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