fixup! 🚧 merge sequences

nextstrain · Aug 27, 2024 · d143872 · d143872
1 parent c099e16
commit d143872
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/augur/merge.py b/augur/merge.py
@@ -285,6 +285,8 @@ def merge_sequences(args):
     # Reversed because seqkit rmdup keeps the first entry but this command
     # should keep the last entry.
     # FIXME: don't use shell. just using it to get a sense of feasibility.
+    # FIXME: is seqkit overkill here? compare to ncov's drop_duplicate_sequences which is plain Python.
+    # https://github.com/nextstrain/ncov/blob/0769ac0429df8456ce70be2f74dc885d7b7fab12/scripts/sanitize_sequences.py#L127
     cat_processes = (f"<({cat(filepath)})" for filepath in reversed(args.sequences))
     shell_cmd = f"cat {' '.join(cat_processes)} | seqkit rmdup"
     print_debug(F"running shell command {shell_cmd!r}")