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//get all the samples and sum them to stdout
//make zstd=1
//gcc -Wall -O2 -I include/ -o get_all_samples test/bench/get_all_samples.c lib/libslow5.a python/slow5threads.c -lm -lz -lzstd -lpthread -fopenmp
#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>
#include <omp.h>
#include <sys/time.h>
#include "../../python/slow5threads.h"
static inline double realtime(void) {
struct timeval tp;
struct timezone tzp;
gettimeofday(&tp, &tzp);
return tp.tv_sec + tp.tv_usec * 1e-6;
}
int main(int argc, char *argv[]) {
if(argc != 5) {
fprintf(stderr, "Usage: %s in_file.blow5 out_file.csv num_thread batch_size\n", argv[0]);
return EXIT_FAILURE;
}
slow5_rec_t **rec = NULL;
int ret=1;
int batch_size = atoi(argv[4]);
int num_thread = atoi(argv[3]);
omp_set_num_threads(num_thread);
uint64_t *sums = malloc(sizeof(uint64_t)*batch_size);
FILE *fp = fopen(argv[2],"w");
if(fp==NULL){
fprintf(stderr,"Error in opening file %s for writing\n",argv[2]);
perror("perr: ");
exit(EXIT_FAILURE);
}
fputs("read_id,samples\n", fp);
double tot_time = 0;
double t0 = realtime();
slow5_file_t *sp = slow5_open(argv[1],"r");
if(sp==NULL){
fprintf(stderr,"Error in opening file\n");
perror("perr: ");
exit(EXIT_FAILURE);
}
tot_time += realtime() - t0;
while(ret > 0){
t0 = realtime();
ret = slow5_get_next_batch(&rec,sp,batch_size,num_thread);
tot_time += realtime() - t0;
fprintf(stderr,"batch loaded with %d reads\n",ret);
#pragma omp parallel for
for(int i=0;i<ret;i++){
uint64_t sum = 0;
for(int j=0; j<rec[i]->len_raw_signal; j++){
sum += rec[i]->raw_signal[j];
}
sums[i] = sum;
}
fprintf(stderr,"batch processed with %d reads\n",ret);
for(int i=0;i<ret;i++){
fprintf(fp,"%s,%ld\n",rec[i]->read_id,sums[i]);
}
fprintf(stderr,"batch printed with %d reads\n",ret);
t0 = realtime();
slow5_free_batch(&rec,ret);
tot_time += realtime() - t0;
if(ret<batch_size){ //this indicates nothing left to read //need to handle errors
break;
}
}
t0 = realtime();
slow5_close(sp);
tot_time += realtime() - t0;
free(sums);
fclose(fp);
fprintf(stderr,"Time for getting samples %f\n", tot_time);
return 0;
}
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