Copious IO inlined in main fuction.

[bryan-lunt]

There is a lot of IO inlined in the main function that could be moved out to an IO.cpp / IO.h file.

The various parsers implemented should be DRY, and should also be absolutely pedantic. (Excess data afterward in a file should cause an error!)

[bryan-lunt]

These Lines 209-294 in master seq2expr.cpp ( https://github.com/UIUCSinhaLab/GEMSTAT/blob/master/src/seq2expr.cpp#L209-L294 ) either into their own file or into IO.cpp/IO.h .

( 221 - 294 in bryanInd ) https://github.com/UIUCSinhaLab/GEMSTAT/blob/bryanInd/src/seq2expr.cpp#L221-L294