fix: check for existence of QC column to appease CI
@@ -58,6 +58,8 @@ if __name__ == '__main__':
to_exclude |= snp_clusters>args.snp_clusters
to_exclude |= rare_mutations>args.rare_mutations
to_exclude |= np.abs(clock_deviation+rare_mutations)>args.clock_plus_rare
+
+ if "QC_mixed_sites" in metadata.columns:
to_exclude |= metadata.QC_mixed_sites=='bad'
# write out file with sequences flagged for exclusion
