docs: swap some stale secondasry -> aux references

fgpyo/sam/__init__.py

@@ -1269,7 +1269,7 @@ def many_from_primary(cls, primary: AlignedSegment) -> list[Self]:
         """
         if primary.is_secondary or primary.is_supplementary:
             raise ValueError(
-                "Cannot derive auxiliary alignments from a non-primary record!"
+                "Cannot build auxiliary alignments from a non-primary record!"
                 f" Found: {primary.query_name}"
             )
         aux_alignments: list[Self] = []
@@ -1350,7 +1350,7 @@ def many_sam_from_primary(cls, primary: AlignedSegment) -> Iterator[AlignedSegme
             aux.is_read1 = primary.is_read1
             aux.is_read2 = primary.is_read2
 
-            # Set some optional, but highly recommended, SAM tags on the secondary alignment.
+            # Set some optional, but highly recommended, SAM tags on the auxiliary alignment.
             aux.set_tag("AS", hit.alignment_score)
             aux.set_tag("NM", hit.edit_distance)
             aux.set_tag("RG", primary.get_tag("RG") if primary.has_tag("RG") else None)
@@ -1393,9 +1393,9 @@ def after_sam_from_primary(
     @classmethod
     def add_to_template(cls, template: Template) -> Template:
         """Rebuild a template by adding auxiliary alignments from the primary alignment tags."""
-        r1_secondaries = iter([]) if template.r1 is None else cls.many_sam_from_primary(template.r1)
-        r2_secondaries = iter([]) if template.r2 is None else cls.many_sam_from_primary(template.r2)
-        return Template.build(chain(template.all_recs(), r1_secondaries, r2_secondaries))
+        r1_aux = iter([]) if template.r1 is None else cls.many_sam_from_primary(template.r1)
+        r2_aux = iter([]) if template.r2 is None else cls.many_sam_from_primary(template.r2)
+        return Template.build(chain(template.all_recs(), r1_aux, r2_aux))
 
 
 @dataclass(frozen=True)