--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcalignmentfile.pyi	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,241 @@
+import array
+import sys
+from typing import (
+    Any,
+    Dict,
+    Type,
+    NamedTuple,
+    Tuple,
+    Optional,
+    Sequence,
+    Union,
+    Callable,
+    List,
+    Iterable,
+)
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Literal
+else:
+    from typing import Literal
+
+from pysam.libchtslib import HTSFile, _HasFileNo
+from pysam.libcalignedsegment import AlignedSegment, PileupColumn
+from pysam.libcfaidx import FastaFile
+
+class IndexStats(NamedTuple):
+    contig: str
+    mapped: int
+    unmapped: int
+    total: int
+
+VALID_HEADER_TYPES: Dict[str, Type]
+VALID_HEADERS: Tuple[str]
+KNOWN_HEADER_FIELDS: Dict[str, Dict[str, Type]]
+VALID_HEADER_ORDER: Dict[str, Tuple[str]]
+
+def build_header_line(fields: Dict[str, str], record: str) -> str: ...
+
+class AlignmentHeader:
+    def __init__(self) -> None: ...
+    @classmethod
+    def _from_text_and_lengths(
+        cls,
+        text: Optional[str],
+        reference_names: Optional[Sequence[str]],
+        reference_lengths: Optional[Sequence[int]],
+    ) -> AlignmentHeader: ...
+    @classmethod
+    def from_text(cls, text: str) -> AlignmentHeader: ...
+    @classmethod
+    def from_dict(cls, header_dict: Dict) -> AlignmentHeader: ...
+    @classmethod
+    def from_references(
+        cls,
+        reference_names: Sequence[str],
+        reference_lengths: Sequence[int],
+        text: Optional[str] = ...,
+        add_sq_text: bool = ...,
+    ) -> AlignmentHeader: ...
+    def __bool__(self) -> bool: ...
+    def copy(self) -> AlignmentHeader: ...
+    @property
+    def nreferences(self) -> int: ...
+    @property
+    def references(self) -> Tuple[str]: ...
+    @property
+    def lengths(self) -> Tuple[int]: ...
+    def to_dict(self) -> Dict: ...
+    def get_reference_name(self, tid: int) -> Optional[str]: ...
+    def get_reference_length(self, reference: str) -> int: ...
+    def is_valid_tid(self, tid: int) -> bool: ...
+    def get_tid(self, reference: str) -> int: ...
+
+# The iterator produced by AlignmentFile is currently itself, but this may
+# change in future and code should not make assumptions about this type.
+AlignmentFileIterator = AlignmentFile
+
+class AlignmentFile(HTSFile):
+    def __init__(
+        self,
+        filename: Union[str, bytes, int, _HasFileNo],
+        mode: Optional[
+            Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0", "rc", "wc"]
+        ] = ...,
+        template: Optional[AlignmentFile] = ...,
+        reference_names: Optional[Sequence[str]] = ...,
+        reference_lengths: Optional[Sequence[int]] = ...,
+        reference_filename: Optional[str] = ...,
+        text: Optional[str] = ...,
+        header: Union[None, Dict, AlignmentHeader] = ...,
+        add_sq_text: bool = ...,
+        add_sam_header: bool = ...,
+        check_sq: bool = ...,
+        index_filename: Optional[str] = ...,
+        filepath_index: Optional[str] = ...,
+        require_index: bool = ...,
+        duplicate_filehandle: bool = ...,
+        ignore_truncation: bool = ...,
+        format_options: Optional[Sequence[str]] = ...,
+        threads: int = ...,
+    ) -> None: ...
+    def has_index(self) -> bool: ...
+    def check_index(self) -> bool: ...
+    def fetch(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        tid: Optional[int] = ...,
+        until_eof: bool = ...,
+        multiple_iterators: bool = ...,
+        reference: Optional[str] = ...,
+        end: int = ...,
+    ) -> IteratorRow: ...
+    def head(self, n: int, multiple_iterators: bool = ...) -> IteratorRow: ...
