Update fgpyo/sam/__init__.py

Co-authored-by: Matt Stone <[email protected]>
fulcrumgenomics · Sep 19, 2024 · 3542b61 · 3542b61
1 parent e610f1e
commit 3542b61
Showing 1 changed file with 3 additions and 0 deletions.
diff --git 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