gffcompare class code "x", what is the minimum overlap? about gffcompare HOT 1 CLOSED

Unfortunately that class code is currently reported for any >=1bp overlap on the opposite strand..
As a side note, the gffcompare documentation has been updated recently (see http://ccb.jhu.edu/software/stringtie/gffcompare.shtml) with a diagram documenting these and other (newer) codes that were added to gffcompare. For example the new code 's' is much more specific as it also involves an intron overlap -- though obviously this is only helpful for multi-exon transcripts.

The C++ code actually retrieves the overlap length but the value is never exposed in the output files produced by gffcompare.
I was playing recently with a faster transcript classification code, temporarily called trmap (full code is in https://github.com/gpertea/trmap) which outputs the full exon structures (along with the class code) of both transcript query along with the overlapped references; I could easily modify that tool to also output the overlap length -- or one can use a post-processing script to filter those 'x' overlaps as needed, based on the exon coordinates.
Eventually this trmap code will likely become part of gffcompare.. but until then it's functional on its own for such quick transcript classification.

from gffcompare.