improve output
@@ -12,7 +12,7 @@ from priorities import sequence_to_int_array
from augur.utils import read_metadata
from datetime import datetime
-tmrca = datetime(2019, 11,15).toordinal()
+tmrca = datetime(2019, 12, 1).toordinal()
def expected_divergence(date):
try:
@@ -99,7 +99,7 @@ if __name__ == '__main__':
if not np.isnan(expected_div) and len(d['snps']) - expected_div > snp_cutoff:
msg += f"too high divergence {len(d['snps']) - expected_div:1.2f}>{snp_cutoff};"
if len(d['clusters']):
- msg += f"snps clusters;"
+ msg += f"{len(d['clusters'])} snp clusters a {','.join([x[2] for x in d['clusters']])} SNPs;"
if d['no_data']>no_data_cutoff:
msg += f"too many Ns ({d['no_data']}>{no_data_cutoff})"
if msg:
