fix: intersect() with mismtached chrom

.github/workflows/run-tests.yaml

@@ -12,6 +12,7 @@ on:
     - "src/**"
     - "tests/**"
 
+
 jobs:
   build:
     strategy:

src/py_interval.cpp

@@ -10,9 +10,9 @@ Copyright (C) 2016-2023 Deep Genomics Inc. All Rights Reserved.
 #define GK_CHECK_REFG(a, b) \
 	GK_CHECK((a).refg == (b).refg, value, "Coordinate system mismatch, {} and {}.", (a), (b));
 
-#define GKPY_INTERVAL_BOOL_METHOD_ONEARG(pyname, method) \
-	GKPY_METHOD_BEGIN_ONEARG(pyname, method) \
-		const Py##pyname::value_t& c = Py##pyname::value(selfo); \
+#define GKPY_INTERVAL_BOOL_METHOD_ONEARG(method) \
+	GKPY_METHOD_BEGIN_ONEARG(Interval, method) \
+		const PyInterval::value_t& c = PyInterval::value(selfo); \
 		if (PyInterval::check(arg)) { const interval_t& a = PyInterval::value(arg); GK_CHECK_REFG(c, a); GKPY_RETURN_BOOL(c.method(a)); } \
 		GK_THROW(type, "argument must be an Interval, not '{}'", Py_TYPE(arg)->tp_name); \
 	GKPY_METHOD_END
@@ -270,6 +270,9 @@ GKPY_METHOD_BEGIN_ONEARG(Interval, intersect)
 	auto x = PyInterval::value(selfo);
 	if (PyInterval::check(arg)) {
 		auto y = PyInterval::value(arg);
+		if (!y.same_strand(x)) {
+			GKPY_RETURN_NONE;
+		}
 		if (((PyInterval*)selfo)->get_anchor() != invalid_pos || ((PyInterval*)arg)->get_anchor() != invalid_pos) {
 			GK_THROW(value, "anchored intersection ({}, {}) is not supported.", x, y);
 		}
@@ -285,11 +288,11 @@ GKPY_METHOD_BEGIN_ONEARG(Interval, intersect)
 	}
 	GK_THROW(type, "argument must be Interval, not '{}'", Py_TYPE(arg)->tp_name);
 GKPY_METHOD_END
-GKPY_INTERVAL_BOOL_METHOD_ONEARG(Interval, upstream_of)
-GKPY_INTERVAL_BOOL_METHOD_ONEARG(Interval, dnstream_of)
-GKPY_INTERVAL_BOOL_METHOD_ONEARG(Interval, contains)
-GKPY_INTERVAL_BOOL_METHOD_ONEARG(Interval, within)
-GKPY_INTERVAL_BOOL_METHOD_ONEARG(Interval, overlaps)
+GKPY_INTERVAL_BOOL_METHOD_ONEARG(upstream_of)
+GKPY_INTERVAL_BOOL_METHOD_ONEARG(dnstream_of)
+GKPY_INTERVAL_BOOL_METHOD_ONEARG(contains)
+GKPY_INTERVAL_BOOL_METHOD_ONEARG(within)
+GKPY_INTERVAL_BOOL_METHOD_ONEARG(overlaps)
 GKPY_INTERVAL_BOOL_METHOD_NOARG(Interval, is_pos_strand)
 GKPY_METHOD_BEGIN_ONEARG(Interval, as_positive_strand)
 	return PyInterval::create(PyInterval::value(selfo).as_pos_strand(), self->get_anchor(), self->get_anchor_offset());

tests/test_interval.py

@@ -443,13 +443,18 @@ def test_comparisons_forward(self):
 
         self.assertTrue(c.upstream_of(a))
         self.assertFalse(b.upstream_of(a))
+        self.assertTrue(a.overlaps(b))
+        self.assertFalse(a.overlaps(c))
 
         self.assertTrue(a.dnstream_of(c))
         self.assertFalse(a.dnstream_of(b))
 
         self.assertTrue(a.contains(d))
         self.assertFalse(a.contains(b))
 
