- ruff

fgpyo/sam/__init__.py

@@ -549,20 +549,20 @@ def length_on_target(self) -> int:
 
     def get_alignment_offsets(self, reverse: bool = False) -> Tuple[int, int]:
         """
-        Get the starting and ending offset for the alignment based on the CIGAR string.
+                Get the starting and ending offset for the alignment based on the CIGAR string.
 
-        Args:
-            reverse: bool Whether to count from the end of the read sequence.
-                Default is False, which counts from the beginning of the read sequence.
+                Args:
+                    reverse: Whether to count from the end of the read sequence.
+                        Default is False, which counts from the beginning of the read sequence.
 
-        Returns: Tuple[int, int] The start and end of the _aligned part_ of the read.
-            0-based, open-ended offsets (to the read sequence.)
-            If 'reverse' is True, the offsets count from the end of the read sequence.
+                Returns: Tuple[int, int] The start and end of the _aligned part_ of the read.
+                    0-based, open-ended offsets (to the read sequence.)
+                    If 'reverse' is True, the offsets count from the end of the read sequence.
 
-# TODO: FIGURE OUT WHY the following three lines causes mkdocs to fail
-# If the Cigar contains no alignment operators that consume sequence bases, or
-# only clipping operators, the start and end offsets will be the same value (indicating
-# an empty region).
+        # TODO: FIGURE OUT WHY the following three lines causes mkdocs to fail
+        # If the Cigar contains no alignment operators that consume sequence bases, or
+        # only clipping operators, the start and end offsets will be the same value (indicating
+        # an empty region).
         """
         start_offset: int = 0
         end_offset: int = 0