handle wes/wgs inheritance edge case

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 2024/10/02 14:46:35
+  Created at 2024/11/04 13:45:23

hail_search/queries/base.py

@@ -472,9 +472,7 @@ def _apply_entry_filters(ht):
     def _filter_single_entries_table(self, ht, project_families, inheritance_filter=None, quality_filter=None, is_merged_ht=False, **kwargs):
         ht, sorted_family_sample_data = self._add_entry_sample_families(ht, project_families, is_merged_ht)
         ht = self._filter_quality(ht, quality_filter, **kwargs)
-        ht, ch_ht = self._filter_inheritance(
-            ht, None, inheritance_filter, sorted_family_sample_data,
-        )
+        ht, ch_ht = self._filter_inheritance(ht, None, inheritance_filter, sorted_family_sample_data)
         ht = self._apply_entry_filters(ht)
         ch_ht = self._apply_entry_filters(ch_ht)
 
@@ -574,7 +572,7 @@ def _get_sample_type(cls, family_index, ht_globals):
 
     def _filter_inheritance(
         self, ht, comp_het_ht, inheritance_filter, sorted_family_sample_data,
-        annotation='family_entries', entries_ht_field='family_entries'
+        annotation='family_entries', entries_ht_field='family_entries', **kwargs
     ):
         any_valid_entry = lambda x: self.GENOTYPE_QUERY_MAP[HAS_ALT](x.GT)
 
@@ -584,14 +582,14 @@ def _filter_inheritance(
             any_valid_entry = lambda x: prev_any_valid_entry(x) & (x.affected_id == AFFECTED_ID)
 
         ht = ht.annotate(**{
-            annotation: ht[entries_ht_field].map(
+            entries_ht_field: ht[entries_ht_field].map(
                 lambda entries: hl.or_missing(entries.any(any_valid_entry), entries)
             )})
 
         if self._has_comp_het_search:
             comp_het_ht = self._annotate_families_inheritance(
                 comp_het_ht if comp_het_ht is not None else ht, COMPOUND_HET, inheritance_filter,
-                sorted_family_sample_data, annotation, entries_ht_field
+                sorted_family_sample_data, annotation, entries_ht_field, **kwargs
             )
 
         if is_any_affected or not (inheritance_filter or self._inheritance_mode):
@@ -600,15 +598,43 @@ def _filter_inheritance(
 
         ht = None if self._inheritance_mode == COMPOUND_HET else self._annotate_families_inheritance(
             ht, self._inheritance_mode, inheritance_filter, sorted_family_sample_data,
-            annotation, entries_ht_field
+            annotation, entries_ht_field, **kwargs
         )
 
         return ht, comp_het_ht
 
     def _annotate_families_inheritance(
         self, ht, inheritance_mode, inheritance_filter, sorted_family_sample_data,
-        annotation, entries_ht_field,
+        annotation, entries_ht_field, family_passes_inheritance_filter = None
     ):
+        if not family_passes_inheritance_filter:
+            family_passes_inheritance_filter = self._get_family_passes_inheritance_filter
+
+        entry_indices_by_gt = self._get_entry_indices_by_gt_map(
+            inheritance_filter, inheritance_mode, sorted_family_sample_data
+        )
+
+        for genotype, entry_indices in entry_indices_by_gt.items():
+            if not entry_indices:
+                continue
+            entry_indices = hl.dict(entry_indices)
+            ht = ht.annotate(**{
+                annotation: hl.enumerate(ht[entries_ht_field]).starmap(
+                    lambda family_idx, family_samples: family_passes_inheritance_filter(
+                        entry_indices, family_idx, genotype, family_samples, ht, annotation
+                    )
+                )
+            })
+
+        return ht
+
+    def _get_family_passes_inheritance_filter(self, entry_indices, family_idx, genotype, family_samples, *args):
+        return hl.or_missing(
+            ~entry_indices.contains(family_idx) | entry_indices[family_idx].all(
+                lambda sample_i: self.GENOTYPE_QUERY_MAP[genotype](family_samples[sample_i].GT)
+        ), family_samples)
+
+    def _get_entry_indices_by_gt_map(self, inheritance_filter, inheritance_mode, sorted_family_sample_data):
         individual_genotype_filter = (inheritance_filter or {}).get('genotype')
 
