jpayne@68: import sys
jpayne@68: from typing import List, Union, NoReturn, Iterable, Any, Tuple, Optional, TypeVar
jpayne@68: 
jpayne@68: if sys.version_info < (3, 8):
jpayne@68:     from typing_extensions import Protocol
jpayne@68: else:
jpayne@68:     from typing import Protocol
jpayne@68: 
jpayne@68: class _HasFileNo(Protocol):
jpayne@68:     def fileno(self) -> int: ...
jpayne@68: 
jpayne@68: def get_verbosity() -> int: ...
jpayne@68: def set_verbosity(level: int): ...
jpayne@68: 
jpayne@68: THFile = TypeVar("THFile", bound="HFile")
jpayne@68: 
jpayne@68: class HFile:
jpayne@68:     def __init__(self, name: Union[int, str], mode: str = ...) -> None: ...
jpayne@68:     def __enter__(self: THFile) -> THFile: ...
jpayne@68:     def __exit__(self, type, value, tb): ...
jpayne@68:     def __iter__(self) -> Any: ...
jpayne@68:     def __next__(self) -> str: ...
jpayne@68:     @property
jpayne@68:     def closed(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def mode(self) -> str: ...
jpayne@68:     @property
jpayne@68:     def name(self) -> Union[int, str]: ...
jpayne@68:     def close(self) -> None: ...
jpayne@68:     def fileno(self) -> int: ...
jpayne@68:     def flush(self) -> None: ...
jpayne@68:     def isatty(self) -> bool: ...
jpayne@68:     def readable(self) -> bool: ...
jpayne@68:     def read(self, size: int = ...) -> bytes: ...
jpayne@68:     def readall(self) -> bytes: ...
jpayne@68:     def readinto(self, buf: Any) -> bytes: ...
jpayne@68:     def readline(self, size: int = ...) -> bytes: ...
jpayne@68:     def readlines(self) -> List[bytes]: ...
jpayne@68:     def seek(self, offset: int, whence: int = ...) -> int: ...
jpayne@68:     def seekable(self) -> bool: ...
jpayne@68:     def tell(self) -> int: ...
jpayne@68:     def truncate(self, *args) -> NoReturn: ...
jpayne@68:     def writable(self) -> bool: ...
jpayne@68:     def write(self, b: bytes) -> int: ...
jpayne@68:     def writelines(self, lines: Iterable[bytes]) -> None: ...
jpayne@68: 
jpayne@68: THTSFile = TypeVar("THTSFile", bound="HTSFile")
jpayne@68: 
jpayne@68: class HTSFile:
jpayne@68:     def __enter__(self: THTSFile) -> THTSFile: ...
jpayne@68:     def __exit__(self, type, value, traceback) -> Any: ...
jpayne@68:     @property
jpayne@68:     def filename(self) -> Any: ...
jpayne@68:     @property
jpayne@68:     def mode(self) -> str: ...
jpayne@68:     @property
jpayne@68:     def threads(self) -> int: ...
jpayne@68:     @property
jpayne@68:     def index_filename(self) -> Optional[str]: ...
jpayne@68:     @property
jpayne@68:     def is_stream(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_remote(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def duplicate_filehandle(self) -> bool: ...
jpayne@68:     def close(self) -> None: ...
jpayne@68:     def flush(self) -> None: ...
jpayne@68:     def check_truncation(self, ignore_truncation: bool = ...) -> None: ...
jpayne@68:     @property
jpayne@68:     def category(self) -> str: ...
jpayne@68:     @property
jpayne@68:     def format(self) -> str: ...
jpayne@68:     @property
jpayne@68:     def version(self) -> Tuple[int, int]: ...
jpayne@68:     @property
jpayne@68:     def compression(self) -> str: ...
jpayne@68:     @property
jpayne@68:     def description(self) -> str: ...
jpayne@68:     @property
jpayne@68:     def is_open(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_closed(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def closed(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_write(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_read(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_sam(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_bam(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_cram(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_vcf(self) -> bool: ...
jpayne@68:     @property
jpayne@68:     def is_bcf(self) -> bool: ...
jpayne@68:     def reset(self) -> None: ...
jpayne@68:     def seek(self, offset: int, whence: int = ...) -> int: ...
jpayne@68:     def tell(self) -> int: ...
jpayne@68:     def add_hts_options(self, format_options: Optional[List[str]] = ...) -> None: ...
jpayne@68:     def parse_region(
jpayne@68:         self,
jpayne@68:         contig: Optional[str] = ...,
jpayne@68:         start: Optional[int] = ...,
jpayne@68:         stop: Optional[int] = ...,
jpayne@68:         region: Optional[str] = ...,
jpayne@68:         tid: Optional[int] = ...,
jpayne@68:         reference: Optional[str] = ...,
jpayne@68:         end: Optional[int] = ...,
jpayne@68:     ) -> Tuple[int, int, int, int]: ...
jpayne@68:     def is_valid_tid(self, tid: int) -> bool: ...
jpayne@68:     def is_valid_reference_name(self, contig: str) -> bool: ...
jpayne@68:     def get_tid(self, contig: str) -> int: ...
jpayne@68:     def get_reference_name(self, tid: int) -> Optional[str]: ...