Fix/contig variants check if ins

neat/variants/contig_variants.py

@@ -49,7 +49,7 @@ def check_if_del(self, other):
 
     def check_if_ins(self, other):
         for insert in self.all_ins:
-            if np.array_equal(other.genotype, insert.genotype) and insert.contains(other):
+            if np.array_equal(other.genotype, insert.genotype) and insert.contains(other.position1):
                 return insert
         return None
 

tests/test_variants/test_check_if_ins.py

@@ -0,0 +1,72 @@
+"""
+Regression test for fix/contig-variants-check-if-ins.
+
+check_if_ins was passing the variant object to Insertion.contains() which
+expects an int (a position). This caused the method to always return None
+even when a variant's position falls within an insertion's span.
+"""
+import numpy as np
+
+from neat.variants.contig_variants import ContigVariants
+from neat.variants import Insertion, SingleNucleotideVariant
+
+
+_GT = np.array([0, 1])
+
+
+def _ins(pos, alt="ACGTT", length=4, gt=None):
+    return Insertion(pos, length, alt, gt if gt is not None else _GT.copy(), "42")
+
+
+def _snv(pos, alt="T", gt=None):
+    return SingleNucleotideVariant(pos, alt, gt if gt is not None else _GT.copy(), "42")
+
+
+def test_check_if_ins_finds_containing_insertion():
+    """SNV inside insertion span is detected."""
+    cv = ContigVariants()
+    ins = _ins(10, "ACGTT", 4)
+    cv.add_variant(ins)
+    snv = _snv(11)  # position1=11 is within [10, 14)
+    result = cv.check_if_ins(snv)
+    assert result is ins
+
+
+def test_check_if_ins_at_insertion_start():
+    """SNV at the insertion's own position is detected."""
+    cv = ContigVariants()
+    ins = _ins(10, "ACGTT", 4)
+    cv.add_variant(ins)
+    snv = _snv(10)
+    assert cv.check_if_ins(snv) is ins
+
+
+def test_check_if_ins_at_insertion_end_exclusive():
+    """Position at insertion start + length is outside the span."""
+    cv = ContigVariants()
+    ins = _ins(10, "ACGTT", 4)  # spans [10, 14)
+    cv.add_variant(ins)
+    snv = _snv(14)
+    assert cv.check_if_ins(snv) is None
+
+
+def test_check_if_ins_outside_span_returns_none():
+    cv = ContigVariants()
+    ins = _ins(10, "ACGTT", 4)
+    cv.add_variant(ins)
+    snv = _snv(50)
+    assert cv.check_if_ins(snv) is None
+
+
+def test_check_if_ins_empty_returns_none():
+    cv = ContigVariants()
+    assert cv.check_if_ins(_snv(10)) is None
+
+
+def test_check_if_ins_genotype_mismatch_returns_none():
+    """Even if position matches, different genotype means no match."""
+    cv = ContigVariants()
+    ins = _ins(10, "ACGTT", 4, gt=np.array([1, 0]))
+    cv.add_variant(ins)
+    snv = _snv(11, gt=np.array([0, 1]))  # different genotype
+    assert cv.check_if_ins(snv) is None