--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libctabix.pyi	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,109 @@
+import sys
+from typing import Optional, List, Any
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Literal
+else:
+    from typing import Literal
+
+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): ...