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// an example programme that uses slow5lib to sequentially read raw SLOW5 records using one thread
// and decode records in prallel 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_BUFFER_SIZE 1024 //number of reads to be loaded in one go
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);
}
//for simplicity assume file has less than READ_BUFFER_SIZE reads
char *mem[READ_BUFFER_SIZE] = {NULL}; //memory to store raw records
size_t bytes[READ_BUFFER_SIZE] = {0}; //memory to store raw record sizes
int n_rec = 0; //number of records read
//read a batch of raw records
for(n_rec=0;n_rec<READ_BUFFER_SIZE;n_rec++){
if(slow5_get_next_bytes(&mem[n_rec],&bytes[n_rec],sp)<0){
if (slow5_errno != SLOW5_ERR_EOF) { //check if end of file has been reached (break the loop) or some other error (exit with error)
fprintf(stderr, "Error reading from SLOW5 file %d", slow5_errno);
exit(EXIT_FAILURE);
} else {
break;
}
}
}
fprintf(stderr, "Read %d raw records\n", n_rec);
//decode a batch of raw records using multiple threads in parallel
#pragma omp parallel for
for(int i=0; i<n_rec; i++) {
slow5_rec_t *rec = NULL; //slow5 record to put the decoded record
int ret = slow5_decode(&mem[i], &bytes[i], &rec, sp); //decode the raw record
if (ret < 0) {
fprintf(stderr, "Error in when decoding the read %d\n",i);
} else {
fprintf(stderr, "Successfully decoded 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(mem[i]); //free the raw record
}
fprintf(stderr, "Decoded %d raw records\n", n_rec);
//close the SLOW5 file
slow5_close(sp);
return 0;
}
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