix bug added to _init where self.params was getting overrided with init_params.  also remove line in same function where emission model is initialized.  this must now be done outside of hmm
fix typos in warning
always accept empty lines
cut down logzero to not cause overflow in EM loop within scikit.  may need to review this
add some updates on new training options to readme
Update README.md