obey seq completeness provided in replicons file

oschwengers · Dec 4, 2023 · 24a43b9 · 24a43b9
1 parent 231788b
commit 24a43b9
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/bakta/utils.py b/bakta/utils.py
@@ -456,10 +456,9 @@ def qc_contigs(contigs: Sequence[dict], replicons: Dict[str, dict]) -> Tuple[Seq
                 if(replicon):
                     contig['type'] = replicon['replicon_type']
                     contig['topology'] = replicon['topology']
+                    contig['complete'] = replicon['replicon_type'] != bc.REPLICON_CONTIG
                     if(replicon['name']):
                         contig['name'] = replicon['name']
-                    if(replicon['replicon_type'] != bc.REPLICON_CONTIG):
-                        contig['complete'] = True
                     if(not cfg.keep_contig_headers):
                         contig['orig_id'] = contig['id']
                         contig['id'] = replicon['new_locus_id'] if replicon['new_locus_id'] else contig['simple_id']