From 570e55527886631eaee22b05dc0667e7b4f06319 Mon Sep 17 00:00:00 2001
From: Joshua Allen <jallen17@illinois.edu>
Date: Sat, 4 Apr 2026 23:21:48 -0500
Subject: [PATCH] Fix check_if_ins to pass position1 int to
 Insertion.contains()

Insertion.contains() expects an int (a reference position), but
check_if_ins was passing the full variant object. This caused the method
to always return None, silently failing to detect variants overlapping
an insertion span.

Adds regression tests in tests/test_variants/test_check_if_ins.py.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 neat/variants/contig_variants.py         |  2 +-
 tests/test_variants/test_check_if_ins.py | 72 ++++++++++++++++++++++++
 2 files changed, 73 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_variants/test_check_if_ins.py

diff --git a/neat/variants/contig_variants.py b/neat/variants/contig_variants.py
index 8a177241..b83a625f 100644
--- a/neat/variants/contig_variants.py
+++ b/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
 
diff --git a/tests/test_variants/test_check_if_ins.py b/tests/test_variants/test_check_if_ins.py
new file mode 100644
index 00000000..e6718885
--- /dev/null
+++ b/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