Changed tab name from 'Required' to 'Important' since SAM/BAMs are
not strictly required. Added asterisks to indicate required fields but
I do not explain to user what asterisks means.
Designing primers on shortest isoform is now the default.
Fix: BJ's bug is related to using different methods for trimming paths.
This would result in keyerrors in constructing the uncommited matrix
for the multinomial em algorithm. The KeyError is now caught, however
this may cause slight problems in calculating psi. Further looking into
how exactly path trims are handled may be useful.