#369 top-match does not work correctly for delimited files

[Kaipo]

The top-match option is not working, as described in this posting to the crux-users group:
https://groups.google.com/forum/#!topic/crux-users/-83jDpsmTfE

[William S Noble]

So this issue has been languishing untouched for a while. The problem stems from some confusion about what --top-match is supposed to for Percolator: is it supposed to filter the input PSMs or the output PSMs? The problem, as I understand it, is that we can't filter the input PSMs because we don't necessarily know which score column is supposed to be used as the ranker. So the only option is to filter at the output (i.e., after SVM training). It sounds, from Brian's description, like this filtering works fine in one format but not tab-delimited. Kaipo, can you fix it so that the output filtering is applied to all formats?