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Remove extra comp het filtering #4430

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merged 3 commits into from
Oct 16, 2024
Merged

Remove extra comp het filtering #4430

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b6d9f42
remove unneeded comp het filter
hanars Oct 15, 2024
5b732c7
undo failed logic negation
hanars Oct 15, 2024
4275809
Merge branch 'dev' of https://github.com/broadinstitute/seqr into com…
hanars Oct 15, 2024
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25 changes: 5 additions & 20 deletions hail_search/queries/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -624,43 +624,28 @@ def _annotate_families_inheritance(
if genotype:
entry_indices_by_gt[genotype][family_index].append(sample_index)

min_unaffected = None
if inheritance_mode == COMPOUND_HET:
family_unaffected_counts = [
len(i) for i in entry_indices_by_gt[INHERITANCE_FILTERS[COMPOUND_HET][UNAFFECTED_ID]].values()
]
self.max_unaffected_samples = max(family_unaffected_counts) if family_unaffected_counts else 0
if self.max_unaffected_samples > 1:
min_unaffected = min(family_unaffected_counts)

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 i, family_samples: self._valid_genotype_family_entries(
family_samples, entry_indices.get(i), genotype, min_unaffected
)
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

@classmethod
def _valid_genotype_family_entries(cls, entries: list, genotype_entry_indices, genotype: str, min_unaffected: int):
is_valid = hl.is_missing(genotype_entry_indices) | genotype_entry_indices.all(
lambda i: cls.GENOTYPE_QUERY_MAP[genotype](entries[i].GT)
)
if min_unaffected is not None and genotype == HAS_REF:
unaffected_filter = genotype_entry_indices.any(
lambda i: cls.GENOTYPE_QUERY_MAP[REF_REF](entries[i].GT)
)
if min_unaffected < 2:
unaffected_filter |= genotype_entry_indices.size() < 2
is_valid &= unaffected_filter
return hl.or_missing(is_valid, entries)

def _get_family_passes_quality_filter(self, quality_filter, ht, **kwargs):
quality_filter = quality_filter or {}

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