jpayne@69: import sys
jpayne@69: from typing import Optional, List, Any
jpayne@69: 
jpayne@69: if sys.version_info < (3, 8):
jpayne@69:     from typing_extensions import Literal
jpayne@69: else:
jpayne@69:     from typing import Literal
jpayne@69: 
jpayne@69: from pysam.libchtslib import HTSFile
jpayne@69: 
jpayne@69: _ParseResult = Any
jpayne@69: 
jpayne@69: class Parser:
jpayne@69:     def __init__(self, encoding: str = ...) -> None: ...
jpayne@69:     def get_encoding(self) -> str: ...
jpayne@69:     def set_encoding(self, encoding: str) -> None: ...
jpayne@69:     def __call__(self, buffer: str, length: int) -> _ParseResult: ...
jpayne@69: 
jpayne@69: class asTuple(Parser): ...
jpayne@69: class asGFF3(Parser): ...
jpayne@69: class asGTF(Parser): ...
jpayne@69: class asBed(Parser): ...
jpayne@69: class asVCF(Parser): ...
jpayne@69: 
jpayne@69: class TabixFile(HTSFile):
jpayne@69:     filename_index: bytes = ...
jpayne@69:     @property
jpayne@69:     def header(self) -> List[str]: ...
jpayne@69:     @property
jpayne@69:     def contigs(self) -> List[str]: ...
jpayne@69:     def __init__(
jpayne@69:         self,
jpayne@69:         filename: str,
jpayne@69:         mode: str = ...,
jpayne@69:         parser: Parser = ...,
jpayne@69:         index: Optional[str] = ...,
jpayne@69:         encoding: str = ...,
jpayne@69:         threads: int = ...,
jpayne@69:         *args,
jpayne@69:         **kwargs
jpayne@69:     ) -> None: ...
jpayne@69:     def fetch(
jpayne@69:         self,
jpayne@69:         reference: Optional[str] = ...,
jpayne@69:         start: Optional[int] = ...,
jpayne@69:         end: Optional[int] = ...,
jpayne@69:         region: Optional[str] = ...,
jpayne@69:         parser: Optional[Parser] = ...,
jpayne@69:         multiple_iterators: bool = ...,
jpayne@69:     ) -> Any: ...
jpayne@69:     def close(self) -> None: ...
jpayne@69: 
jpayne@69: class TabixIterator:
jpayne@69:     def __init__(self, encoding: str = ...) -> None: ...
jpayne@69:     def __iter__(self) -> TabixIterator: ...
jpayne@69:     def __next__(self) -> str: ...
jpayne@69: 
jpayne@69: class EmptyIterator:
jpayne@69:     def __iter__(self) -> Any: ...
jpayne@69:     def __next__(self) -> Any: ...
jpayne@69: 
jpayne@69: class TabixIteratorParsed(TabixIterator):
jpayne@69:     def __init__(self, parser: Parser) -> None: ...
jpayne@69:     def __next__(self) -> Any: ...
jpayne@69: 
jpayne@69: class GZIterator:
jpayne@69:     def __init__(
jpayne@69:         self, filename: str, bufer_size: int = ..., encoding: str = ...
jpayne@69:     ) -> None: ...
jpayne@69:     def __iter__(self) -> GZIterator: ...
jpayne@69:     def __next__(self) -> str: ...
jpayne@69: 
jpayne@69: class GZIteratorHead(GZIterator): ...
jpayne@69: 
jpayne@69: class GZIteratorParsed(GZIterator):
jpayne@69:     def __init__(self, parser: Parser) -> None: ...
jpayne@69:     def __next__(self) -> _ParseResult: ...
jpayne@69: 
jpayne@69: def tabix_compress(filename_in: str, filename_out: str, force: bool = ...) -> None: ...
jpayne@69: def tabix_index(
jpayne@69:     filename: str,
jpayne@69:     force: bool = ...,
jpayne@69:     seq_col: Optional[int] = ...,
jpayne@69:     start_col: Optional[int] = ...,
jpayne@69:     end_col: Optional[int] = ...,
jpayne@69:     preset: Optional[Literal["gff", "bed", "sam", "vcf", "psltbl", "pileup"]] = ...,
jpayne@69:     meta_char: str = ...,
jpayne@69:     line_skip: int = ...,
jpayne@69:     zerobased: bool = ...,
jpayne@69:     min_shift: int = ...,
jpayne@69:     index: Optional[str] = ...,
jpayne@69:     keep_original: bool = ...,
jpayne@69:     csi: bool = ...,
jpayne@69: ) -> str: ...
jpayne@69: 
jpayne@69: class tabix_file_iterator:
jpayne@69:     def __init__(self, infile: str, parser: Parser, buffer_size: int = ...) -> None: ...
jpayne@69:     def __iter__(self) -> tabix_file_iterator: ...
jpayne@69:     def __next__(self) -> _ParseResult: ...
jpayne@69: 
jpayne@69: class tabix_generic_iterator:
jpayne@69:     def __init__(self, infile: str, parser: Parser) -> None: ...
jpayne@69:     def __iter__(self) -> tabix_generic_iterator: ...
jpayne@69:     def __next__(self) -> _ParseResult: ...
jpayne@69: 
jpayne@69: def tabix_iterator(infile: str, parser: Optional[Parser]) -> _ParseResult: ...
jpayne@69: 
jpayne@69: # backwards compatibility
jpayne@69: class Tabixfile(TabixFile): ...