How to provide a GFF/GTF file to Chromonomer
I think the part of the code that should allow you to do this is in chromomer.cc.

Lines 2857-2983 form the function parse_command_line. Nowhere is there any reference to anything resembling parsing a GFF file, so I think the documentation is not in line with the code at this point.

For reference, I looked at version 1.07. It would be helpful if the code were on github.