Split subpaths selected by extract path range into discrete fragments.

When `domagi extract` is given a path range, it may select
discontinuous fragments of other paths. These fragments must be output
as separate paths, not erroneously merged together.

1 files changed, 21 insertions, 0 deletions

diff --git a/tests/test_domagi.py b/tests/test_domagi.py
index 8f92de6..ade24cd 100644
--- a/tests/test_domagi.py
+++ b/tests/test_domagi.py
@@ -265,6 +265,27 @@ def test_domagi_extract_path(tmp_path, request, domagi_db_name, path_range, expe
     with open(expected_output) as file:
         assert_gfa_equal(file, io.StringIO(result.stdout))
 
+@pytest.mark.parametrize("domagi_db_name, path_range, expected_output",
+                         [("domagi_db_test1",
+                           "x:10-20",
+                           Path("test-data/expected-output/test1-extract-path-no-bridge-10-20.gfa"))])
+def test_domagi_extract_path_no_bridge(tmp_path, request, domagi_db_name, path_range, expected_output):
+    domagi_db = request.getfixturevalue(domagi_db_name)
+    output_duckdb_path = tmp_path / f"{domagi_db.stem}-output.db"
+    runner = CliRunner()
+    result = runner.invoke(main, ["extract",
+                                  "--db", domagi_db,
+                                  "--path-range", path_range,
+                                  "--max-distance-subpaths", "0",
+                                  "--out", output_duckdb_path])
+    assert result.exit_code == 0
+    result = runner.invoke(main, ["view",
+                                  "--to-gfa",
+                                  "--db", output_duckdb_path])
+    assert result.exit_code == 0
+    with open(expected_output) as file:
+        assert_gfa_equal(file, io.StringIO(result.stdout))
+
 @pytest.mark.parametrize("domagi_db_name, expected_output",
                          [("domagi_db_test1",
                            Path("test-data/expected-output/test1-matrix")),