--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcfaidx.pxd	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,81 @@
+# cython: language_level=3
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+from libc.stdlib cimport malloc, calloc, realloc, free
+from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
+from libc.stdio cimport FILE, printf
+cimport cython
+
+from cpython cimport array
+from pysam.libchtslib cimport faidx_t, kstring_t, BGZF
+
+# These functions are put here and not in chtslib.pxd in order
+# to avoid warnings for unused functions.
+cdef extern from "pysam_stream.h" nogil:
+
+    ctypedef struct kstream_t:
+        pass
+
+    ctypedef struct kseq_t:
+        kstring_t name
+        kstring_t comment
+        kstring_t seq
+        kstring_t qual
+
+    kseq_t *kseq_init(BGZF *)
+    int kseq_read(kseq_t *)
+    void kseq_destroy(kseq_t *)
+    kstream_t *ks_init(BGZF *)
+    void ks_destroy(kstream_t *)
+
+    # Retrieve characters from stream until delimiter
+    # is reached placing results in str.
+    int ks_getuntil(kstream_t *,
+                    int delimiter,
+                    kstring_t * str,
+                    int * dret)
+
+cdef class FastaFile:
+    cdef bint is_remote
+    cdef object _filename, _references, _lengths, reference2length
+    cdef faidx_t* fastafile
+    cdef char* _fetch(self, char* reference,
+                      int start, int end, int* length) except? NULL
+
+
+cdef class FastqProxy:
+    cdef kseq_t * _delegate
+    cdef cython.str to_string(self)
+    cdef cython.str tostring(self)
+    cpdef array.array get_quality_array(self, int offset=*)
+
+
+cdef class FastxRecord:
+    """
+    Python container for pysam.libcfaidx.FastqProxy with persistence.
+    """
+    cdef public str comment, quality, sequence, name
+    cdef cython.str to_string(self)
+    cdef cython.str tostring(self)
+    cpdef array.array get_quality_array(self, int offset=*)
+
+cdef class FastxFile:
+    cdef object _filename
+    cdef BGZF * fastqfile
+    cdef kseq_t * entry
+    cdef bint persist
+    cdef bint is_remote
+
+    cdef kseq_t * getCurrent(self)
+    cdef int cnext(self)
+
+
+# Compatibility Layer for pysam 0.8.1
+cdef class FastqFile(FastxFile):
+    pass
+
+
+# Compatibility Layer for pysam < 0.8
+cdef class Fastafile(FastaFile):
+    pass
+