         # Create a mapping of genotypes to check against a list of samples for a family
@@ -630,21 +656,7 @@ def _annotate_families_inheritance(
             ]
             self.max_unaffected_samples = max(family_unaffected_counts) if family_unaffected_counts else 0
 
-        for genotype, entry_indices in entry_indices_by_gt.items():
-            if not entry_indices:
-                continue
-            entry_indices = hl.dict(entry_indices)
-            ht = ht.annotate(**{
-                annotation: hl.enumerate(ht[entries_ht_field]).starmap(
-                    lambda family_i, family_samples: hl.or_missing(
-                        ~entry_indices.contains(family_i) | entry_indices[family_i].all(
-                            lambda sample_i: self.GENOTYPE_QUERY_MAP[genotype](family_samples[sample_i].GT)
-                        ), family_samples,
-                    ),
-                )
-            })
-
-        return ht
+        return entry_indices_by_gt
 
     def _get_family_passes_quality_filter(self, quality_filter, ht, **kwargs):
         quality_filter = quality_filter or {}

hail_search/queries/mito.py

@@ -205,37 +205,62 @@ def _filter_entries_ht_both_sample_types(
             )
 
         ch_ht = None
-        family_guid_idx_map = defaultdict(dict)
+        family_idx_map = defaultdict(dict)
         for sample_type, sorted_family_sample_data in sample_types:
+            ht = self._annotate_initial_passes_inheritance(ht, sample_type)
+            ch_ht = self._annotate_initial_passes_inheritance(ch_ht, sample_type)
             ht, ch_ht = self._filter_inheritance(
                 ht, ch_ht, inheritance_filter, sorted_family_sample_data,
-                annotation=sample_type.passes_inheritance_field, entries_ht_field=sample_type.family_entries_field
+                annotation=sample_type.passes_inheritance_field, entries_ht_field=sample_type.family_entries_field,
+                family_passes_inheritance_filter=self._get_family_passes_inheritance_filter_both_sample_types
             )
             for family_idx, samples in enumerate(sorted_family_sample_data):
                 family_guid = samples[0]['familyGuid']
-                family_guid_idx_map[family_guid][sample_type.value] = family_idx
+                family_idx_map[family_guid][sample_type.value] = family_idx
 
-        family_idx_map = hl.dict(family_guid_idx_map)
+        family_idx_map = hl.dict(family_idx_map)
         ht = self._apply_multi_sample_type_entry_filters(ht, family_idx_map)
         ch_ht = self._apply_multi_sample_type_entry_filters(ch_ht, family_idx_map)
         return ht, ch_ht
 
+    @staticmethod
+    def _annotate_initial_passes_inheritance(ht, sample_type):
+        if ht is None:
+            return ht
+
+        return ht.annotate(**{
+            sample_type.passes_inheritance_field: ht[sample_type.family_entries_field].map(
+                lambda family_entries: hl.array(
+                    hl.range(0, hl.len(family_entries)).map(lambda _: True)
+                )
+            )})
+
+    def _get_family_passes_inheritance_filter_both_sample_types(
+        self, entry_indices, family_idx, genotype, family_samples, ht, annotation
+    ):
+        return hl.enumerate(ht[annotation][family_idx]).starmap(
+            lambda sample_idx, passes: (hl.case()
+                .when(~entry_indices.get(family_idx).contains(sample_idx), passes)
+                .when(~self.GENOTYPE_QUERY_MAP[genotype](family_samples[sample_idx].GT), False)
+                .default(passes))
+        )
+
     def _apply_multi_sample_type_entry_filters(self, ht, family_idx_map):
         if ht is None:
             return ht
 
