AGAT-v0.3.0

• 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_by_attribute_* 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.

AGAT-v0.2.3

• new script: agat_convert_sp_gff2zff.pl
• script name modified: agat_convert_sp_gxf_to_gxf.pl to agat_convert_sp_gxf2gxf.pl
• update pods

AGAT-v0.2.2

• improve agat_convert_bed2gff.pl to re-create CDS too (default behaviour)
• improve agat_convert_sp_gff2gtf.pl to be able to select output among all GTF versions available + update help
• fix error message when json file fails to load
• improve agat_sp_kraken_assess_liftover.pl to deal with output in a non-local file.
• update README

AGAT-v0.2.1

fix wrong calculation in the script agat_convert_sp_gff2bed.pl

AGAT-v0.2.0

Fixes:
#22 update printSurrounded to avoid line truncation
#23 agat_sq_basic_statistics.pl, add parameter to inflate multi-parent features
#24 agat_sp_extract_sequences.pl, now deals with seq < 3 nucleotide or empty translation
#25 update message in agat_sp_merge_annotations.pl
#27 add converter agat_convert_genscan2gff.pl

New scripts:
agat_convert_sp_gff2gtf.pl
agat_convert_sp_gxf_to_gxf.pl (copy of agat_sp_gxf_to_gff3.pl)
agat_convert_embl2gff.pl
agat_convert_mfannot2gff.pl
agat_convert_sp_gff2bed.pl
agat_sp_kraken_assess_lift_coverage.pl
agat_convert_genscan2gff.pl

Updates:
update features_level.json to handle more ensembl feature types

• esthetic changes
  fix STDOUT for agat_sp_filter_feature_by_attribute_presence.pl
  fix CDS starting offset in agat_sp_extract_sequences (translation in protein was wrong if starting CDS phase was different than 0. We clip now 1 or 2 nucleotide when needed to start in the correct frame)
  add test for the new scripts
  update OmniscienI to deal with no_check_skip option as an array + lower case key in uniqID hash + deal differently in _check_l2_linked_to_l3 to better create l2 feature (update gff_syntax test case9 to reflect the change).
  ...

AGAT-v0.1.1

• fixing agat_sq_mask.pl script
• Update README.md
• update tests
• update script helps
• fix #16
• fix #15
• add gff syntax case 33 and case 34 (to be compatible with the weird gff from nf-core dataset)
• add transcription_end_site in features_level3.json
• fix lowercase ID to stay uppercase when uppercase ID are created by the Omniscient constants

AGAT-v0.1.0

• Fix #6,#7,#8,#9,#10,#11
• 5 new scripts:
  agat_sp_filter_feature_by_attribute_value.pl
  agat_sp_compare_two_annotations.pl
  agat_sp_compare_two_BUSCOs.pl
  agat_sp_sensitivity_specificity.pl
  agat_sp_filter_feature_by_attribute_value.pl (to replace maker_select_models_by_AED_score.pl from GAAS repo. It is standardised here that make it able to perform more advance tasks)
• Modification of agat_sp_manage_IDs.pl to get shorter default ID naming. The previous style is still available with the --ensembl option
• add tests
• Improve/fix output path and names for some scripts
• cosmetic changes: Clean code, improve help, factored some code (moved into utilities mod

AGAT-v0.0.3

Create utilities module for clarity.
Add function get_proper_codon_table to check codon table because previous version of bioperl set codon table to 1 even is 0 is asked.
Update of all script that use codon table, and update the output of agat_sp_fix_longest_ORF.pl that was varying depending bioperl version used. => this fix the test step problem in bioconda
fix typo.

AGAT-v0.0.2

Test suite improve (result based) for a better code coverage.
Fix regression when introducing handling of off headers and top features (source, chromosomes).
Improve access to json data (now saved in Omniscient in 'other' level)
Header saved in omniscient (now saved in 'other' level)
Fix scripts that were looping over every levels... now have to skip 'other' level.
Add MANISFEST.SKIP
Fix scripts that were not running after transplanting the code from GAAS to AGAT
Add 'sort keys' in many scripts to be able to compare results (less efficient but good for reproducibility)
Update README - add installation from Bioconda

AGAT-v0.0.1

First AGAT release.