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

* feat: improve parent/child s&r

* Update pedigree.py

Author: bpblanken

v03_pipeline/lib/misc/family_loading_failures.py

@@ -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__)
 
 
@@ -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

v03_pipeline/lib/misc/pedigree.py

@@ -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'
@@ -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: