Merge pull request #1014 from broadinstitute/dev

Dev

Author: bpblanken

v03_pipeline/lib/misc/validation.py

@@ -151,10 +151,16 @@ def validate_imputed_sex_ploidy(
             )
         ),
     )
-    discrepant_rate = mt.aggregate_cols(hl.agg.fraction(mt.discrepant))
-    if discrepant_rate:
-        msg = f'{discrepant_rate:.2%} of samples have misaligned ploidy with their provided imputed sex.'
-        raise SeqrValidationError(msg)
+    discrepant_samples = mt.aggregate_cols(
+        hl.agg.filter(mt.discrepant, hl.agg.collect_as_set(mt.s)),
+    )
+    if discrepant_samples:
+        sorted_discrepant_samples = sorted(discrepant_samples)
+        msg = f'Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : {sorted_discrepant_samples[:10]}'
+        raise SeqrValidationError(
+            msg,
+            {'imputed_sex_ploidy_failures': sorted_discrepant_samples},
+        )
 
 
 def validate_sample_type(