NBISweden/AGAT: AGAT-v0.5.1

Update Readme, add a troubleshooting paragraph Fix #83 in agat_convert_sp_gff2gtf.pl: remove stop codon from the CDS when converting to GTF (works only if stop_codon feature exists) Fix #82 add parameter to translate alternative start codon by a M in agat_sp_extract_sequences.pl Fix #78 fix mispelling in statistics report Fix #80 Update Help in agat_sp_flag_premature_stop_codons.pl Fix #77 bug in agat_convert_sp_gff2bed.pl. When several isoform only one is printed Fix #75 add verbosity for a specific message in OmniscientI.pm Fix ID when several similar blast name in agat_sp_manage_functional_annotation.pl Fix #71 log file based on input file Fix #69 fix the --expose option in agat_convert_sp_gxf2gxf.pl that was not working anymore (to display the json files) add lncrna in features_level2.json