1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
|
#cython: language_level=3
from libc.stdio cimport *
from libc.stdint cimport *
from libc.stdlib cimport *
cdef extern from "pyslow5.h":
cdef enum slow5_aux_type:
SLOW5_INT8_T = 0,
SLOW5_INT16_T,
SLOW5_INT32_T,
SLOW5_INT64_T,
SLOW5_UINT8_T,
SLOW5_UINT16_T,
SLOW5_UINT32_T,
SLOW5_UINT64_T,
SLOW5_FLOAT,
SLOW5_DOUBLE,
SLOW5_CHAR,
SLOW5_ENUM,
SLOW5_INT8_T_ARRAY,
SLOW5_INT16_T_ARRAY,
SLOW5_INT32_T_ARRAY,
SLOW5_INT64_T_ARRAY,
SLOW5_UINT8_T_ARRAY,
SLOW5_UINT16_T_ARRAY,
SLOW5_UINT32_T_ARRAY,
SLOW5_UINT64_T_ARRAY,
SLOW5_FLOAT_ARRAY,
SLOW5_DOUBLE_ARRAY,
SLOW5_STRING,
SLOW5_ENUM_ARRAY
ctypedef struct slow5_aux_meta_t:
pass
ctypedef struct slow5_hdr_data_t:
pass
ctypedef struct slow5_version:
uint8_t major
uint8_t minor
uint8_t patch
ctypedef struct slow5_press_t:
pass
ctypedef struct slow5_hdr_t:
slow5_version version;
uint32_t num_read_groups;
slow5_hdr_data_t data;
slow5_aux_meta_t *aux_meta;
ctypedef struct slow5_idx_t:
pass
ctypedef enum slow5_fmt:
pass
ctypedef struct slow5_file_meta_t:
pass
ctypedef struct slow5_file_t:
FILE *fp
slow5_fmt format
slow5_press_t *compress
slow5_hdr_t *header
slow5_idx_t *index
slow5_file_meta_t meta
ctypedef struct slow5_rec_t:
uint16_t read_id_len
char* read_id
uint32_t read_group
double digitisation
double offset
double range
double sampling_rate
uint64_t len_raw_signal
int16_t* raw_signal
pass
# Open a slow5 file
slow5_file_t *slow5_open(const char *pathname, const char *mode);
const char **slow5_get_hdr_keys(const slow5_hdr_t *header, uint64_t *len);
char *slow5_hdr_get(const char *attr, uint32_t read_group, const slow5_hdr_t *header);
void slow5_idx_unload(slow5_file_t *s5p);
int slow5_close(slow5_file_t *s5p);
int slow5_idx_load(slow5_file_t *s5p);
int slow5_get(const char *read_id, slow5_rec_t **read, slow5_file_t *s5p);
int slow5_get_next(slow5_rec_t **read, slow5_file_t *s5p);
char **slow5_get_aux_names(const slow5_hdr_t *header, uint64_t *len);
slow5_aux_type *slow5_get_aux_types(const slow5_hdr_t *header, uint64_t *len);
void slow5_rec_free(slow5_rec_t *read);
char **slow5_get_rids(const slow5_file_t *s5p, uint64_t *len);
int8_t slow5_aux_get_int8(const slow5_rec_t *read, const char *attr, int *err);
int16_t slow5_aux_get_int16(const slow5_rec_t *read, const char *attr, int *err);
int32_t slow5_aux_get_int32(const slow5_rec_t *read, const char *attr, int *err);
int64_t slow5_aux_get_int64(const slow5_rec_t *read, const char *attr, int *err);
uint8_t slow5_aux_get_uint8(const slow5_rec_t *read, const char *attr, int *err);
uint16_t slow5_aux_get_uint16(const slow5_rec_t *read, const char *attr, int *err);
uint32_t slow5_aux_get_uint32(const slow5_rec_t *read, const char *attr, int *err);
uint64_t slow5_aux_get_uint64(const slow5_rec_t *read, const char *attr, int *err);
float slow5_aux_get_float(const slow5_rec_t *read, const char *attr, int *err);
double slow5_aux_get_double(const slow5_rec_t *read, const char *attr, int *err);
char slow5_aux_get_char(const slow5_rec_t *read, const char *attr, int *err);
uint8_t slow5_aux_get_enum(const slow5_rec_t *read, const char *field, int *err);
int8_t *slow5_aux_get_int8_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
int16_t *slow5_aux_get_int16_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
int32_t *slow5_aux_get_int32_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
int64_t *slow5_aux_get_int64_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
uint8_t *slow5_aux_get_uint8_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
uint16_t *slow5_aux_get_uint16_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
uint32_t *slow5_aux_get_uint32_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
uint64_t *slow5_aux_get_uint64_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
float *slow5_aux_get_float_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
double *slow5_aux_get_double_array(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
char *slow5_aux_get_string(const slow5_rec_t *read, const char *attr, uint64_t *len, int *err);
uint8_t *slow5_aux_get_enum_array(const slow5_rec_t *read, const char *field, uint64_t *len, int *err);
# Write slow5 file
# from slow5.h
int slow5_set_press(slow5_file_t *s5p, int rec_press, int sig_press);
int slow5_hdr_add_attr(const char *attr, slow5_hdr_t *header);
int slow5_hdr_set(const char *attr, const char *value, uint32_t read_group, slow5_hdr_t *header);
int64_t slow5_hdr_add_rg(slow5_hdr_t *header);
slow5_rec_t *slow5_rec_init();
# Write slow5 file
int slow5_hdr_write(slow5_file_t *sf);
int slow5_write(slow5_rec_t *rec, slow5_file_t *sf);
int slow5_aux_add(const char *attr, slow5_aux_type type, slow5_hdr_t *header);
int slow5_aux_set(slow5_rec_t *read, const char *attr, const void *data, slow5_hdr_t *header);
int slow5_aux_set_string(slow5_rec_t *read, const char *attr, const char *data, slow5_hdr_t *header);
cdef extern from "slow5threads.h":
int slow5_get_batch(slow5_rec_t ***read, slow5_file_t *s5p, char **rid, int num_rid, int num_threads);
int slow5_get_next_batch(slow5_rec_t ***read, slow5_file_t *s5p, int batch_size, int num_threads);
int slow5_write_batch(slow5_rec_t **read, slow5_file_t *s5p, int batch_size, int num_threads);
void slow5_free_batch(slow5_rec_t ***read, int num_rec);
|
