NBISweden / AGAT / 12653278232

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Fix #512 (#515)

* fix bug when list of id to keep is empty (that would result in an empty file) it was seen as if no idlist was provided (which result in filter behavior to not be applied) which finally print the whole omniscienthash instead of nothing. It affects agat_sp_flag_premature_stop_codons.pl / agat_sp_filter_record_by_coordinates.pl / agat_convert_sp_gff2tsv.pl / agat_sp_prokka_fix_fragmented_gene_annotations.pl

* stick to a default expected behaviour: In the case of isoforms, the isoforms that do not pass the test are removed. If all isoforms are removed, the gene is removed.

* update test accordingly

51 of 51 new or added lines in 2 files covered. (100.0%)

12446 of 15347 relevant lines covered (81.1%)

2113.06 hits per line