NBISweden/AGAT: AGAT-v1.4.1

What's Changed

• Allow agat_sp_filter_feature_by_attribute_value to filter with multiple values - fix #426 by @Juke34 in https://github.com/NBISweden/AGAT/pull/464
• Add possibility to output agat_sp_statistics.pl result in yaml format - fix #401 by @Juke34 in https://github.com/NBISweden/AGAT/pull/466
• fix #420. Now table 0 can be called (bioperl >= april 2024 must be pr… by @Juke34 in https://github.com/NBISweden/AGAT/pull/470
• Fix #471 - agat_sp_filter_feature_by_attribute_value.pl to allow the use of "!" test by @Juke34 in https://github.com/NBISweden/AGAT/pull/473
• Fix #475 : Added an option for agat_sp_merge_annotations.pl to refer a folder of GFF files by @IvanUgrin in https://github.com/NBISweden/AGAT/pull/476
• Mfannot - agat_convert_mfannot2gff.pl - big improvement in handling this conversion by @Juke34 in https://github.com/NBISweden/AGAT/pull/483
• sort tag L2 for better reproducibility in a function of OmniscientO by @Juke34 in https://github.com/NBISweden/AGAT/pull/487
• fix #484 by @Juke34 in https://github.com/NBISweden/AGAT/pull/488 - CDS must not be attached to Level2 if no Parent/ID relationship and locus name not the same as previous L2. Should be parsed using locus instead of sequential (as expected).
• fix #307 - Update agat_sp_statistics.pl to provide median and percentile statistics by @Juke34 in https://github.com/NBISweden/AGAT/pull/489
• remove transcript ID in Level1 feature when creating it from another feature used as template (clean_clone) by @Juke34 in https://github.com/NBISweden/AGAT/pull/491

Documentation:

• Update documentation of agat_convert_minimap2_bam2gff.md by @Juke34 in https://github.com/NBISweden/AGAT/pull/452
• Update README - Update Zenodo to always point to latest DOI
• rename agat_sp_fix_cds_frame.pl to agat_sp_fix_cds_phase.pl in pod of the script and its corresponding md doc file
• fix mispelling script name in doc. fix #456 by @Juke34 in https://github.com/NBISweden/AGAT/pull/465
• remove unused inflate option from agat_convert_genscan2gff.pl and agat_convert_genscan2gff.md fix #477 by @Juke34 in https://github.com/NBISweden/AGAT/pull/481
• update doc agat_sp_compare_two_annotations.pl by @Juke34 in https://github.com/NBISweden/AGAT/pull/490
• Shift AGAT documentation from readthedocs to Mkdocs (gh-pages of GitHub now) by @Juke34 in https://github.com/NBISweden/AGAT/pull/482

New Contributors

• @IvanUgrin made their first contribution in https://github.com/NBISweden/AGAT/pull/476 (fix #475)

Full Changelog: https://github.com/NBISweden/AGAT/compare/v1.4.0...v1.4.1