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Ignore cache row if lineage is Unassigned (because of QC failure when…
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… cache was created). Otherwise, in generate_final_report, scorpio override logic's expanded_pango_lineage.startswith() gets an exception because 'Unassigned' expands to None. fixes cov-lineages#410
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AngieHinrichs committed Apr 6, 2022
1 parent cbf0778 commit 9cee885
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion pangolin/scripts/usher.smk
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ rule usher_cache:
writer.writeheader()
for row in reader:
hash = row["hash"]
if hash in seqs_to_assign:
if hash in seqs_to_assign and row["lineage"] != UNASSIGNED_LINEAGE_REPORTED:
cache_note = "Assigned from cache"
if not row["note"]:
row["note"] = cache_note
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