--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcbcf.pxd	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,144 @@
+# cython: language_level=3
+###############################################################################
+###############################################################################
+## Cython wrapper for htslib VCF/BCF reader/writer
+###############################################################################
+#
+# The MIT License
+#
+# Copyright (c) 2015, 2016 Kevin Jacobs (jacobs@bioinformed.com)
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+
+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, memmove, strncpy, strlen, strdup
+
+from pysam.libchtslib cimport *
+
+
+cdef class VariantHeader(object):
+    cdef bcf_hdr_t *ptr
+
+    cdef _add_sample(self, name)
+    cdef _hdr_sync(self)
+    cdef _subset_samples(self, include_samples)
+
+
+cdef class VariantHeaderRecord(object):
+    cdef readonly VariantHeader header
+    cdef bcf_hrec_t *ptr
+
+
+cdef class VariantHeaderRecords(object):
+    cdef readonly VariantHeader header
+
+
+cdef class VariantHeaderContigs(object):
+    cdef readonly VariantHeader header
+
+
+cdef class VariantHeaderSamples(object):
+    cdef readonly VariantHeader header
+
+
+cdef class VariantContig(object):
+    cdef readonly VariantHeader header
+    cdef int id
+
+
+cdef class VariantMetadata(object):
+    cdef readonly VariantHeader header
+    cdef int type
+    cdef int id
+
+
+cdef class VariantHeaderMetadata(object):
+    cdef readonly VariantHeader header
+    cdef int32_t type
+
+
+cdef class VariantRecord(object):
+    cdef readonly VariantHeader header
+    cdef bcf1_t *ptr
+
+
+cdef class VariantRecordFilter(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordFormat(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordInfo(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordSamples(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordSample(object):
+    cdef VariantRecord record
+    cdef readonly int32_t index
+
+
+cdef class BaseIndex(object):
+    cdef tuple refs
+    cdef dict refmap
+
+
+cdef class BCFIndex(BaseIndex):
+    cdef readonly VariantHeader header
+    cdef hts_idx_t *ptr
+
+
+cdef class TabixIndex(BaseIndex):
+    cdef tbx_t *ptr
+
+
+cdef class BaseIterator(object):
+    cdef VariantFile bcf
+    cdef hts_itr_t  *iter
+
+
+cdef class BCFIterator(BaseIterator):
+    cdef BCFIndex index
+
+
+cdef class TabixIterator(BaseIterator):
+    cdef TabixIndex index
+    cdef kstring_t line_buffer
+
+
+cdef class VariantFile(HTSFile):
+    cdef readonly VariantHeader  header
+    cdef readonly BaseIndex      index
+
+    cdef readonly bint           drop_samples  # true if sample information is to be ignored
+
+    # FIXME: Temporary, use htsFormat when it is available
+    cdef readonly bint       is_reading     # true if file has begun reading records
+    cdef readonly bint       header_written # true if header has already been written
+
+    cpdef int write(self, VariantRecord record) except -1