Skip writing force-inclusions a second time

This fixes double-writing of the same record.
nextstrain · Jun 30, 2022 · 4859b5d · 4859b5d
1 parent 0bfd28a
commit 4859b5d
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/augur/filter.py b/augur/filter.py
@@ -1429,6 +1429,10 @@ def run(args):
                 output_log_writer.writerow(filtered_strain)
 
         if group_by:
+            # Prevent force-included sequences from being included again during
+            # subsampling.
+            seq_keep = seq_keep - distinct_force_included_strains
+
             # If grouping, track the highest priority metadata records or
             # count the number of records per group. First, we need to get
             # the groups for the given records.