--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcfaidx.pyi	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,82 @@
+import array
+from typing import Optional, Any, Sequence, Iterator
+
+class FastaFile:
+    def __init__(
+        self,
+        filename: str,
+        filepath_index: Optional[str] = ...,
+        filepath_index_compressed: Optional[str] = ...,
+    ) -> None: ...
+    def is_open(self) -> bool: ...
+    def __len__(self) -> int: ...
+    def close(self) -> None: ...
+    def __enter__(self) -> FastaFile: ...
+    def __exit__(self, type, value, traceback) -> Any: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def filename(self) -> str: ...
+    @property
+    def references(self) -> Sequence[str]: ...
+    @property
+    def nreferences(self) -> Optional[int]: ...
+    @property
+    def lengths(self) -> Sequence[int]: ...
+    def fetch(
+        self,
+        reference: Optional[str] = ...,
+        start: Optional[int] = ...,
+        end: Optional[int] = ...,
+        region: Optional[str] = ...,
+    ) -> str: ...
+    def get_reference_length(self, reference: str) -> int: ...
+    def __getitem__(self, reference: str) -> str: ...
+    def __contains__(self, reference: str) -> bool: ...
+
+        
+class FastqProxy:
+    @property
+    def name(self) -> str: ...
+    @property
+    def sequence(self) -> str: ...
+    @property
+    def comment(self) -> Optional[str]: ...
+    @property
+    def quality(self) -> Optional[str]: ...
+    def to_string(self) -> str: ...
+    def get_quality_array(self, offset: int = ...) -> Optional[array.array]: ...
+    
+        
+class FastxRecord:
+    comment: Optional[str] = ...
+    quality: Optional[str] = ...
+    sequence: Optional[str] = ...
+    name: Optional[str] = ...
+    def __init__(
+        self,
+        name: Optional[str] = ...,
+        comment: Optional[str] = ...,
+        sequence: Optional[str] = ...,
+        quality: Optional[str] = ...,
+    ) -> None: ...
+    def set_name(self, name: str) -> None: ...
+    def set_comment(self, comment: str) -> None: ...
+    def set_sequence(self, sequence: str, quality: Optional[str] = ...) -> None: ...
+    def get_quality_array(self, offset: int = ...) -> array.array: ...
+
+class FastxFile:
+    def __init__(self, filename: str, persist: bool = ...) -> None: ...
+    def is_open(self) -> bool: ...
+    def close(self) -> None: ...
+    def __enter__(self) -> FastxFile: ...
+    def __exit__(self, type, value, traceback) -> Any: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def filename(self) -> str: ...
+    def __iter__(self) -> Iterator[FastxRecord]: ...
+    def __next__(self) -> FastxRecord: ...
+
+# deprecated
+class FastqFile(FastxFile): ...