How to provide a GFF/GTF file to Chromonomer I am trying to use Chromonomer. It should be possible (according to the software page and a paper) to add a GFF/GTF file to the analysis.

Alas, neither the built-in help nor some light source code browsing were enough to find a way of passing the file to the software.

How can I use a GFF or a GTF file with 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.