In both AGP 1.1 and AGP 2.0 there is support for comment lines prefixed with the hash character (#). In the latter case,comments are restricted to the header only i.e. all comment lines must occur at the top of the file.
Current Gap5 seg faults if there are any comments at the top of the AGP file.
In addition, it's not obvious which AGP version(s) are supported by gap5. Since AGP 1.1 is deprecated by NCBI, it makes sense to only support version 2.0:
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