TLDR: Change the default settings to NOT remove regions with duplicate GeneIDs
GeneID is an optional parameters that is missing in most kinds our input files. The default action of the script is to remove duplicate GeneIDs which is very problematic when the input file has not Gene ID and the user is selecting some other column as GeneID, e.g. the coordinate column. In this case some regions with non-unique coordinates get filtered out
TLDR: Change the default settings to NOT remove regions with duplicate GeneIDs
GeneID is an optional parameters that is missing in most kinds our input files. The default action of the script is to remove duplicate GeneIDs which is very problematic when the input file has not Gene ID and the user is selecting some other column as GeneID, e.g. the coordinate column. In this case some regions with non-unique coordinates get filtered out