update fixtures (#4563)

hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/README.txt

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-  Written with version 0.2.130-bea04d9c79b5
-  Created at 2024/11/04 13:45:23
+  Written with version 0.2.133-4c60fddb171a
+  Created at 2025/01/02 12:26:15

hail_search/test_search.py

@@ -14,9 +14,9 @@
     EXPECTED_SAMPLE_DATA_WITH_SEX, SV_WGS_SAMPLE_DATA_WITH_SEX, VARIANT_LOOKUP_VARIANT, \
     MULTI_PROJECT_SAMPLE_TYPES_SAMPLE_DATA, FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA, \
     VARIANT1_BOTH_SAMPLE_TYPES, VARIANT2_BOTH_SAMPLE_TYPES, FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA_MISSING_PARENTAL_WGS, \
-    VARIANT3_BOTH_SAMPLE_TYPES, VARIANT4_BOTH_SAMPLE_TYPES, VARIANT2_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, \
+    VARIANT4_BOTH_SAMPLE_TYPES, VARIANT2_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, \
     VARIANT1_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, \
-    VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY
+    VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, VARIANT4_WES_ONLY, VARIANT3_WES_ONLY
 from hail_search.web_app import init_web_app, sync_to_async_hail_query
 from hail_search.queries.base import BaseHailTableQuery
 
@@ -370,10 +370,11 @@ async def test_both_sample_types_search(self):
 
         # Variant 1 is de novo in exome but inherited and homozygous in genome.
         # Variant 2 is inherited and homozygous in exome and de novo and homozygous in genome.
-        # Variant 3 is inherited in both sample types. Variant 4 is de novo in both sample types.
+        # Variant 3 is inherited in both sample types.
+        # Variant 4 is de novo in exome, but inherited in genome in the same parent that has variant 3.
         inheritance_mode = 'recessive'
         await self._assert_expected_search(
-            [VARIANT1_BOTH_SAMPLE_TYPES, VARIANT2_BOTH_SAMPLE_TYPES, [VARIANT3_BOTH_SAMPLE_TYPES, VARIANT4_BOTH_SAMPLE_TYPES]],
+            [VARIANT1_BOTH_SAMPLE_TYPES, VARIANT2_BOTH_SAMPLE_TYPES, [VARIANT3_WES_ONLY, VARIANT4_WES_ONLY]],
             sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA, inheritance_mode=inheritance_mode,
             **COMP_HET_ALL_PASS_FILTERS
         )

hail_search/test_utils.py

@@ -380,27 +380,19 @@
     'CAID': 'CA10960369',
 }
 
-VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY = deepcopy(VARIANT3)
-genotypes = VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes']
-VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes'] = {
-    'I000004_hg00731': [
-        genotypes['I000004_hg00731'],
-        {**genotypes['I000004_hg00731'], 'sampleType': 'WGS'}
-    ],
+VARIANT3_WES_ONLY = deepcopy(VARIANT3)
+genotypes = VARIANT3_WES_ONLY['genotypes']
+VARIANT3_WES_ONLY['genotypes'] = {
+    'I000004_hg00731': [genotypes['I000004_hg00731']],
     'I000005_hg00732': [genotypes['I000005_hg00732']],
     'I000006_hg00733': [genotypes['I000006_hg00733']],
 }
 
-VARIANT3_BOTH_SAMPLE_TYPES = deepcopy(VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY)
-genotypes = VARIANT3_BOTH_SAMPLE_TYPES['genotypes']
-VARIANT3_BOTH_SAMPLE_TYPES['genotypes']['I000005_hg00732'] = [
-    *genotypes['I000005_hg00732'],
-    {**genotypes['I000005_hg00732'][0], 'sampleType': 'WGS'}
-]
-VARIANT3_BOTH_SAMPLE_TYPES['genotypes']['I000006_hg00733'] = [
-    *genotypes['I000006_hg00733'],
-    {**genotypes['I000006_hg00733'][0], 'sampleType': 'WGS'}
-]
+VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY = deepcopy(VARIANT3_WES_ONLY)
+genotypes = VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes']
+VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes']['I000004_hg00731'].append(
+    {**genotypes['I000004_hg00731'][0], 'sampleType': 'WGS'}
+)
 
 VARIANT4 = {
     'variantId': '1-91511686-T-G',
@@ -475,17 +467,20 @@
     'CAID': 'CA341062623',
 }
 
-VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY = deepcopy(VARIANT4)
-genotypes = VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes']
-VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes'] = {
-    'I000004_hg00731': [
-        genotypes['I000004_hg00731'],
-        {**genotypes['I000004_hg00731'], 'sampleType': 'WGS'}
-    ],
+VARIANT4_WES_ONLY = deepcopy(VARIANT4)
+genotypes = VARIANT4_WES_ONLY['genotypes']
+VARIANT4_WES_ONLY['genotypes'] = {
+    'I000004_hg00731': [genotypes['I000004_hg00731']],
     'I000005_hg00732': [genotypes['I000005_hg00732']],
     'I000006_hg00733': [genotypes['I000006_hg00733']],
 }
 
+VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY = deepcopy(VARIANT4_WES_ONLY)
+genotypes = VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes']
+VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY['genotypes']['I000004_hg00731'].append(
+    {**genotypes['I000004_hg00731'][0], 'sampleType': 'WGS'}
+)
+
 VARIANT4_BOTH_SAMPLE_TYPES = deepcopy(VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY)
 genotypes = VARIANT4_BOTH_SAMPLE_TYPES['genotypes']
 VARIANT4_BOTH_SAMPLE_TYPES['genotypes']['I000005_hg00732'] = [
@@ -494,7 +489,7 @@
 ]
 VARIANT4_BOTH_SAMPLE_TYPES['genotypes']['I000006_hg00733'] = [
     *genotypes['I000006_hg00733'],
-    {**genotypes['I000006_hg00733'][0], 'sampleType': 'WGS'}
+    {**genotypes['I000006_hg00733'][0], 'numAlt': 2, 'sampleType': 'WGS'}
 ]
 
 VARIANT_LOOKUP_VARIANT = {