NBISweden/AGAT: AGAT-v1.2.0

new script:

• agat_sp_add_intergenic_regions.pl

• agat_sp_add_splice_sites.pl

• agat_convert_minimap2_bam2gff.pl : fix #363 save AS information from BAM into GFF score (instead of phase) and put a dot for the phase

• Update statistics rendering (e.g. agat_sp_statistics.pl): Avoid to display twice stats when there is no isoform, add "(bp)" to clarify what means the numbers.
• new features in feature_levels.yaml :
  • pseudogenic_region
  • pseudogenic_cds
  • intergenic_region
  • protein_bind
  • regulatory
  • five_prime_cis_splice_site
  • three_prime_cis_splice_site
• remove JSON from MYMETA.yml
• fix #346 : config.yaml is now called by default agar_config.yaml. It is now possible to create one at the fly with a chosen name. It is also possible to call all script specifying a config file located and named as wished.
• fix #368 - Avoid seq_id 0 to be replaced by default SEQ value

• fix #378 - fix auto format detection for sq scripts

• homogenize input/ouput

  • use exclusively AGAT::BioperlGFF (_sq_script was using Bio::Tools::GFF for input/output; sp script were using AGAT::BioperlGFF for input and Bio::Tools::GFF for output)
  • improving AGAT::BioperlGFF to take care of GFF and GTF output (adding parameter VERSION and TYPE). Remind AGAT::BioperlGFF is an improved version of Bio::Tools::GFF
  • simplify code by factorizing OmniscientToGTF.pm and BioperlGFF.pm by implementing redundant function into BioperlGFF (e.g. filtering feature by GTF version; _gff25_string_JD and _gff25_string to fix incorrect GTF output provided by bioperl, etc)

new test:

• agat_convert_minimap2_bam2gff.pl
• agat_sq_add_attributes_from_tsv.pl
• agat_sp_add_intergenic_regions.pl
• agat_sp_add_splice_sites.pl

doc:

• remove 0 from agat config file which is not a correct to select for GTF version
• remove agat_sq_manage_ID from doc (official script is agat_sq_manage_IDs)
• update pod (removing option not used)
• update doc .md