manually add

arrow/commands/annotations/load_gff3.py

@@ -33,6 +33,11 @@
     help="Disable CDS recalculation and instead use the one provided",
     is_flag=True
 )
+@click.option(
+    "--cds_cleaning",
+    help="This changes the behaviour of creating GFF3 features in apollo to match more closely to what it expects. Generally you'll probably want this on if you have transcripts with multiple exons and CDSs, but we don't want to change existing scripts so we are not defaulting this on."
+    is_flag=True
+)
 @click.option(
     "--timing",
     help="Output loading performance metrics",
@@ -41,11 +46,11 @@
 @pass_context
 @custom_exception
 @str_output
-def cli(ctx, organism, gff3, source="", batch_size=1, test=False, use_name=False, disable_cds_recalculation=False, timing=False):
+def cli(ctx, organism, gff3, source="", batch_size=1, test=False, use_name=False, disable_cds_recalculation=False, cds_cleaning=False, timing=False):
     """Load a full GFF3 into annotation track
 
 Output:
 
     Loading report
     """
-    return ctx.gi.annotations.load_gff3(organism, gff3, source=source, batch_size=batch_size, test=test, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation, timing=timing)
+    return ctx.gi.annotations.load_gff3(organism, gff3, source=source, batch_size=batch_size, test=test, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation, cds_cleaning=cds_cleaning, timing=timing)