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.