From eb5f7c2ea2340f417e109014faa3712c8cf28cda Mon Sep 17 00:00:00 2001 From: Gosuke Shibahara Date: Wed, 17 Dec 2025 21:11:49 +0000 Subject: [PATCH 1/2] fix --- pysam/libcalignedsegment.pyi | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/pysam/libcalignedsegment.pyi b/pysam/libcalignedsegment.pyi index 66da76ed5..ea41f312f 100644 --- a/pysam/libcalignedsegment.pyi +++ b/pysam/libcalignedsegment.pyi @@ -135,22 +135,22 @@ class AlignedSegment: def get_forward_qualities(self) -> Optional[array]: ... @overload - def get_aligned_pairs(self, matches_only: Literal[True], with_seq: Literal[False] = ..., with_cigar: Literal[False] = ...) -> List[Tuple[int, int]]: ... + def get_aligned_pairs(self, matches_only: Literal[True] = ..., with_seq: Literal[False] = ..., with_cigar: Literal[False] = ...) -> List[Tuple[int, int]]: ... @overload - def get_aligned_pairs(self, matches_only: Literal[True], with_seq: Literal[False], with_cigar: Literal[True]) -> List[Tuple[int, int, CIGAR_OPS]]: ... + def get_aligned_pairs(self, matches_only: Literal[True] = ..., with_seq: Literal[False] = ..., with_cigar: Literal[True] = ...) -> List[Tuple[int, int, CIGAR_OPS]]: ... @overload - def get_aligned_pairs(self, matches_only: Literal[True], with_seq: Literal[True], with_cigar: Literal[False] = ...) -> List[Tuple[int, int, str]]: ... + def get_aligned_pairs(self, matches_only: Literal[True] = ..., with_seq: Literal[True] = ..., with_cigar: Literal[False] = ...) -> List[Tuple[int, int, str]]: ... @overload - def get_aligned_pairs(self, matches_only: Literal[True], with_seq: Literal[True], with_cigar: Literal[True]) -> List[Tuple[int, int, str, CIGAR_OPS]]: ... + def get_aligned_pairs(self, matches_only: Literal[True] = ..., with_seq: Literal[True] = ..., with_cigar: Literal[True] = ...) -> List[Tuple[int, int, str, CIGAR_OPS]]: ... @overload - def get_aligned_pairs(self, matches_only: bool = ..., with_seq: Literal[False] = ..., with_cigar: Literal[False] = ...) -> List[Tuple[Optional[int], Optional[int]]]: ... + def get_aligned_pairs(self, matches_only: Literal[False] = ..., with_seq: Literal[False] = ..., with_cigar: Literal[False] = ...) -> List[Tuple[Optional[int], Optional[int]]]: ... @overload - def get_aligned_pairs(self, matches_only: bool, with_seq: Literal[False], with_cigar: Literal[True]) -> List[Tuple[Optional[int], Optional[int], CIGAR_OPS]]: ... + def get_aligned_pairs(self, matches_only: Literal[False] = ..., with_seq: Literal[False] = ..., with_cigar: Literal[True] = ...) -> List[Tuple[Optional[int], Optional[int], CIGAR_OPS]]: ... @overload - def get_aligned_pairs(self, matches_only: bool, with_seq: Literal[True], with_cigar: Literal[False] = ...) -> List[Tuple[Optional[int], Optional[int], Optional[str]]]: ... + def get_aligned_pairs(self, matches_only: Literal[False] = ..., with_seq: Literal[True] = ..., with_cigar: Literal[False] = ...) -> List[Tuple[Optional[int], Optional[int], Optional[str]]]: ... @overload - def get_aligned_pairs(self, matches_only: bool, with_seq: Literal[True], with_cigar: Literal[True]) -> List[Tuple[Optional[int], Optional[int], Optional[str], CIGAR_OPS]]: ... + def get_aligned_pairs(self, matches_only: Literal[False] = ..., with_seq: Literal[True] = ..., with_cigar: Literal[True] = ...) -> List[Tuple[Optional[int], Optional[int], Optional[str], CIGAR_OPS]]: ... @overload def get_aligned_pairs(self, matches_only: bool = ..., with_seq: bool = ..., with_cigar: bool = ...) -> List[Tuple]: ... From b1fb4cf68d1faba7e9ae9dbb67be2982585e78ad Mon Sep 17 00:00:00 2001 From: Gosuke Shibahara Date: Thu, 18 Dec 2025 17:12:30 +0000 Subject: [PATCH 2/2] trigger ci