From ed247db9c92bcc8414316ee647911e00ff7d9a4e Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Wed, 18 Sep 2024 21:05:34 -0400 Subject: [PATCH] - ruff --- fgpyo/sam/__init__.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py index cc6d7ee8..f847aac0 100644 --- a/fgpyo/sam/__init__.py +++ b/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