Skip to content

Fix type hints for get_aligned_pairs #1371

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gshiba wants to merge 3 commits into
base: master
Choose a base branch
from
+8 −8
Open

Fix type hints for get_aligned_pairs #1371

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
eb5f7c2
fix
gshiba Dec 17, 2025
b1fb4cf
trigger ci
gshiba Dec 18, 2025
dc5561e
Merge remote-tracking branch 'upstream/master' into get-ap
gshiba Dec 18, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 8 additions & 8 deletions pysam/libcalignedsegment.pyi
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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]: ...
Expand Down
Loading