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from typing import Optional, Literal, List, Any
from pysam.libchtslib import HTSFile
_ParseResult = Any
class Parser:
def __init__(self, encoding: str = ...) -> None: ...
def get_encoding(self) -> str: ...
def set_encoding(self, encoding: str) -> None: ...
def __call__(self, buffer: str, length: int) -> _ParseResult: ...
class asTuple(Parser): ...
class asGFF3(Parser): ...
class asGTF(Parser): ...
class asBed(Parser): ...
class asVCF(Parser): ...
class TabixFile(HTSFile):
filename_index: bytes = ...
@property
def header(self) -> List[str]: ...
@property
def contigs(self) -> List[str]: ...
def __init__(
self,
filename: str,
mode: str = ...,
parser: Parser = ...,
index: Optional[str] = ...,
encoding: str = ...,
threads: int = ...,
*args,
**kwargs
) -> None: ...
def fetch(
self,
reference: Optional[str] = ...,
start: Optional[int] = ...,
end: Optional[int] = ...,
region: Optional[str] = ...,
parser: Optional[Parser] = ...,
multiple_iterators: bool = ...,
) -> Any: ...
def close(self) -> None: ...
class TabixIterator:
def __init__(self, encoding: str = ...) -> None: ...
def __iter__(self) -> TabixIterator: ...
def __next__(self) -> str: ...
class EmptyIterator:
def __iter__(self) -> Any: ...
def __next__(self) -> Any: ...
class TabixIteratorParsed(TabixIterator):
def __init__(self, parser: Parser) -> None: ...
def __next__(self) -> Any: ...
class GZIterator:
def __init__(
self, filename: str, bufer_size: int = ..., encoding: str = ...
) -> None: ...
def __iter__(self) -> GZIterator: ...
def __next__(self) -> str: ...
class GZIteratorHead(GZIterator): ...
class GZIteratorParsed(GZIterator):
def __init__(self, parser: Parser) -> None: ...
def __next__(self) -> _ParseResult: ...
def tabix_compress(filename_in: str, filename_out: str, force: bool = ...) -> None: ...
def tabix_index(
filename: str,
force: bool = ...,
seq_col: Optional[int] = ...,
start_col: Optional[int] = ...,
end_col: Optional[int] = ...,
preset: Optional[Literal["gff", "bed", "sam", "vcf", "psltbl", "pileup"]] = ...,
meta_char: str = ...,
line_skip: int = ...,
zerobased: bool = ...,
min_shift: int = ...,
index: Optional[str] = ...,
keep_original: bool = ...,
csi: bool = ...,
) -> str: ...
class tabix_file_iterator:
def __init__(self, infile: str, parser: Parser, buffer_size: int = ...) -> None: ...
def __iter__(self) -> tabix_file_iterator: ...
def __next__(self) -> _ParseResult: ...
class tabix_generic_iterator:
def __init__(self, infile: str, parser: Parser) -> None: ...
def __iter__(self) -> tabix_generic_iterator: ...
def __next__(self) -> _ParseResult: ...
def tabix_iterator(infile: str, parser: Optional[Parser]) -> _ParseResult: ...
# backwards compatibility
class Tabixfile(TabixFile): ...
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