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// an example programme that uses slow5lib to randomly access records in a SLOW5 file using multiple threads (pthreads)
#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>
#include <pthread.h>
#include <errno.h>
#define FILE_PATH "examples/example.slow5"
#define NUM_THREADS 4
#define READ_LIST_SIZE 4 //for simplicity number of threads are equal to number of reads to access, we assign one thread for each access
char * read_id_list[READ_LIST_SIZE] = {"r4", "r1", "r3", "r4"};
/* arguments for a thread */
typedef struct {
slow5_file_t *sp;
char *read_id;
} pthread_arg;
/* thread function */
void* access_read(void* voidargs) {
pthread_arg *args = (pthread_arg*)voidargs; //cast the void pointer to pthread_arg pointer
slow5_rec_t *rec = NULL; //slow5 record to be read
//fetch the read with read_id assigned to this thread
int ret = slow5_get(args->read_id, &rec, args->sp);
if (ret < 0) {
fprintf(stderr, "Error when when fetching the read %s\n",args->read_id);
} else {
fprintf(stderr, "Successfully fetched the read %s with %ld raw signal samples\n", rec->read_id, rec->len_raw_signal);
// .... do the processing here as needed
}
//free the SLOW5 record
slow5_rec_free(rec);
pthread_exit(0);
}
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,t = 0; //for return value and thread index
//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);
}
//thread IDs and arguments
pthread_t tids[NUM_THREADS];
pthread_arg args[NUM_THREADS];
//create threads
for(t = 0; t < NUM_THREADS; t++){
args[t].sp = sp; //assign the SLOW5 file pointer
args[t].read_id = read_id_list[t]; //assign a read_id to each thread
ret = pthread_create(&tids[t], NULL, access_read, (void*)(&args[t]));
if(ret < 0){
fprintf(stderr, "Error creating thread\n");
exit(EXIT_FAILURE);
}
}
//pthread joining
for (t = 0; t < NUM_THREADS; t++) {
int ret = pthread_join(tids[t], NULL);
if(ret < 0){
fprintf(stderr, "Error creating thread\n");
exit(EXIT_FAILURE);
}
}
//free the SLOW5 index
slow5_idx_unload(sp);
//close the SLOW5 file
slow5_close(sp);
return 0;
}
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