--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcalignedsegment.pxd	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,103 @@
+# cython: language_level=3
+from pysam.libchtslib cimport *
+
+cdef extern from "htslib_util.h":
+
+    # add *nbytes* into the variable length data of *src* at *pos*
+    bam1_t * pysam_bam_update(bam1_t * b,
+           	         size_t nbytes_old,
+                         size_t nbytes_new,
+                         uint8_t * pos)
+
+    # now: static
+    int aux_type2size(int)
+
+    char * pysam_bam_get_qname(bam1_t * b)
+    uint32_t * pysam_bam_get_cigar(bam1_t * b)
+    uint8_t * pysam_bam_get_seq(bam1_t * b)
+    uint8_t * pysam_bam_get_qual(bam1_t * b)
+    uint8_t * pysam_bam_get_aux(bam1_t * b)
+    int pysam_bam_get_l_aux(bam1_t * b)
+    char pysam_bam_seqi(uint8_t * s, int i)
+
+    uint8_t pysam_get_qual(bam1_t * b)
+    uint32_t pysam_get_n_cigar(bam1_t * b)
+    void pysam_set_qual(bam1_t * b, uint8_t v)
+    void pysam_set_n_cigar(bam1_t * b, uint32_t v)
+    void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
+
+
+from pysam.libcalignmentfile cimport AlignmentFile, AlignmentHeader
+ctypedef AlignmentFile AlignmentFile_t
+
+
+# Note: need to declare all C fields and methods here
+cdef class AlignedSegment:
+
+    # object that this AlignedSegment represents
+    cdef bam1_t * _delegate
+
+    # the header that a read is associated with
+    cdef readonly AlignmentHeader header
+
+    # caching of array properties for quick access
+    cdef object cache_query_qualities
+    cdef object cache_query_alignment_qualities
+    cdef object cache_query_sequence
+    cdef object cache_query_alignment_sequence
+
+    # add an alignment tag with value to the AlignedSegment
+    # an existing tag of the same name will be replaced.
+    cpdef set_tag(self, tag, value, value_type=?, replace=?)
+
+    # get an alignment tag from the AlignedSegment
+    cpdef get_tag(self, tag, with_value_type=?)
+
+    # return true if tag exists
+    cpdef has_tag(self, tag)
+
+    # returns a valid sam alignment string
+    cpdef to_string(self)
+
+    # returns a valid sam alignment string (deprecated)
+    cpdef tostring(self, htsfile=*)
+
+
+cdef class PileupColumn:
+    cdef const bam_pileup1_t ** plp
+    cdef int tid
+    cdef int pos
+    cdef int n_pu
+    cdef AlignmentHeader header
+    cdef uint32_t min_base_quality
+    cdef kstring_t buf
+    cdef char * reference_sequence
+
+cdef class PileupRead:
+    cdef int32_t  _qpos
+    cdef AlignedSegment _alignment
+    cdef int _indel
+    cdef int _level
+    cdef uint32_t _is_del
+    cdef uint32_t _is_head
+    cdef uint32_t _is_tail
+    cdef uint32_t _is_refskip
+
+# factory methods
+cdef AlignedSegment makeAlignedSegment(
+    bam1_t * src,
+    AlignmentHeader header)
+
+cdef PileupColumn makePileupColumn(
+    const bam_pileup1_t ** plp,
+    int tid,
+    int pos,
+    int n_pu,
+    uint32_t min_base_quality,
+    char * reference_sequence,
+    AlignmentHeader header)
+
+cdef PileupRead makePileupRead(const bam_pileup1_t * src,
+		               AlignmentHeader header)
+
+cdef uint32_t get_alignment_length(bam1_t * src)