debug for -per-contig --per-gene --gene-transcript-map to ensure gene…

… is output in geneID column
CGATOxford · Jun 11, 2024 · a122c6d · a122c6d
1 parent 10c6495
commit a122c6d
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/umi_tools/group.py b/umi_tools/group.py
@@ -287,7 +287,10 @@ def main(argv=None):
                     if options.tsv:
                         if options.per_gene:
                             if options.per_contig:
-                                gene = read.reference_name
+                                if options.options.gene_transcript_map:
+                                    gene = read.get_tag(gene_tag)
+                                else:
+                                    gene = read.reference_name
                             else:
                                 gene = read.get_tag(gene_tag)
                         else: