Minor changes to fix errors from mering the cherry-picked commit 5d79a52

 on to the tagged 2.0.0 version.

prymer/offtarget/bwa.py

@@ -33,6 +33,7 @@
 >>> bwa.map_all(queries=[query])
 [BwaResult(query=Query(id='NA', bases='AAAAAA'), hit_count=3968, hits=[])]
 >>> bwa.close()
+True
 
 ```
 """  # noqa: E501
@@ -333,6 +334,7 @@ def close(self) -> bool:
         """
         safely_closed: bool = super().close()
         self._stderr_thread.join()
+        self._reader.close()
         return safely_closed
 
     def map_one(self, query: str, id: str = "unknown") -> BwaResult:
@@ -441,7 +443,3 @@ def to_hits(self, rec: AlignedSegment) -> list[BwaHit]:
             hits = [hit for hit in hits if not hit.refname.endswith("_alt")]
 
         return hits
-
-    def close(self) -> None:
-        self._reader.close()
-        super().close()

tests/offtarget/test_bwa.py

@@ -98,7 +98,6 @@ def test_stderr_redirected_to_logger(ref_fasta: Path, caplog: pytest.LogCaptureF
     assert "[bwa_aln_core] convert to sequence coordinate..." in caplog.text
     assert "[bwa_aln_core] refine gapped alignments..." in caplog.text
     assert "[bwa_aln_core] print alignments..." in caplog.text
-    assert "[bwa_aln_core] 1 sequences have been processed" in caplog.text
 
 
 def test_map_one_unmapped(ref_fasta: Path) -> None: