diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py
index 78c3386..395e842 100644
--- a/fgpyo/sam/__init__.py
+++ b/fgpyo/sam/__init__.py
@@ -572,11 +572,14 @@ def get_alignment_offsets(self, reverse: bool = False) -> Tuple[int, int]:
         elements = self.elements if not reverse else reversed(self.elements)
         for cig_el in elements:
             if cig_el.operator.is_clipping and not alignment_began:
+                # We are in the clipping operators preceding the alignment
                 start_offset += cig_el.length_on_query
                 end_offset += cig_el.length_on_query
             elif cig_el.operator.is_clipping:
+                # We have exited the alignment and are in the clipping operators after the alignment
                 break
             else:
+                # We are within the alignment
                 alignment_began = True
                 end_offset += cig_el.length_on_query