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// an example programme that uses slow5lib to randomly access records in a SLOW5 file using multiple threads (openMP)
#include <omp.h>
#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>
#define FILE_PATH "examples/example.slow5"
#define READ_LIST_SIZE 4
char * read_id_list[READ_LIST_SIZE] = {"r4", "r1", "r3", "r4"};
int main(){
//open the SLOW5 file
slow5_file_t *sp = slow5_open(FILE_PATH,"r");
if(sp==NULL){
fprintf(stderr,"Error in opening file\n");
exit(EXIT_FAILURE);
}
int ret=0; //for return value
//load the SLOW5 index (will be built if not present)
ret = slow5_idx_load(sp);
if (ret < 0) {
fprintf(stderr, "Error in loading index\n");
exit(EXIT_FAILURE);
}
#pragma omp parallel for
for(int32_t i=0; i<READ_LIST_SIZE; i++) {
slow5_rec_t *rec = NULL; //slow5 record to be read
ret = slow5_get(read_id_list[i], &rec, sp); //fetch the read
if (ret < 0) {
fprintf(stderr, "Error in when fetching the read %s\n",read_id_list[i]);
} else {
fprintf(stderr, "Successfully fetched the read %s with %ld raw signal samples\n", rec->read_id, rec->len_raw_signal);
}
slow5_rec_free(rec); //free the SLOW5 record
}
//free the SLOW5 index
slow5_idx_unload(sp);
//close the SLOW5 file
slow5_close(sp);
return 0;
}
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