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