--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libchtslib.pyi	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,116 @@
+import sys
+from typing import List, Union, NoReturn, Iterable, Any, Tuple, Optional, TypeVar
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Protocol
+else:
+    from typing import Protocol
+
+class _HasFileNo(Protocol):
+    def fileno(self) -> int: ...
+
+def get_verbosity() -> int: ...
+def set_verbosity(level: int): ...
+
+THFile = TypeVar("THFile", bound="HFile")
+
+class HFile:
+    def __init__(self, name: Union[int, str], mode: str = ...) -> None: ...
+    def __enter__(self: THFile) -> THFile: ...
+    def __exit__(self, type, value, tb): ...
+    def __iter__(self) -> Any: ...
+    def __next__(self) -> str: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def mode(self) -> str: ...
+    @property
+    def name(self) -> Union[int, str]: ...
+    def close(self) -> None: ...
+    def fileno(self) -> int: ...
+    def flush(self) -> None: ...
+    def isatty(self) -> bool: ...
+    def readable(self) -> bool: ...
+    def read(self, size: int = ...) -> bytes: ...
+    def readall(self) -> bytes: ...
+    def readinto(self, buf: Any) -> bytes: ...
+    def readline(self, size: int = ...) -> bytes: ...
+    def readlines(self) -> List[bytes]: ...
+    def seek(self, offset: int, whence: int = ...) -> int: ...
+    def seekable(self) -> bool: ...
+    def tell(self) -> int: ...
+    def truncate(self, *args) -> NoReturn: ...
+    def writable(self) -> bool: ...
+    def write(self, b: bytes) -> int: ...
+    def writelines(self, lines: Iterable[bytes]) -> None: ...
+
+THTSFile = TypeVar("THTSFile", bound="HTSFile")
+
+class HTSFile:
+    def __enter__(self: THTSFile) -> THTSFile: ...
+    def __exit__(self, type, value, traceback) -> Any: ...
+    @property
+    def filename(self) -> Any: ...
+    @property
+    def mode(self) -> str: ...
+    @property
+    def threads(self) -> int: ...
+    @property
+    def index_filename(self) -> Optional[str]: ...
+    @property
+    def is_stream(self) -> bool: ...
+    @property
+    def is_remote(self) -> bool: ...
+    @property
+    def duplicate_filehandle(self) -> bool: ...
+    def close(self) -> None: ...
+    def flush(self) -> None: ...
+    def check_truncation(self, ignore_truncation: bool = ...) -> None: ...
+    @property
+    def category(self) -> str: ...
+    @property
+    def format(self) -> str: ...
+    @property
+    def version(self) -> Tuple[int, int]: ...
+    @property
+    def compression(self) -> str: ...
+    @property
+    def description(self) -> str: ...
+    @property
+    def is_open(self) -> bool: ...
+    @property
+    def is_closed(self) -> bool: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def is_write(self) -> bool: ...
+    @property
+    def is_read(self) -> bool: ...
+    @property
+    def is_sam(self) -> bool: ...
+    @property
+    def is_bam(self) -> bool: ...
+    @property
+    def is_cram(self) -> bool: ...
+    @property
+    def is_vcf(self) -> bool: ...
+    @property
+    def is_bcf(self) -> bool: ...
+    def reset(self) -> None: ...
+    def seek(self, offset: int, whence: int = ...) -> int: ...
+    def tell(self) -> int: ...
+    def add_hts_options(self, format_options: Optional[List[str]] = ...) -> None: ...
+    def parse_region(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        tid: Optional[int] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+    ) -> Tuple[int, int, int, int]: ...
+    def is_valid_tid(self, tid: int) -> bool: ...
+    def is_valid_reference_name(self, contig: str) -> bool: ...
+    def get_tid(self, contig: str) -> int: ...
+    def get_reference_name(self, tid: int) -> Optional[str]: ...