text: user1649: 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?
  
  user196: 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.
  
original_text: 1649: <p>I am trying to use <a href="http://catchenlab.life.illinois.edu/chromonomer/" rel="nofollow noreferrer">Chromonomer</a>. It should be possible (according to the software page and a paper) to add a GFF/GTF file to the analysis.</p>
  
  <p>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.</p>
  
  <p>How can I use a GFF or a GTF file with Chromonomer?</p>
   196: <p>I think the part of the code that should allow you to do this is in <code>chromomer.cc</code>.</p>
  
  <p>Lines 2857-2983 form the function <code>parse_command_line</code>. 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.</p>
  
  <p>For reference, I looked at version 1.07. It would be helpful if the code were on github.</p>
  