Update prymer/offtarget/bwa.py

Co-authored-by: Tim Fennell <[email protected]>

prymer/offtarget/bwa.py

@@ -374,14 +374,17 @@ def _to_result(self, query: Query, rec: pysam.AlignedSegment) -> BwaResult:
             )
 
         num_hits: int = int(rec.get_tag("HN")) if rec.has_tag("HN") else 0
-        hits: list[BwaHit] = self.to_hits(rec=rec) if 0 < num_hits < self.max_hits else []
-
         # `to_hits()` removes artifactual hits which span the boundary between concatenated
         # reference sequences. If we are reporting a list of hits, the number of hits should match
         # the size of this list. Otherwise, we either have zero hits, or more than the maximum
         # number of hits. In both of the latter cases, we have to rely on the count reported in the
         # `HN` tag.
-        num_hits = len(hits) if hits else num_hits
+        hits: list[BwaHit]
+        if 0 < num_hits < self.max_hits:
+            hits = self.to_hits(rec=rec)
+            num_hits = len(hits)
+        else:
+            hits = []
 
         return BwaResult(query=query, hit_count=num_hits, hits=hits)