--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libctabix.pxd	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,128 @@
+# 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
+
+# Note: this replaces python "open"!
+cdef extern from "fcntl.h":
+    int open(char *pathname, int flags)
+
+cdef extern from "unistd.h" nogil:
+    ctypedef int ssize_t
+    ssize_t read(int fd, void *buf, size_t count)
+    int close(int fd)
+
+from pysam.libchtslib cimport hts_idx_t, hts_itr_t, htsFile, \
+    tbx_t, kstring_t, BGZF, HTSFile
+
+
+# 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 tabix_file_iterator:
+    cdef BGZF * fh
+    cdef kstream_t * kstream
+    cdef kstring_t buffer
+    cdef size_t size
+    cdef Parser parser
+    cdef int fd
+    cdef int duplicated_fd
+    cdef infile
+
+    cdef __cnext__(self)
+
+
+cdef class TabixFile(HTSFile):
+    # pointer to index structure
+    cdef tbx_t * index
+
+    cdef readonly object filename_index
+
+    cdef Parser parser
+
+    cdef encoding    
+
+
+cdef class Parser:
+    cdef encoding
+    cdef parse(self, char * buffer, int len)
+
+
+cdef class asTuple(Parser):
+    cdef parse(self, char * buffer, int len)
+
+
+cdef class asGTF(Parser):
+    pass
+
+
+cdef class asGFF3(Parser):
+    pass
+
+
+cdef class asBed(Parser):
+    pass
+
+
+cdef class asVCF(Parser):
+    pass
+
+
+cdef class TabixIterator:
+    cdef hts_itr_t * iterator
+    cdef TabixFile tabixfile
+    cdef kstring_t buffer
+    cdef encoding
+    cdef int __cnext__(self)
+
+
+cdef class TabixIteratorParsed(TabixIterator):
+    cdef Parser parser
+
+
+cdef class GZIterator:
+    cdef object _filename
+    cdef BGZF * gzipfile
+    cdef kstream_t * kstream
+    cdef kstring_t buffer
+    cdef int __cnext__(self)
+    cdef encoding
+
+
+cdef class GZIteratorHead(GZIterator):
+    pass
+
+
+cdef class GZIteratorParsed(GZIterator):
+    cdef Parser parser
+
+
+# Compatibility Layer for pysam < 0.8
+cdef class Tabixfile(TabixFile):
+    pass