Possible bug (v1.0 and 1.2)

[robertewhite]

Hi

I have been using AGAT to assemble GFF3 files for Epstein-Barr virus, and have had some odd error messages in the log file. As far as I can tell, the output GFF3 looks fine, but it is a lot to analyse in forensic detail.

The message is:
"Use of uninitialized value in lc at /Users/xxx/miniconda3/envs/agatenv3/lib/perl5/site_perl/AGAT/OmniscientI.pm line 1069, line 511. [and same on many other lines]

Since I have used AGAT a lot for a string of files (iteratively correcting my input) and initially this did not appear, but subsequently appeared more and more frequently in the output, I thought it might be a corruption in my installation, so I installed 1.2 in a new environment, and the error persisted.

Attaching the log and the input file so you can see if you can reproduce this issue. [the orphan features in the GFF3 file are deliberate]

Cheers
Rob
WTw_withWp.agat.log
WTw_withWp.gff3 copy.txt