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;
}