Consistent error handling

[bjpop]

I think a useful contribution would be to demonstrate good error handling practices.

One thing I was thinking of is a command line argument to decide whether the program will stop if it encounters a bad input FASTA file, or whether it should continue processing the remaining files.

We should try to make the error handling and output of the different versions the same.

[tseemann]

You don't often see a --continue-on-error option but I can see it has a use-case. Still annoying :)

[bjpop]

It has been decided that this enhancement won't be included in the interests of avoiding too much complexity.