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
|
# slow5_get_batch
## NAME
slow5_get_batch - fetches a batch of SLOW5 records corresponding to a given batch of read ID
## SYNOPSYS
`int slow5_get_batch(slow5_mt_t *mt, slow5_batch_t *read_batch, char **rid, int num_rid)`
## DESCRIPTION
`slow5_get_batch()` fetches a batch of record from a SLOW5 file associated with *mt* for a specified list of read IDs. The list of read must be pointed by *rid* and the the size of the list must be specified by *num_rid*.
## RETURN VALUE
The number of records fetched.
## NOTES
*num_rid* 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.
## NOTES
## 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;
ret = slow5_idx_load(sp);
if(ret<0){
fprintf(stderr,"Error in loading index\n");
exit(EXIT_FAILURE);
}
int num_rid = 4;
int num_thread = 2;
int batch_size = 4096;
char *rid[num_rid];
rid[0]="r4";
rid[1]="r1",
rid[2]="r2";
rid[3]="r5";
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);
}
ret = slow5_get_batch(mt, read_batch, rid, num_rid);
if(ret!=num_rid){
fprintf(stderr,"Error in fetching all records\n");
exit(EXIT_FAILURE);
}
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);
}
slow5_free_batch(read_batch);
slow5_free_mt(mt);
slow5_idx_unload(sp);
slow5_close(sp);
return 0;
}
```
## SEE ALSO
[slow5_get()](slow5_get_next_batch.md)
|