Merge remote-tracking branch 'origin/main' into cv_fix_mates_secondar…

…y_supplementary

fgpyo/sam/__init__.py

@@ -665,7 +665,7 @@ def from_recs(  # noqa: C901  # `from_recs` is too complex (11 > 10)
 
         if rec2 is None:
             if not rec1.has_tag("MC"):
-                raise ValueError('Cannot determine proper pair status without a mate cigar ("MC")!')
+                raise ValueError('Cannot determine pair orientation without a mate cigar ("MC")!')
             rec2_cigar = Cigar.from_cigarstring(str(rec1.get_tag("MC")))
             rec2_reference_end = rec1.next_reference_start + rec2_cigar.length_on_target()
         else:
@@ -966,16 +966,16 @@ def set_mate_info_on_supplementary(supp: AlignedSegment, mate_primary: AlignedSe
 def set_pair_info(r1: AlignedSegment, r2: AlignedSegment, proper_pair: bool = True) -> None:
     """Resets mate pair information between reads in a pair.
 
-    Requires that both r1 and r2 are mapped. Can be handed reads that already have pairing flags
-    setup or independent R1 and R2 records that are currently flagged as SE reads.
+    Can be handed reads that already have pairing flags setup or independent R1 and R2 records that
+    are currently flagged as SE reads.
 
     Args:
         r1: Read 1 (first read in the template).
         r2: Read 2 with the same query name as r1 (second read in the template).
         proper_pair: whether the pair is proper or not.
     """
     if r1.query_name != r2.query_name:
-        raise ValueError("Cannot pair reads with different query names!")
+        raise ValueError("Cannot set pair info on reads with different query names!")
 
     for r in [r1, r2]:
         r.is_paired = True
@@ -984,6 +984,7 @@ def set_pair_info(r1: AlignedSegment, r2: AlignedSegment, proper_pair: bool = Tr
     r1.is_read2 = False
     r2.is_read2 = True
     r2.is_read1 = False
+
     set_mate_info(r1=r1, r2=r2, is_proper_pair=lambda a, b: proper_pair)