--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/utils.py	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,126 @@
+from typing import (
+    Callable,
+    List,
+    Optional,
+    Tuple,
+    Iterable,
+    Union,
+)
+
+from pysam.libcutils import _pysam_dispatch
+
+
+class SamtoolsError(Exception):
+    '''exception raised in case of an error incurred in the samtools
+    library.'''
+
+    def __init__(self, value):
+        self.value = value
+
+    def __str__(self):
+        return repr(self.value)
+
+
+class PysamDispatcher(object):
+    '''The dispatcher emulates the samtools/bctools command line.
+
+    Captures stdout and stderr.
+
+    Raises a :class:`pysam.SamtoolsError` exception in case samtools
+    exits with an error code other than 0.
+
+    Some command line options are associated with parsers.  For
+    example, the samtools command "pileup -c" creates a tab-separated
+    table on standard output. In order to associate parsers with
+    options, an optional list of parsers can be supplied. The list
+    will be processed in order checking for the presence of each
+    option.
+
+    If no parser is given or no appropriate parser is found, the
+    stdout output of samtools/bcftools commands will be returned.
+
+    '''
+
+    dispatch = None
+    parsers = None
+    collection = None
+
+    def __init__(
+        self,
+        collection: str,
+        dispatch: str,
+        parsers: Optional[Iterable[Tuple[str, Callable[[Union[str, List[str]]], Union[str, List[str]]]]]] = None,
+    ):
+        self.collection = collection
+        self.dispatch = dispatch
+        self.parsers = parsers
+        self.stderr = []
+
+    def __call__(self, *args: str, **kwargs) -> Union[str, List[str]]:
+        '''
+        execute a samtools command.
+
+        Keyword arguments:
+        catch_stdout -- redirect stdout from the samtools command and
+            return as variable (default True)
+        save_stdout -- redirect stdout to a filename.
+        raw -- ignore any parsers associated with this samtools command.
+        split_lines -- return stdout (if catch_stdout is True and stderr
+                       as a list of strings.
+        '''
+        retval, stderr, stdout = _pysam_dispatch(
+            self.collection,
+            self.dispatch,
+            args,
+            catch_stdout=kwargs.get("catch_stdout", True),
+            save_stdout=kwargs.get("save_stdout", None))
+
+        if kwargs.get("split_lines", False):
+            stdout = stdout.splitlines()
+            if stderr:
+                stderr = stderr.splitlines()
+
+        if retval:
+            raise SamtoolsError(
+                "%s returned with error %i: "
+                "stdout=%s, stderr=%s" %
+                (self.collection,
+                 retval,
+                 stdout,
+                 stderr))
+
+        self.stderr = stderr
+
+        # call parser for stdout:
+        if not kwargs.get("raw") and stdout and self.parsers:
+            for options, parser in self.parsers:
+                for option in options:
+                    if option not in args:
+                        break
+                else:
+                    return parser(stdout)
+
+        return stdout
+
+    def get_messages(self):
+        return self.stderr
+
+    def usage(self):
+        '''return the samtools usage information for this command'''
+        retval, stderr, stdout = _pysam_dispatch(
+            self.collection,
+            self.dispatch,
+            is_usage=True,
+            catch_stdout=True)
+        # some tools write usage to stderr, such as mpileup
+        if stderr:
+            return stderr
+        else:
+            return stdout
+
+
+class unquoted_str(str):
+    '''Tag a value as an unquoted string. Meta-information in the VCF
+    header takes the form of key=value pairs. By default, pysam will
+    enclose the value in quotation marks. Tagging that value with
+    unquoted_str will prevent this quoting.'''