+    def mate(self, read: AlignedSegment) -> AlignedSegment: ...
+    def pileup(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+        truncate: bool = ...,
+        max_depth: int = ...,
+        stepper: str = ...,
+        fastafile: Optional[FastaFile] = ...,
+        ignore_overlaps: bool = ...,
+        flag_filter: int = ...,
+        flag_require: int = ...,
+        ignore_orphans: bool = ...,
+        min_base_quality: int = ...,
+        adjust_capq_threshold: int = ...,
+        min_mapping_quality: int = ...,
+        compute_baq: bool = ...,
+        redo_baq: bool = ...,
+    ) -> IteratorColumn: ...
+    def count(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        until_eof: bool = ...,
+        read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+    ) -> int: ...
+    def count_coverage(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        quality_threshold: int = ...,
+        read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+    ) -> Tuple[array.array, array.array, array.array, array.array]: ...
+    def find_introns_slow(
+        self, read_iterator: Iterable[AlignedSegment]
+    ) -> Dict[Tuple[int, int], int]: ...
+    def find_introns(
+        self, read_iterator: Iterable[AlignedSegment]
+    ) -> Dict[Tuple[int, int], int]: ...
+    def close(self) -> None: ...
+    def write(self, read: AlignedSegment) -> int: ...
+    def __enter__(self) -> AlignmentFile: ...
+    def __exit__(self, exc_type, exc_value, traceback): ...
+    @property
+    def mapped(self) -> int: ...
+    @property
+    def unmapped(self) -> int: ...
+    @property
+    def nocoordinate(self) -> int: ...
+    def get_index_statistics(self) -> List[IndexStats]: ...
+    def __iter__(self) -> AlignmentFileIterator: ...
+    def __next__(self) -> AlignedSegment: ...
+    def is_valid_tid(self, tid: int) -> bool: ...
+    def get_tid(self, reference: str) -> int: ...
+    def get_reference_name(self, tid: int) -> str: ...
+    def get_reference_length(self, reference: str) -> int: ...
+    @property
+    def nreferences(self) -> int: ...
+    @property
+    def references(self) -> Tuple[str, ...]: ...
+    @property
+    def lengths(self) -> Tuple[int, ...]: ...
+    @property
+    def reference_filename(self) -> Optional[str]: ...
+    @property
+    def header(self) -> AlignmentHeader: ...
+
+class IteratorRow:
+    def __iter__(self) -> IteratorRow: ...
+    def __next__(self) -> AlignedSegment: ...
+
+class IteratorRowAll(IteratorRow): ...
+class IteratorRowAllRefs(IteratorRow): ...
+class IteratorRowHead(IteratorRow): ...
+class IteratorRowRegion(IteratorRow): ...
+class IteratorRowSelection(IteratorRow): ...
+
+class IteratorColumn:
+    def __iter__(self) -> IteratorColumn: ...
+    def __next__(self) -> PileupColumn: ...
+    @property
+    def seq_len(self) -> int: ...
+    def add_reference(self, fastafile: FastaFile) -> None: ...
+    def has_reference(self) -> bool: ...
+
+class IteratorColumnAll(IteratorColumn): ...
+class IteratorColumnAllRefs(IteratorColumn): ...
+class IteratorColumnRegion(IteratorColumn): ...
+
+class SNPCall:
+    @property
+    def tid(self) -> int: ...
+    @property
+    def pos(self) -> int: ...
+    @property
+    def reference_base(self) -> str: ...
+    @property
+    def genotype(self) -> str: ...
+    @property
+    def consensus_quality(self) -> int: ...
+    @property
+    def snp_quality(self) -> int: ...
+    @property
+    def mapping_quality(self) -> int: ...
+    @property
+    def coverage(self) -> int: ...
+
+class IndexedReads:
+    def __init__(
+        self, samfile: AlignmentFile, multiple_iterators: bool = ...
+    ) -> None: ...
+    def build(self) -> None: ...
+    def find(self, query_name: str) -> IteratorRow: ...