-        # Keep family from both sample types if either passes quality AND inheritance
         for sample_type in SampleType:
             ht = ht.annotate(**{
                 sample_type.family_entries_field: hl.enumerate(ht[sample_type.family_entries_field]).starmap(
-                    lambda i, family_samples: hl.or_missing(
-                        hl.bind(
-                            lambda other_sample_type_idx: (
-                                self._family_has_valid_sample_type_entries(ht, sample_type, i) |
-                                self._family_has_valid_sample_type_entries(ht, sample_type.other_sample_type, other_sample_type_idx)
-                            ),
-                            family_idx_map.get(hl.coalesce(family_samples)[0]['familyGuid']).get(sample_type.other_sample_type.value),
-                       ), family_samples)
+                    lambda family_idx, family_samples: hl.or_missing(
+                        hl.bind(lambda other_sample_type_family_idx: ((
+                            self._family_has_valid_quality(ht, sample_type, family_idx) |
+                            self._family_has_valid_quality(ht, sample_type.other_sample_type, other_sample_type_family_idx)
+                             ) &
+                            self._family_has_valid_inheritance(ht, sample_type, family_idx, other_sample_type_family_idx) &
+                            self._family_has_valid_inheritance(ht, sample_type.other_sample_type, other_sample_type_family_idx, family_idx)
+                        ), family_idx_map.get(hl.coalesce(family_samples)[0]['familyGuid']).get(sample_type.other_sample_type.value),
+                    ), family_samples)
                 )})
 
         # Merge family entries and filters from both sample types
@@ -253,13 +278,29 @@ def _apply_multi_sample_type_entry_filters(self, ht, family_idx_map):
         return ht.filter(ht.family_entries.any(hl.is_defined))
 
     @staticmethod
-    def _family_has_valid_sample_type_entries(ht, sample_type, sample_type_family_idx):
-        # Note: This logic does not sufficiently handle case 2 here https://docs.google.com/presentation/d/1hqDV8ulhviUcR5C4PtNUqkCLXKDsc6pccgFVlFmWUAU/edit?usp=sharing
-        # and will need to be changed to support it - https://github.com/broadinstitute/seqr/issues/4403
+    def _family_has_valid_quality(ht, sample_type, sample_type_family_idx):
         return (
             hl.is_defined(sample_type_family_idx) &
-            hl.is_defined(ht[sample_type.passes_quality_field][sample_type_family_idx]) &
-            hl.is_defined(ht[sample_type.passes_inheritance_field][sample_type_family_idx])
+            hl.is_defined(ht[sample_type.passes_quality_field][sample_type_family_idx])
+        )
+
+    @staticmethod
+    def _family_has_valid_inheritance(ht, sample_type, family_idx, other_sample_type_family_idx):
+        return hl.bind(
+            lambda sample_type_fail_samples, other_sample_type_pass_samples: (
+                sample_type_fail_samples.all(other_sample_type_pass_samples.contains)
+            ), hl.enumerate(ht[sample_type.family_entries_field][family_idx]).starmap(
+                lambda sample_idx, sample: hl.or_missing(
+                    ~ht[sample_type.passes_inheritance_field][family_idx][sample_idx],
+                    sample['sampleId'],
+                )
+            ).filter(hl.is_defined),
+            hl.enumerate(ht[sample_type.other_sample_type.family_entries_field][other_sample_type_family_idx]).starmap(
+                lambda sample_idx, sample: hl.or_missing(
+                    ht[sample_type.other_sample_type.passes_inheritance_field][other_sample_type_family_idx][sample_idx],
+                    sample['sampleId'],
+                )
+            ).filter(hl.is_defined),
         )
 
     def _get_sample_genotype(self, samples, r=None, include_genotype_overrides=False, select_fields=None, **kwargs):

hail_search/test_search.py

@@ -13,7 +13,10 @@
     FAMILY_2_MITO_SAMPLE_DATA, FAMILY_2_ALL_SAMPLE_DATA, MITO_VARIANT1, MITO_VARIANT2, MITO_VARIANT3, \
     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
+    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, \
+    VARIANT1_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, \
+    VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY
 from hail_search.web_app import init_web_app, sync_to_async_hail_query
 from hail_search.queries.base import BaseHailTableQuery
 