+        self.assertTrue(d.within(a))
+        self.assertFalse(b.within(a))
+
         self.assertTrue(a.upstream_of(Interval.from_rna1('chr1', 21, 21, 'hg19')))
         self.assertFalse(a.upstream_of(Interval.from_rna1('chr1', 20, 20, 'hg19')))
         self.assertFalse(a.upstream_of(Interval.from_rna1('chr1', 19, 19, 'hg19')))
@@ -476,6 +481,18 @@ def test_comparisons_forward(self):
         with self.assertRaises(ValueError):
             d != e
 
+        # test incompatible strand/chromosome
+        self.assertFalse(c.upstream_of(a.as_opposite_strand()))
+        self.assertFalse(c.upstream_of(Interval('chr2', a.strand, a.start, a.end, a.refg)))
+        self.assertFalse(a.dnstream_of(c.as_opposite_strand()))
+        self.assertFalse(a.dnstream_of(Interval('chr2', c.strand, c.start, c.end, c.refg)))
+        self.assertFalse(a.contains(d.as_opposite_strand()))
+        self.assertFalse(a.contains(Interval('chr2', d.strand, d.start, d.end, d.refg)))
+        self.assertFalse(d.within(a.as_opposite_strand()))
+        self.assertFalse(d.within(Interval('chr2', a.strand, a.start, a.end, a.refg)))
+        self.assertFalse(a.overlaps(b.as_opposite_strand()))
+        self.assertFalse(a.overlaps(Interval('chr2', b.strand, b.start, b.end, b.refg)))
+
     def test_comparisons_reverse(self):
         a = Interval.from_rna1('chr1', -20, -10, 'hg19')
         b = Interval.from_rna1('chr1', -15, -5, 'hg19')
@@ -485,6 +502,7 @@ def test_comparisons_reverse(self):
         self.assertTrue(a.upstream_of(c))
         self.assertFalse(a.upstream_of(b))
         self.assertTrue(a.overlaps(b))
+        self.assertFalse(a.overlaps(c))
 
         self.assertTrue(c.dnstream_of(a))
         self.assertFalse(b.dnstream_of(a))
@@ -502,6 +520,17 @@ def test_comparisons_reverse(self):
         self.assertTrue(a.dnstream_of(Interval.from_rna1('chr1', -21, -21, 'hg19')))
         self.assertFalse(a.dnstream_of(Interval.from_rna1('chr1', -20, -20, 'hg19')))
 
+        # test incompatible strand/chromosome
+        self.assertFalse(a.upstream_of(c.as_opposite_strand()))
+        self.assertFalse(a.upstream_of(Interval('chr2', c.strand, c.start, c.end, c.refg)))
+        self.assertFalse(c.dnstream_of(a.as_opposite_strand()))
+        self.assertFalse(c.dnstream_of(Interval('chr2', a.strand, a.start, a.end, a.refg)))
+        self.assertFalse(a.contains(d.as_opposite_strand()))
+        self.assertFalse(a.contains(Interval('chr2', d.strand, d.start, d.end, d.refg)))
+        self.assertFalse(d.within(Interval('chr2', a.strand, a.start, a.end, a.refg)))
+        self.assertFalse(a.overlaps(b.as_opposite_strand()))
+        self.assertFalse(a.overlaps(Interval('chr2', b.strand, b.start, b.end, b.refg)))
+
     def test_input_validation(self):
 
         with self.assertRaises(ValueError):
@@ -693,6 +722,7 @@ def test_intersect(self):
         self.assertEqual(neg_mid.intersect(neg_inside), neg_inside)
 
         self.assertIsNone(left.intersect(Interval(left.chrom, left.strand, left.start, left.end, 'hg38.p12')))
+        self.assertIsNone(left.intersect(Interval('chr2', left.strand, left.start, left.end, left.reference_genome)))
         self.assertIsNone(neg_left.intersect(left))
 
         with self.assertRaises(ValueError):