Merge pull request #796 from broadinstitute/dev

main <- dev

Author: bpblanken

v03_pipeline/lib/misc/family_loading_failures.py

@@ -175,7 +175,10 @@ def get_families_failed_sex_check(
     failed_families = defaultdict(list)
     for family in families:
         for sample_id in family.samples:
-            if family.samples[sample_id].sex != sex_check_lookup[sample_id]:
+            if family.samples[sample_id].sex not in {
+                sex_check_lookup[sample_id],
+                Sex.UNKNOWN,
+            }:  # NB: Unknown samples in pedigree are excluded from sex check.
                 failed_families[family].append(
                     f'Sample {sample_id} has pedigree sex {family.samples[sample_id].sex.value} but imputed sex {sex_check_lookup[sample_id].value}',
                 )

v03_pipeline/lib/misc/family_loading_failures_test.py

@@ -202,7 +202,6 @@ def test_get_families_failed_sex_check(self):
             [
                 [
                     'Sample ROS_006_18Y03226_D1 has pedigree sex F but imputed sex M',
-                    'Sample ROS_006_18Y03227_D1 has pedigree sex M but imputed sex F',
                 ],
             ],
         )

v03_pipeline/lib/misc/pedigree_test.py

@@ -316,7 +316,7 @@ def test_parse_project(self) -> None:
                     samples={
                         'BBL_BC1-000345_01_D1': Sample(
                             sample_id='BBL_BC1-000345_01_D1',
-                            sex=Sex.FEMALE,
+                            sex=Sex.UNKNOWN,
                             mother='BBL_BC1-000345_03_D1',
                             father='BBL_BC1-000345_02_D1',
                             maternal_grandmother=None,

v03_pipeline/lib/model/definitions.py

@@ -11,6 +11,7 @@ class AccessControl(Enum):
 class Sex(Enum):
     FEMALE = 'F'
     MALE = 'M'
+    UNKNOWN = 'U'
 
 
 class PipelineVersion(Enum):

v03_pipeline/var/test/pedigrees/test_pedigree_2.tsv

@@ -6,6 +6,6 @@ R0111_tgg_bblanken_wes	BBL_HT-007-5195_1	BBL_HT-007-5195	BBL_HT-007-5195_03_D1
 R0111_tgg_bblanken_wes	BBL_HT-007-5195_1	BBL_HT-007-5195	BBL_HT-007-5195_04_D1	BBL_HT-007-5195_02_D1	BBL_HT-007-5195_03_D1	M
 R0111_tgg_bblanken_wes	BBL_HT-007-5195_1	BBL_HT-007-5195	BBL_HT-007-5195_05_D1	BBL_HT-007-5195_02_D1	BBL_HT-007-5195_03_D1	F
 R0111_tgg_bblanken_wes	BBL_HT-007-5195_1	BBL_HT-007-5195	BBL_HT-007-5195_06_D1	BBL_HT-007-5195_02_D1	BBL_HT-007-5195_03_D1	M
-R0111_tgg_bblanken_wes	BBL_BC1-000345_1	BBL_BC1-000345	BBL_BC1-000345_01_D1	BBL_BC1-000345_02_D1	BBL_BC1-000345_03_D1	F
+R0111_tgg_bblanken_wes	BBL_BC1-000345_1	BBL_BC1-000345	BBL_BC1-000345_01_D1	BBL_BC1-000345_02_D1	BBL_BC1-000345_03_D1	U
 R0111_tgg_bblanken_wes	BBL_BC1-000345_1	BBL_BC1-000345	BBL_BC1-000345_02_D1			M
 R0111_tgg_bblanken_wes	BBL_BC1-000345_1	BBL_BC1-000345	BBL_BC1-000345_03_D1			F

v03_pipeline/var/test/pedigrees/test_pedigree_6.tsv

@@ -1,6 +1,6 @@
 Project_GUID	Family_GUID	Family_ID	Individual_ID	Paternal_ID	Maternal_ID	Sex
 R0116_sex_check_project2	family_1	family_1	ROS_006_18Y03226_D1			F
-R0116_sex_check_project2	family_1	family_1	ROS_006_18Y03227_D1			M
+R0116_sex_check_project2	family_1	family_1	ROS_006_18Y03227_D1			U
 R0116_sex_check_project2	family_1	family_1	ROS_006_18Y03228_D1	ROS_006_18Y03226_D1	ROS_006_18Y03227_D1	F
 R0116_sex_check_project2	family_2	family_2	ROS_007_19Y05919_D1			F
 R0116_sex_check_project2	family_2	family_2	ROS_007_19Y05939_D1			F