--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcsamfile.pxd	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,46 @@
+# cython: language_level=3
+from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile
+
+#################################################
+# Compatibility Layer for pysam < 0.8
+
+# import all declarations from htslib
+from pysam.libchtslib cimport *
+
+cdef class AlignedRead(AlignedSegment):
+    pass
+
+cdef class Samfile(AlignmentFile):
+    pass
+
+# import the conversion functions
+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)
+
+    uint16_t pysam_get_bin(bam1_t * b)
+    uint8_t pysam_get_qual(bam1_t * b)
+    uint8_t pysam_get_l_qname(bam1_t * b)
+    uint16_t pysam_get_flag(bam1_t * b)
+    uint32_t pysam_get_n_cigar(bam1_t * b)
+    void pysam_set_bin(bam1_t * b, uint16_t v)
+    void pysam_set_qual(bam1_t * b, uint8_t v)
+    void pysam_set_l_qname(bam1_t * b, uint8_t v)
+    void pysam_set_flag(bam1_t * b, uint16_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)