Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcsamfile.pxd @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 # cython: language_level=3
2 from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile
3
4 #################################################
5 # Compatibility Layer for pysam < 0.8
6
7 # import all declarations from htslib
8 from pysam.libchtslib cimport *
9
10 cdef class AlignedRead(AlignedSegment):
11 pass
12
13 cdef class Samfile(AlignmentFile):
14 pass
15
16 # import the conversion functions
17 cdef extern from "htslib_util.h":
18
19 # add *nbytes* into the variable length data of *src* at *pos*
20 bam1_t * pysam_bam_update(bam1_t * b,
21 size_t nbytes_old,
22 size_t nbytes_new,
23 uint8_t * pos)
24
25 # now: static
26 int aux_type2size(int)
27
28 char * pysam_bam_get_qname(bam1_t * b)
29 uint32_t * pysam_bam_get_cigar(bam1_t * b)
30 uint8_t * pysam_bam_get_seq(bam1_t * b)
31 uint8_t * pysam_bam_get_qual(bam1_t * b)
32 uint8_t * pysam_bam_get_aux(bam1_t * b)
33 int pysam_bam_get_l_aux(bam1_t * b)
34 char pysam_bam_seqi(uint8_t * s, int i)
35
36 uint16_t pysam_get_bin(bam1_t * b)
37 uint8_t pysam_get_qual(bam1_t * b)
38 uint8_t pysam_get_l_qname(bam1_t * b)
39 uint16_t pysam_get_flag(bam1_t * b)
40 uint32_t pysam_get_n_cigar(bam1_t * b)
41 void pysam_set_bin(bam1_t * b, uint16_t v)
42 void pysam_set_qual(bam1_t * b, uint8_t v)
43 void pysam_set_l_qname(bam1_t * b, uint8_t v)
44 void pysam_set_flag(bam1_t * b, uint16_t v)
45 void pysam_set_n_cigar(bam1_t * b, uint32_t v)
46 void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)