Add new script agat_convert_minimap2_bam2gff.pl Add new feature type in json files Add function activate_warning_limit in utilities Add test for agat_convert_minimap2_bam2gff.pl (and add minimap sam and bam files for future tests) Add gff_syntax test 35 Add warnings when no phase specified within the CDS and enhance how we deal with cds phase in case of no phase at all Add option to remove offset in agat_sp_extract_sequences.pl to deal with offset even when we do not translate the sequence. Add log file for omniscient (activated by default for agat_convert_sp_gxf2gxf.pl) and polish logging messages Rename agat_sp_to_tabulated.pl to agat_convert_sp_gff2tsv.pl and fix it (number of column can vary now and we put N/A when info not applicable for the feature.) Rename Change agat_sp_split_by_level2_feature.pl into agat_sp_separate_by_record_type.pl because now deal with topfeature and standalone features. Rename agat_sq_manage_ID.pl into agat_sq_manage_IDs.pl Remove constant LEVEL1 LEVEL2 etc in OmniscientI Remove redundant info (topfeature dedicated hash. Info already exists in the value of other->level->level1). Create new function to access to json values stored into omniscient and adapt scripts accessing topfeatures. Remove agat_sp_gxf_to_gff3.pl because the same as agat_convert_sp_gxf2gxf.pl. It allows to avoid to take care of this 2 scripts in parallel. Fix potential problem for agat_sp_filter_feature_byattribute* because features were removed from omniscient while we looped over in the same time. Fix agat_sp_compare_two_BUSCOs.pl to deal with BUSCOv4 too Fix #33 #34 #35 #38 #40 Fix typo and update pod/help Update AGAT to deal with standalone features (l1 without children. Before it was removing them). Modify test files and scripts to include those standalone features. Update agat_sp_statistics.pl add number of overlapping genes within the statistics. Update to take topfeature and standalone features into account. Update ontology to use complete one instead of SOFA within AGAT Move JSON related code to OmniscientJson.pm Use of OntologyEngineI in OmniscientI.pm to filter ontology terms to follow the GFF3 rules: Feature type must be sequence_feature (SO:0000110) or an is_a child of it.