diff options
| -rw-r--r-- | domagi/domagi.py | 12 | ||||
| -rw-r--r-- | tests/test_domagi.py | 1 |
2 files changed, 10 insertions, 3 deletions
diff --git a/domagi/domagi.py b/domagi/domagi.py index 6175c08..4d9bb45 100644 --- a/domagi/domagi.py +++ b/domagi/domagi.py @@ -259,10 +259,18 @@ def extract(con, outfile, segment_name, path_range, steps, threads, progress): SELECT id, 0 FROM initial_segment UNION ALL SELECT DISTINCT to_segment, distance+1 FROM cte - INNER JOIN link ON from_segment=id + INNER JOIN ( + -- Eliminate directionality of the link table. We must traverse both + -- to segments leading out of and to segments leading into the + -- current segment. + SELECT from_segment, to_segment FROM link + UNION + SELECT to_segment AS from_segment, from_segment AS to_segment FROM link + ) + ON from_segment=id WHERE distance<? ) - SELECT id FROM cte; + SELECT DISTINCT id FROM cte; """, [steps]) con.execute(f""" diff --git a/tests/test_domagi.py b/tests/test_domagi.py index 3312247..d7190a0 100644 --- a/tests/test_domagi.py +++ b/tests/test_domagi.py @@ -206,7 +206,6 @@ def test_domagi_depth_bed_windows(tmp_path, request, domagi_db_name, bed_windows pd.read_csv(io.StringIO(result.stdout), sep="\t"), check_dtype=False) -@pytest.mark.xfail @pytest.mark.parametrize("domagi_db_name, context_steps, expected_output", [("domagi_db_test1", 1, |