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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 (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 5 //for simplicity assume number of threads is equal to number of reads in the file
#define READ_BUFFER_SIZE 1024 //number of reads to be loaded in one go
/* arguments for a thread */
typedef struct {
slow5_file_t *sp;
char *mem;
size_t bytes;
} 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 put the decoded record
//decode the read assigned to this thread
int ret = slow5_decode(&args->mem, &args->bytes, &rec, args->sp); //decode the raw record
if (ret < 0) {
fprintf(stderr, "Error in when decoding the read\n");
} else {
fprintf(stderr, "Successfully decoded 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);
//free the raw record
free(args->mem);
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
//for simplicity assume the file has less than READ_BUFFER_SIZE reads
// and that the number of reads is equal to NUM_THREADS
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);
//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].mem = mem[t]; //assign a raw read record to each thread
args[t].bytes = bytes[t]; //assign the size of the raw record 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);
}
}
//close the SLOW5 file
slow5_close(sp);
return 0;
}
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