not applicable

Author: jklugherz

v03_pipeline/lib/misc/family_loading_failures.py

@@ -213,5 +213,5 @@ def get_families_failed_imputed_sex_ploidy(
             sorted_discrepant_samples = sorted(discrepant_loadable_samples)
             failed_families[
                 family
-            ] = f'Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : {sorted_discrepant_samples[:10]}'
+            ] = f'Found samples with misaligned ploidy with their provided imputed sex: {sorted_discrepant_samples}'
     return failed_families

v03_pipeline/lib/misc/family_loading_failures_test.py

@@ -416,7 +416,7 @@ def test_get_families_failed_imputed_sex_ploidy(self) -> None:
         self.assertCountEqual(
             failed_families.values(),
             [
-                "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']",
+                "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1', 'HG00732_1', 'NA20889_1', 'NA20899_1']",
             ],
         )
 
@@ -435,6 +435,6 @@ def test_get_families_failed_imputed_sex_ploidy(self) -> None:
         self.assertCountEqual(
             failed_families.values(),
             [
-                "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['HG00731_1']",
+                "Found samples with misaligned ploidy with their provided imputed sex: ['HG00731_1']",
             ],
         )

v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py

@@ -181,19 +181,19 @@ def test_write_remapped_and_subsetted_callset_task_failed_some_family_checks(
                         ploidy_check={
                             '234_1': hl.Struct(
                                 samples=['NA19678_1'],
-                                reasons="Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA19678_1']",
+                                reasons="Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']",
                             ),
                             '567_1': hl.Struct(
                                 samples=['NA20872_1'],
-                                reasons="Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20872_1']",
+                                reasons="Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']",
                             ),
                             'bcd_1': hl.Struct(
                                 samples=['NA20878_1'],
-                                reasons="Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20878_1']",
+                                reasons="Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']",
                             ),
                             'cde_1': hl.Struct(
                                 samples=['NA20881_1'],
-                                reasons="Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20881_1']",
+                                reasons="Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']",
                             ),
                         },
                     ),
@@ -300,19 +300,19 @@ def test_write_remapped_and_subsetted_callset_task_all_families_failed(
                         'ploidy_check': {
                             'cde_1': {
                                 'samples': ['NA20881_1'],
-                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20881_1']",
+                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex: ['NA20881_1']",
                             },
                             '234_1': {
                                 'samples': ['NA19678_1'],
-                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA19678_1']",
+                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex: ['NA19678_1']",
                             },
                             'bcd_1': {
                                 'samples': ['NA20878_1'],
-                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20878_1']",
+                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex: ['NA20878_1']",
                             },
                             '567_1': {
                                 'samples': ['NA20872_1'],
-                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex (first 10, if applicable) : ['NA20872_1']",
+                                'reasons': "Found samples with misaligned ploidy with their provided imputed sex: ['NA20872_1']",
                             },
                         },
                     },