output Core from netmhciipan

[kippakers]

Class II predictions have a lot of redundancy in the peptides they spit out which can be reduced by looking at the Core sequence. Currently topiary doesn't output the Core of a peptide (to match the classI output), but I think it's necessary for class II.

Would adding an extra column to the output csv be detrimental to downstream stuff?

[iskandr]

Sorry for the long delay in thinking about this. I can pass along the binding core, though it might clutter the downstream slightly. Do you still need this?

[kippakers]

I think it's important, but maybe to keep clutter down for other users it's best to use a flag to turn this on.