test regions simulated; closes #1577

tests/test_genomes.py

@@ -215,6 +215,36 @@ def test_chromosome_segment(self):
             assert contig.origin == f"{chromosome}:{left}-{right}"
             assert contig.length == length
 
+    def test_not_simulated_outside_region(self):
+        # test that when left, right are specified
+        # we legit don't simulate anything outside that region
+        species = stdpopsim.get_species("AraTha")
+        model = stdpopsim.PiecewiseConstantSize(100)
+        samples = {"pop_0": 50}
+
+        left, right = 100000, 900000
+        contig = species.get_contig("1", left=left, right=right)
+
+        engine = stdpopsim.get_engine("msprime")
+        ts = engine.simulate(
+            model,
+            contig,
+            samples,
+            seed=236,
+        )
+
+        assert ts.sequence_length > right
+        assert ts.num_sites > 0
+        assert left in ts.breakpoints()
+        assert right in ts.breakpoints()
+        assert left <= min(ts.sites_position)
+        assert max(ts.sites_position) < right
+        assert ts.num_trees > 2
+        for t in ts.trees(root_threshold=2):
+            tl, tr = t.interval
+            if tl > right or tr < left:
+                assert t.num_roots == 0
+
     def test_chromosome_segment_with_genetic_map(self):
         chr_id = "chr2"
         left = 1000001

tests/test_slim_engine.py

@@ -1175,6 +1175,41 @@ def test_off_by_one(self):
         self.verify_recombination_map(contig, ts)
         assert list(ts.breakpoints()) == [0.0, midpoint, contig.length]
 
+    def test_not_simulated_outside_region(self):
+        # test that when left, right are specified
+        # we legit don't simulate anything outside that region
+        species = stdpopsim.get_species("AraTha")
+        model = stdpopsim.PiecewiseConstantSize(100)
+        samples = {"pop_0": 50}
+
+        left, right = 100000, 900000
+        contig = species.get_contig("1", left=left, right=right)
+        dfe = species.get_dfe("Gamma_H18")
+        exons = species.get_annotations("araport_11_exons")
+        exon_intervals = exons.get_chromosome_annotations("1")
+        contig.add_dfe(intervals=exon_intervals, DFE=dfe)
+
+        engine = stdpopsim.get_engine("slim")
+        ts = engine.simulate(
+            model,
+            contig,
+            samples,
+            seed=236,
+            slim_burn_in=100,
+        )
+
+        assert ts.sequence_length > right
+        assert ts.num_sites > 0
+        assert left in ts.breakpoints()
+        assert right in ts.breakpoints()
+        assert left <= min(ts.sites_position)
+        assert max(ts.sites_position) < right
+        assert ts.num_trees > 2
+        for t in ts.trees(root_threshold=2):
+            tl, tr = t.interval
+            if tl > right or tr < left:
+                assert t.num_roots == 0
+
 
 @pytest.mark.skipif(IS_WINDOWS, reason="SLiM not available on windows")
 class TestGenomicElementTypes(PiecewiseConstantSizeMixin):