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