@@ -365,34 +368,31 @@ async def test_both_sample_types_search(self):
             MULTI_PROJECT_BOTH_SAMPLE_TYPE_VARIANTS, gene_counts=GENE_COUNTS, sample_data=MULTI_PROJECT_SAMPLE_TYPES_SAMPLE_DATA,
         )
 
-        # Variant1 in family_2 is de novo in exome but maternally inherited in genome.
-        # Genome passes quality and inheritance, show genotypes for both sample types.
-        variant1_interval = ['1', 10438, 10440]
+        # 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.
         inheritance_mode = 'recessive'
         await self._assert_expected_search(
-            [VARIANT1_BOTH_SAMPLE_TYPES], sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA, inheritance_mode=inheritance_mode,
-            **COMP_HET_ALL_PASS_FILTERS, intervals=[variant1_interval]
+            [VARIANT1_BOTH_SAMPLE_TYPES, VARIANT2_BOTH_SAMPLE_TYPES, [VARIANT3_BOTH_SAMPLE_TYPES, VARIANT4_BOTH_SAMPLE_TYPES]],
+            sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA, inheritance_mode=inheritance_mode,
+            **COMP_HET_ALL_PASS_FILTERS
         )
-        # Exome passes quality and inheritance, show genotypes for both sample types.
-        inheritance_mode = 'de_novo'
         await self._assert_expected_search(
-            [VARIANT1_BOTH_SAMPLE_TYPES], sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA, inheritance_mode=inheritance_mode,
-            intervals=[variant1_interval]
+            [VARIANT1_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, VARIANT2_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY,
+             [VARIANT3_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY]],
+            sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA_MISSING_PARENTAL_WGS, inheritance_mode=inheritance_mode,
+            **COMP_HET_ALL_PASS_FILTERS
         )
 
-        # Variant 2 in family_2 is inherited in exome and there is no parental data in genome.
-        # Genome and exome pass quality and inheritance, show genotypes for both sample types.
-        variant2_interval = ['1', 38724418, 38724420]
-        inheritance_mode = 'recessive'
+        inheritance_mode = 'de_novo'
         await self._assert_expected_search(
-            [VARIANT2_BOTH_SAMPLE_TYPES], sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA_MISSING_PARENTAL_WGS,
-            inheritance_mode=inheritance_mode, **COMP_HET_ALL_PASS_FILTERS, intervals=[variant2_interval]
+            [VARIANT1_BOTH_SAMPLE_TYPES, VARIANT2_BOTH_SAMPLE_TYPES, VARIANT4_BOTH_SAMPLE_TYPES],
+            sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA, inheritance_mode=inheritance_mode,
         )
-        # Genome passes quality and inheritance exome fails inheritance (parental data shows variant is inherited).
-        inheritance_mode = 'de_novo'
+        # Variant 2 fails inheritance when parental data is missing in genome
         await self._assert_expected_search(
-            [VARIANT2_BOTH_SAMPLE_TYPES], sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA_MISSING_PARENTAL_WGS,
-            inheritance_mode=inheritance_mode, intervals=[variant2_interval]
+            [VARIANT1_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY, VARIANT4_BOTH_SAMPLE_TYPES_PROBAND_WGS_ONLY],
+            sample_data=FAMILY_2_BOTH_SAMPLE_TYPE_SAMPLE_DATA_MISSING_PARENTAL_WGS, inheritance_mode=inheritance_mode,
         )
 
     async def test_inheritance_filter(self):