Jacques Dainat
This script if for a particular purpose and avoid overlap of the end of genes to be exactly at the same position ( a peculiarity for submission to public archive)...
If you work on 2 files use agat_sp_merge_annotations.pl If you work on a single file then use the gxf2gxf script but you must first activate the merge option in the...
What vesion of AGAT do you use? To be able to merge gene without CDS, both gene must be of the same type (level1 must be similar e.g. `gene` and...
Right if two genes have CDS it is at CDS level that the overlap will be taken into account to decide to merge the gene or not. You would like...
`agat_sp_fix_overlaping_genes.pl` is not made for that purpose. Either use `agat_sp_merge_annotations.pl` or activate the merge_loci param `agat config --expose --merge_loci` and use any script (most appropriate is agat_convert_sp_gxf2gxf.pl). But for now...
Compare to EVM, AGAT does not use any specific logic to decide if one gene is more reliable than another, so your concern about relying on AGAT is worthwhile. It...
Thank you for your involvement. Could you update the regex to recognize gtf and gff file? If there is a way to minimize the external library to use it would...
Can you share a sample with what you provide in and pointing what is missing in the output?
Thank you for the feedback. This is a remaining from another script used to develop this one. This has no place here. I will remove that.
Fixed in last PR