Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libchtslib.pyi @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 import sys
2 from typing import List, Union, NoReturn, Iterable, Any, Tuple, Optional, TypeVar
3
4 if sys.version_info < (3, 8):
5 from typing_extensions import Protocol
6 else:
7 from typing import Protocol
8
9 class _HasFileNo(Protocol):
10 def fileno(self) -> int: ...
11
12 def get_verbosity() -> int: ...
13 def set_verbosity(level: int): ...
14
15 THFile = TypeVar("THFile", bound="HFile")
16
17 class HFile:
18 def __init__(self, name: Union[int, str], mode: str = ...) -> None: ...
19 def __enter__(self: THFile) -> THFile: ...
20 def __exit__(self, type, value, tb): ...
21 def __iter__(self) -> Any: ...
22 def __next__(self) -> str: ...
23 @property
24 def closed(self) -> bool: ...
25 @property
26 def mode(self) -> str: ...
27 @property
28 def name(self) -> Union[int, str]: ...
29 def close(self) -> None: ...
30 def fileno(self) -> int: ...
31 def flush(self) -> None: ...
32 def isatty(self) -> bool: ...
33 def readable(self) -> bool: ...
34 def read(self, size: int = ...) -> bytes: ...
35 def readall(self) -> bytes: ...
36 def readinto(self, buf: Any) -> bytes: ...
37 def readline(self, size: int = ...) -> bytes: ...
38 def readlines(self) -> List[bytes]: ...
39 def seek(self, offset: int, whence: int = ...) -> int: ...
40 def seekable(self) -> bool: ...
41 def tell(self) -> int: ...
42 def truncate(self, *args) -> NoReturn: ...
43 def writable(self) -> bool: ...
44 def write(self, b: bytes) -> int: ...
45 def writelines(self, lines: Iterable[bytes]) -> None: ...
46
47 THTSFile = TypeVar("THTSFile", bound="HTSFile")
48
49 class HTSFile:
50 def __enter__(self: THTSFile) -> THTSFile: ...
51 def __exit__(self, type, value, traceback) -> Any: ...
52 @property
53 def filename(self) -> Any: ...
54 @property
55 def mode(self) -> str: ...
56 @property
57 def threads(self) -> int: ...
58 @property
59 def index_filename(self) -> Optional[str]: ...
60 @property
61 def is_stream(self) -> bool: ...
62 @property
63 def is_remote(self) -> bool: ...
64 @property
65 def duplicate_filehandle(self) -> bool: ...
66 def close(self) -> None: ...
67 def flush(self) -> None: ...
68 def check_truncation(self, ignore_truncation: bool = ...) -> None: ...
69 @property
70 def category(self) -> str: ...
71 @property
72 def format(self) -> str: ...
73 @property
74 def version(self) -> Tuple[int, int]: ...
75 @property
76 def compression(self) -> str: ...
77 @property
78 def description(self) -> str: ...
79 @property
80 def is_open(self) -> bool: ...
81 @property
82 def is_closed(self) -> bool: ...
83 @property
84 def closed(self) -> bool: ...
85 @property
86 def is_write(self) -> bool: ...
87 @property
88 def is_read(self) -> bool: ...
89 @property
90 def is_sam(self) -> bool: ...
91 @property
92 def is_bam(self) -> bool: ...
93 @property
94 def is_cram(self) -> bool: ...
95 @property
96 def is_vcf(self) -> bool: ...
97 @property
98 def is_bcf(self) -> bool: ...
99 def reset(self) -> None: ...
100 def seek(self, offset: int, whence: int = ...) -> int: ...
101 def tell(self) -> int: ...
102 def add_hts_options(self, format_options: Optional[List[str]] = ...) -> None: ...
103 def parse_region(
104 self,
105 contig: Optional[str] = ...,
106 start: Optional[int] = ...,
107 stop: Optional[int] = ...,
108 region: Optional[str] = ...,
109 tid: Optional[int] = ...,
110 reference: Optional[str] = ...,
111 end: Optional[int] = ...,
112 ) -> Tuple[int, int, int, int]: ...
113 def is_valid_tid(self, tid: int) -> bool: ...
114 def is_valid_reference_name(self, contig: str) -> bool: ...
115 def get_tid(self, contig: str) -> int: ...
116 def get_reference_name(self, tid: int) -> Optional[str]: ...