Allow missing calls when checking Male ploidy discrepancy

Author: bpblanken

v03_pipeline/lib/misc/validation.py

@@ -104,8 +104,8 @@ def validate_imputed_sex_ploidy(
     mt = mt.select_cols(
         discrepant=(
             (
-                # All calls are diploid but the sex is Male
-                hl.agg.all(mt.GT.is_diploid())
+                # All calls are diploid or missing but the sex is Male
+                hl.agg.all(mt.GT.is_diploid() | hl.is_missing(mt.GT))
                 & (sex_check_ht[mt.s].predicted_sex == Sex.MALE.value)
             )
             | (

v03_pipeline/lib/misc/validation_test.py

@@ -106,19 +106,21 @@ def test_validate_imputed_sex_ploidy(self) -> None:
                     ),
                 ],
             },
-            cols={'s': ['HG00731_1', 'HG00732_1']},
+            # Male, Female, Male
+            cols={'s': ['HG00731_1', 'HG00732_1', 'NA19678_1']},
             entries={
                 'GT': [
                     [
                         hl.Call(alleles=[0], phased=False),
                         hl.Call(alleles=[0], phased=False),
+                        hl.missing(hl.tcall),
                     ],
                 ],
             },
         ).key_rows_by('locus')
         self.assertRaisesRegex(
             SeqrValidationError,
-            '50.00% of samples have misaligned ploidy',
+            '66.67% of samples have misaligned ploidy',
             validate_imputed_sex_ploidy,
             mt,
             sex_check_ht,