NBISweden/AGAT: 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). ...