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import sys
from typing import List, Union, NoReturn, Iterable, Any, Tuple, Optional, TypeVar
if sys.version_info < (3, 8):
from typing_extensions import Protocol
else:
from typing import Protocol
class _HasFileNo(Protocol):
def fileno(self) -> int: ...
def get_verbosity() -> int: ...
def set_verbosity(level: int): ...
THFile = TypeVar("THFile", bound="HFile")
class HFile:
def __init__(self, name: Union[int, str], mode: str = ...) -> None: ...
def __enter__(self: THFile) -> THFile: ...
def __exit__(self, type, value, tb): ...
def __iter__(self) -> Any: ...
def __next__(self) -> str: ...
@property
def closed(self) -> bool: ...
@property
def mode(self) -> str: ...
@property
def name(self) -> Union[int, str]: ...
def close(self) -> None: ...
def fileno(self) -> int: ...
def flush(self) -> None: ...
def isatty(self) -> bool: ...
def readable(self) -> bool: ...
def read(self, size: int = ...) -> bytes: ...
def readall(self) -> bytes: ...
def readinto(self, buf: Any) -> bytes: ...
def readline(self, size: int = ...) -> bytes: ...
def readlines(self) -> List[bytes]: ...
def seek(self, offset: int, whence: int = ...) -> int: ...
def seekable(self) -> bool: ...
def tell(self) -> int: ...
def truncate(self, *args) -> NoReturn: ...
def writable(self) -> bool: ...
def write(self, b: bytes) -> int: ...
def writelines(self, lines: Iterable[bytes]) -> None: ...
THTSFile = TypeVar("THTSFile", bound="HTSFile")
class HTSFile:
def __enter__(self: THTSFile) -> THTSFile: ...
def __exit__(self, type, value, traceback) -> Any: ...
@property
def filename(self) -> Any: ...
@property
def mode(self) -> str: ...
@property
def threads(self) -> int: ...
@property
def index_filename(self) -> Optional[str]: ...
@property
def is_stream(self) -> bool: ...
@property
def is_remote(self) -> bool: ...
@property
def duplicate_filehandle(self) -> bool: ...
def close(self) -> None: ...
def check_truncation(self, ignore_truncation: bool = ...) -> None: ...
@property
def category(self) -> str: ...
@property
def format(self) -> str: ...
@property
def version(self) -> Tuple[int, int]: ...
@property
def compression(self) -> str: ...
@property
def description(self) -> str: ...
@property
def is_open(self) -> bool: ...
@property
def is_closed(self) -> bool: ...
@property
def closed(self) -> bool: ...
@property
def is_write(self) -> bool: ...
@property
def is_read(self) -> bool: ...
@property
def is_sam(self) -> bool: ...
@property
def is_bam(self) -> bool: ...
@property
def is_cram(self) -> bool: ...
@property
def is_vcf(self) -> bool: ...
@property
def is_bcf(self) -> bool: ...
def reset(self) -> None: ...
def seek(self, offset: int, whence: int = ...) -> int: ...
def tell(self) -> int: ...
def add_hts_options(self, format_options: Optional[List[str]] = ...) -> None: ...
def parse_region(
self,
contig: Optional[str] = ...,
start: Optional[int] = ...,
stop: Optional[int] = ...,
region: Optional[str] = ...,
tid: Optional[int] = ...,
reference: Optional[str] = ...,
end: Optional[int] = ...,
) -> Tuple[int, int, int, int]: ...
def is_valid_tid(self, tid: int) -> bool: ...
def is_valid_reference_name(self, contig: str) -> bool: ...
def get_tid(self, contig: str) -> int: ...
def get_reference_name(self, tid: int) -> Optional[str]: ...
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