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feat: increase relatedness tolerance for parent/child relationships #1067

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Merged
merged 2 commits into from
Apr 15, 2025
Merged

feat: increase relatedness tolerance for parent/child relationships #1067

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d739ba3
feat: improve parent/child s&r
bpblanken Apr 2, 2025
f774f48
Update pedigree.py
bpblanken Apr 2, 2025
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9 changes: 1 addition & 8 deletions v03_pipeline/lib/misc/family_loading_failures.py
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Original file line number Diff line number Diff line change
@@ -1,14 +1,11 @@
from collections import defaultdict

import hail as hl
import numpy as np

from v03_pipeline.lib.logger import get_logger
from v03_pipeline.lib.misc.pedigree import Family, Relation, Sample
from v03_pipeline.lib.model import Sex

RELATEDNESS_TOLERANCE = 0.2

logger = get_logger(__name__)


Expand All @@ -26,11 +23,7 @@ def passes_relatedness_check(
(min(sample_id, other_id), max(sample_id, other_id)),
)
if not coefficients or not any(
np.allclose(
coefficients,
relation.coefficients,
atol=RELATEDNESS_TOLERANCE,
)
relation.coefficients_equal(coefficients)
for relation in (
[expected_relation, additional_allowed_relation]
if additional_allowed_relation
Expand Down
17 changes: 17 additions & 0 deletions v03_pipeline/lib/misc/pedigree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,13 @@
from enum import Enum

import hail as hl
import numpy as np

from v03_pipeline.lib.model import Sex

DEFAULT_RELATEDNESS_TOLERANCE = 0.2
PARENT_CHILD_RELATEDNESS_TOLERANCE = 0.4


class Relation(Enum):
PARENT_CHILD = 'parent_child'
Expand All @@ -24,6 +28,19 @@ def coefficients(self):
Relation.AUNT_NEPHEW: [0.5, 0.5, 0, 0.25],
}[self]

def coefficients_equal(self, coefficients: list[float]) -> bool:
if self == Relation.PARENT_CHILD:
return (coefficients[0] == self.coefficients[0]) and np.allclose(
coefficients[1:],
self.coefficients[1:],
atol=DEFAULT_RELATEDNESS_TOLERANCE,
)
return np.allclose(
coefficients,
self.coefficients,
atol=DEFAULT_RELATEDNESS_TOLERANCE,
)


@dataclass
class Sample:
Expand Down