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
|
# slow5_get_next_batch
## NAME
slow5_get_next_batch - fetches the next batch of records at the current file pointer of a SLOW5 file
## SYNOPSYS
`int slow5_get_next_batch(slow5_mt_t *mt, slow5_batch_t *read_batch, int num_reads)`
## DESCRIPTION
`slow5_get_next_batch()` fetches the next *num_reads* number of records from a SLOW5 file associated with *mt* at the current file pointer into a *slow5_batch_t*.
## RETURN VALUE
The number of records fetched.
## NOTES
*num_reads* must be less than or equal to the capacity of the read_batch.
## ERRORS
Currently, in case of error, this function will exit the programme. Proper error handling might be introduced in future, where a negative number return is indicative of error.
## EXAMPLES
```
#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>
#include <slow5/slow5_mt.h>
#define FILE_PATH "examples/example.slow5"
int main(){
slow5_file_t *sp = slow5_open(FILE_PATH,"r");
if(sp==NULL){
fprintf(stderr,"Error in opening file\n");
exit(EXIT_FAILURE);
}
slow5_rec_t **rec = NULL;
int ret=0;
int batch_size = 4096;
int num_thread = 8;
slow5_mt_t *mt = slow5_init_mt(num_thread,sp);
if (mt==NULL){ //currently not useful, but better have this for future proofing
fprintf(stderr,"Error in initialising multi-thread struct\n");
exit(EXIT_FAILURE);
}
slow5_batch_t *read_batch = slow5_init_batch(batch_size);
if (read_batch==NULL){ //currently not useful, but better have this for future proofing
fprintf(stderr,"Error in initialising slow5 record batch\n");
exit(EXIT_FAILURE);
}
while((ret = slow5_get_next_batch(mt,read_batch,4096)) > 0){
for(int i=0;i<ret;i++){
rec = read_batch->slow5_rec;
uint64_t len_raw_signal = rec[i]->len_raw_signal;
printf("%s\t%ld\n",rec[i]->read_id,len_raw_signal);
}
if(ret<4096){ //this indicates nothing left to read //better handling of errors may be introduced in future
break;
}
}
slow5_free_batch(read_batch);
slow5_free_mt(mt);
slow5_close(sp);
return 0;
}
```
## SEE ALSO
[slow5_get()](slow5_get_batch.md)
|
