jpayne@68: import sys
jpayne@68: from typing import Optional, List, Any
jpayne@68: 
jpayne@68: if sys.version_info < (3, 8):
jpayne@68:     from typing_extensions import Literal
jpayne@68: else:
jpayne@68:     from typing import Literal
jpayne@68: 
jpayne@68: from pysam.libchtslib import HTSFile
jpayne@68: 
jpayne@68: _ParseResult = Any
jpayne@68: 
jpayne@68: class Parser:
jpayne@68:     def __init__(self, encoding: str = ...) -> None: ...
jpayne@68:     def get_encoding(self) -> str: ...
jpayne@68:     def set_encoding(self, encoding: str) -> None: ...
jpayne@68:     def __call__(self, buffer: str, length: int) -> _ParseResult: ...
jpayne@68: 
jpayne@68: class asTuple(Parser): ...
jpayne@68: class asGFF3(Parser): ...
jpayne@68: class asGTF(Parser): ...
jpayne@68: class asBed(Parser): ...
jpayne@68: class asVCF(Parser): ...
jpayne@68: 
jpayne@68: class TabixFile(HTSFile):
jpayne@68:     filename_index: bytes = ...
jpayne@68:     @property
jpayne@68:     def header(self) -> List[str]: ...
jpayne@68:     @property
jpayne@68:     def contigs(self) -> List[str]: ...
jpayne@68:     def __init__(
jpayne@68:         self,
jpayne@68:         filename: str,
jpayne@68:         mode: str = ...,
jpayne@68:         parser: Parser = ...,
jpayne@68:         index: Optional[str] = ...,
jpayne@68:         encoding: str = ...,
jpayne@68:         threads: int = ...,
jpayne@68:         *args,
jpayne@68:         **kwargs
jpayne@68:     ) -> None: ...
jpayne@68:     def fetch(
jpayne@68:         self,
jpayne@68:         reference: Optional[str] = ...,
jpayne@68:         start: Optional[int] = ...,
jpayne@68:         end: Optional[int] = ...,
jpayne@68:         region: Optional[str] = ...,
jpayne@68:         parser: Optional[Parser] = ...,
jpayne@68:         multiple_iterators: bool = ...,
jpayne@68:     ) -> Any: ...
jpayne@68:     def close(self) -> None: ...
jpayne@68: 
jpayne@68: class TabixIterator:
jpayne@68:     def __init__(self, encoding: str = ...) -> None: ...
jpayne@68:     def __iter__(self) -> TabixIterator: ...
jpayne@68:     def __next__(self) -> str: ...
jpayne@68: 
jpayne@68: class EmptyIterator:
jpayne@68:     def __iter__(self) -> Any: ...
jpayne@68:     def __next__(self) -> Any: ...
jpayne@68: 
jpayne@68: class TabixIteratorParsed(TabixIterator):
jpayne@68:     def __init__(self, parser: Parser) -> None: ...
jpayne@68:     def __next__(self) -> Any: ...
jpayne@68: 
jpayne@68: class GZIterator:
jpayne@68:     def __init__(
jpayne@68:         self, filename: str, bufer_size: int = ..., encoding: str = ...
jpayne@68:     ) -> None: ...
jpayne@68:     def __iter__(self) -> GZIterator: ...
jpayne@68:     def __next__(self) -> str: ...
jpayne@68: 
jpayne@68: class GZIteratorHead(GZIterator): ...
jpayne@68: 
jpayne@68: class GZIteratorParsed(GZIterator):
jpayne@68:     def __init__(self, parser: Parser) -> None: ...
jpayne@68:     def __next__(self) -> _ParseResult: ...
jpayne@68: 
jpayne@68: def tabix_compress(filename_in: str, filename_out: str, force: bool = ...) -> None: ...
jpayne@68: def tabix_index(
jpayne@68:     filename: str,
jpayne@68:     force: bool = ...,
jpayne@68:     seq_col: Optional[int] = ...,
jpayne@68:     start_col: Optional[int] = ...,
jpayne@68:     end_col: Optional[int] = ...,
jpayne@68:     preset: Optional[Literal["gff", "bed", "sam", "vcf", "psltbl", "pileup"]] = ...,
jpayne@68:     meta_char: str = ...,
jpayne@68:     line_skip: int = ...,
jpayne@68:     zerobased: bool = ...,
jpayne@68:     min_shift: int = ...,
jpayne@68:     index: Optional[str] = ...,
jpayne@68:     keep_original: bool = ...,
jpayne@68:     csi: bool = ...,
jpayne@68: ) -> str: ...
jpayne@68: 
jpayne@68: class tabix_file_iterator:
jpayne@68:     def __init__(self, infile: str, parser: Parser, buffer_size: int = ...) -> None: ...
jpayne@68:     def __iter__(self) -> tabix_file_iterator: ...
jpayne@68:     def __next__(self) -> _ParseResult: ...
jpayne@68: 
jpayne@68: class tabix_generic_iterator:
jpayne@68:     def __init__(self, infile: str, parser: Parser) -> None: ...
jpayne@68:     def __iter__(self) -> tabix_generic_iterator: ...
jpayne@68:     def __next__(self) -> _ParseResult: ...
jpayne@68: 
jpayne@68: def tabix_iterator(infile: str, parser: Optional[Parser]) -> _ParseResult: ...
jpayne@68: 
jpayne@68: # backwards compatibility
jpayne@68: class Tabixfile(TabixFile): ...