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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcalignedsegment.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.libchtslib cimport *
3
4 cdef extern from "htslib_util.h":
5
6 # add *nbytes* into the variable length data of *src* at *pos*
7 bam1_t * pysam_bam_update(bam1_t * b,
8 size_t nbytes_old,
9 size_t nbytes_new,
10 uint8_t * pos)
11
12 # now: static
13 int aux_type2size(int)
14
15 char * pysam_bam_get_qname(bam1_t * b)
16 uint32_t * pysam_bam_get_cigar(bam1_t * b)
17 uint8_t * pysam_bam_get_seq(bam1_t * b)
18 uint8_t * pysam_bam_get_qual(bam1_t * b)
19 uint8_t * pysam_bam_get_aux(bam1_t * b)
20 int pysam_bam_get_l_aux(bam1_t * b)
21 char pysam_bam_seqi(uint8_t * s, int i)
22
23 uint8_t pysam_get_qual(bam1_t * b)
24 uint32_t pysam_get_n_cigar(bam1_t * b)
25 void pysam_set_qual(bam1_t * b, uint8_t v)
26 void pysam_set_n_cigar(bam1_t * b, uint32_t v)
27 void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
28
29
30 from pysam.libcalignmentfile cimport AlignmentFile, AlignmentHeader
31 ctypedef AlignmentFile AlignmentFile_t
32
33
34 # Note: need to declare all C fields and methods here
35 cdef class AlignedSegment:
36
37 # object that this AlignedSegment represents
38 cdef bam1_t * _delegate
39
40 # the header that a read is associated with
41 cdef readonly AlignmentHeader header
42
43 # caching of array properties for quick access
44 cdef object cache_query_qualities
45 cdef object cache_query_alignment_qualities
46 cdef object cache_query_sequence
47 cdef object cache_query_alignment_sequence
48
49 # add an alignment tag with value to the AlignedSegment
50 # an existing tag of the same name will be replaced.
51 cpdef set_tag(self, tag, value, value_type=?, replace=?)
52
53 # get an alignment tag from the AlignedSegment
54 cpdef get_tag(self, tag, with_value_type=?)
55
56 # return true if tag exists
57 cpdef has_tag(self, tag)
58
59 # returns a valid sam alignment string
60 cpdef to_string(self)
61
62 # returns a valid sam alignment string (deprecated)
63 cpdef tostring(self, htsfile=*)
64
65
66 cdef class PileupColumn:
67 cdef const bam_pileup1_t ** plp
68 cdef int tid
69 cdef int pos
70 cdef int n_pu
71 cdef AlignmentHeader header
72 cdef uint32_t min_base_quality
73 cdef kstring_t buf
74 cdef char * reference_sequence
75
76 cdef class PileupRead:
77 cdef int32_t _qpos
78 cdef AlignedSegment _alignment
79 cdef int _indel
80 cdef int _level
81 cdef uint32_t _is_del
82 cdef uint32_t _is_head
83 cdef uint32_t _is_tail
84 cdef uint32_t _is_refskip
85
86 # factory methods
87 cdef AlignedSegment makeAlignedSegment(
88 bam1_t * src,
89 AlignmentHeader header)
90
91 cdef PileupColumn makePileupColumn(
92 const bam_pileup1_t ** plp,
93 int tid,
94 int pos,
95 int n_pu,
96 uint32_t min_base_quality,
97 char * reference_sequence,
98 AlignmentHeader header)
99
100 cdef PileupRead makePileupRead(const bam_pileup1_t * src,
101 AlignmentHeader header)
102
103 cdef uint32_t get_alignment_length(bam1_t * src)