debug

tests/test_bwapy.py

@@ -161,28 +161,28 @@ def test_bwamem(ref_fasta: Path, fastx_record: FastxRecord) -> None:
     assert rec.cigarstring == "80M"
     # TODO: test multi-mapping, reverse strand, etc
 
-
-def test_bwamem_threading(ref_fasta: Path, fastx_record: FastxRecord) -> None:
-    opt = BwaMemOptions(threads=2)
-    bwa = BwaMem(prefix=ref_fasta)
-
-    revcomp_seq = None if not fastx_record.sequence else reverse_complement(fastx_record.sequence)
-    revcomp_record = FastxRecord(name="revcomp", sequence=revcomp_seq)
-
-    queries = [fastx_record if i % 2 == 0 else revcomp_record for i in range(100)]
-    list_of_recs = bwa.align(opt=opt, queries=queries)
-    assert len(list_of_recs) == len(queries)
-    for i, recs in enumerate(list_of_recs):
-        assert len(recs) == 1
-        rec = recs[0]
-        if i % 2 == 0:
-            assert rec.query_name == "test"
-            assert rec.is_forward
-        else:
-            assert rec.query_name == "revcomp"
-            assert rec.is_reverse
-        assert not rec.is_paired
-        assert not rec.is_read1
-        assert not rec.is_read2
-        assert rec.reference_start == 80
-        assert rec.cigarstring == "80M"
+#
+# def test_bwamem_threading(ref_fasta: Path, fastx_record: FastxRecord) -> None:
+#     opt = BwaMemOptions(threads=2)
+#     bwa = BwaMem(prefix=ref_fasta)
+#
+#     revcomp_seq = None if not fastx_record.sequence else reverse_complement(fastx_record.sequence)
+#     revcomp_record = FastxRecord(name="revcomp", sequence=revcomp_seq)
+#
+#     queries = [fastx_record if i % 2 == 0 else revcomp_record for i in range(100)]
+#     list_of_recs = bwa.align(opt=opt, queries=queries)
+#     assert len(list_of_recs) == len(queries)
+#     for i, recs in enumerate(list_of_recs):
+#         assert len(recs) == 1
+#         rec = recs[0]
+#         if i % 2 == 0:
+#             assert rec.query_name == "test"
+#             assert rec.is_forward
+#         else:
+#             assert rec.query_name == "revcomp"
+#             assert rec.is_reverse
+#         assert not rec.is_paired
+#         assert not rec.is_read1
+#         assert not rec.is_read2
+#         assert rec.reference_start == 80
+#         assert rec.cigarstring == "80M"