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jpayne@69
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1 # cython: language_level=3
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jpayne@69
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2 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
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3 from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
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4 from libc.stdlib cimport malloc, calloc, realloc, free
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5 from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
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6 from libc.stdio cimport FILE, printf
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7
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8 # Note: this replaces python "open"!
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9 cdef extern from "fcntl.h":
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10 int open(char *pathname, int flags)
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11
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12 cdef extern from "unistd.h" nogil:
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13 ctypedef int ssize_t
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14 ssize_t read(int fd, void *buf, size_t count)
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15 int close(int fd)
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16
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17 from pysam.libchtslib cimport hts_idx_t, hts_itr_t, htsFile, \
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18 tbx_t, kstring_t, BGZF, HTSFile
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19
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20
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21 # These functions are put here and not in chtslib.pxd in order
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22 # to avoid warnings for unused functions.
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23 cdef extern from "pysam_stream.h" nogil:
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24
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25 ctypedef struct kstream_t:
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26 pass
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27
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28 ctypedef struct kseq_t:
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29 kstring_t name
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30 kstring_t comment
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31 kstring_t seq
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32 kstring_t qual
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33
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34 kseq_t *kseq_init(BGZF *)
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35 int kseq_read(kseq_t *)
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36 void kseq_destroy(kseq_t *)
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37 kstream_t *ks_init(BGZF *)
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38 void ks_destroy(kstream_t *)
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39
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40 # Retrieve characters from stream until delimiter
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41 # is reached placing results in str.
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42 int ks_getuntil(kstream_t *,
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43 int delimiter,
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44 kstring_t * str,
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45 int * dret)
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46
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47
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48 cdef class tabix_file_iterator:
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49 cdef BGZF * fh
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50 cdef kstream_t * kstream
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51 cdef kstring_t buffer
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52 cdef size_t size
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53 cdef Parser parser
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54 cdef int fd
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55 cdef int duplicated_fd
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56 cdef infile
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57
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58 cdef __cnext__(self)
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59
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60
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61 cdef class TabixFile(HTSFile):
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62 # pointer to index structure
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63 cdef tbx_t * index
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64
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65 cdef readonly object filename_index
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66
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67 cdef Parser parser
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68
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69 cdef encoding
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70
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71
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72 cdef class Parser:
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73 cdef encoding
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74 cdef parse(self, char * buffer, int len)
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75
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76
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77 cdef class asTuple(Parser):
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78 cdef parse(self, char * buffer, int len)
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79
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80
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81 cdef class asGTF(Parser):
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82 pass
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83
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84
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85 cdef class asGFF3(Parser):
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86 pass
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87
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88
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89 cdef class asBed(Parser):
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90 pass
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91
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92
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93 cdef class asVCF(Parser):
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94 pass
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95
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96
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97 cdef class TabixIterator:
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98 cdef hts_itr_t * iterator
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99 cdef TabixFile tabixfile
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100 cdef kstring_t buffer
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101 cdef encoding
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102 cdef int __cnext__(self)
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103
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104
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105 cdef class TabixIteratorParsed(TabixIterator):
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106 cdef Parser parser
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107
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108
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109 cdef class GZIterator:
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110 cdef object _filename
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111 cdef BGZF * gzipfile
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112 cdef kstream_t * kstream
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113 cdef kstring_t buffer
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114 cdef int __cnext__(self)
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115 cdef encoding
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116
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117
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118 cdef class GZIteratorHead(GZIterator):
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119 pass
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120
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121
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122 cdef class GZIteratorParsed(GZIterator):
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123 cdef Parser parser
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124
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125
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126 # Compatibility Layer for pysam < 0.8
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127 cdef class Tabixfile(TabixFile):
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128 pass
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