Add test for checking CigarHit.gaps() lengths

cfe-lab · Nov 14, 2023 · eb712a3 · eb712a3
1 parent 7f3cdc0
commit eb712a3
Showing 1 changed file with 12 additions and 1 deletion.
diff --git a/micall/tests/test_cigar_tools.py b/micall/tests/test_cigar_tools.py
@@ -4,7 +4,7 @@
 import itertools
 
 from micall.utils.consensus_aligner import CigarActions
-from micall.utils.cigar_tools import Cigar, CigarHit, connect_cigar_hits
+from micall.utils.cigar_tools import Cigar, CigarHit, connect_cigar_hits, CoordinateMapping
 
 
 cigar_mapping_cases = [
@@ -383,6 +383,17 @@ def test_cigar_hit_gaps_no_m_or_i(hit):
         assert 'I' not in str(gap.cigar)
 
 
+@pytest.mark.parametrize('hit', [x[0] for x in cigar_hit_ref_cut_cases
+                                 if not isinstance(x[2], Exception)])
+def test_cigar_hit_gaps_lengths(hit):
+    gaps = list(hit.gaps())
+
+    for gap in gaps:
+        assert gap.query_length == 0
+        assert gap.ref_length > 0
+        assert gap.coordinate_mapping == CoordinateMapping()
+
+
 @pytest.mark.parametrize("reference_seq, query_seq, cigar, expected_reference, expected_query", [
     ('ACTG',   'ACTG',   '4M',     'ACTG',   'ACTG'),
     ('ACTG',   '',       '4D',     'ACTG',   '----'),