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//get all the samples and sum them to stdout
//make zstd=1
//gcc -Wall -O2 -I include/ -o get_selected_read_ids_read_number test/bench/get_selected_read_ids_read_number.c lib/libslow5.a python/slow5threads.c -lm -lz -lzstd -lpthread
#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 != 6) {
fprintf(stderr, "Usage: %s in_file.blow5 inread_id.csv out_file.csv num_thread batch_size\n", argv[0]);
return EXIT_FAILURE;
}
int ret=0;
int batch_size = atoi(argv[5]);
int num_thread = atoi(argv[4]);
uint64_t *sums = malloc(sizeof(uint64_t)*batch_size);
char tmp[1024];
FILE *fpr = fopen(argv[2],"r");
if(fpr==NULL){
fprintf(stderr,"Error in opening file %s for reading\n",argv[2]);
perror("perr: ");;
exit(EXIT_FAILURE);
}
if(fscanf(fpr,"%s",tmp)<1 || strcmp(tmp,",read_id")!=0){
fprintf(stderr,"Bad input CSV file. CSV header is expected to have read_id\n");
exit(EXIT_FAILURE);
}
FILE *fpw = fopen(argv[3],"w");
if(fpw==NULL){
fprintf(stderr,"Error in opening file %s for writing\n",argv[3]);
perror("perr: ");;
exit(EXIT_FAILURE);
}
fputs("read_id,read_number\n", fpw);
double tot_time = 0;
double t0 = realtime();
slow5_rec_t **rec = NULL;
slow5_file_t *sp = slow5_open(argv[1],"r");
if(sp==NULL){
fprintf(stderr,"Error in opening file\n");
exit(EXIT_FAILURE);
}
ret = slow5_idx_load(sp);
if(ret<0){
fprintf(stderr,"Error in loading index\n");
exit(EXIT_FAILURE);
}
tot_time += realtime() - t0;
char **rid = malloc(sizeof(char*)*batch_size);
while(1){
int i=0;
for(i=0; i<batch_size; i++){
int crap;
if (fscanf(fpr,"%d,%s",&crap,tmp) < 2) {
break;
}
rid[i] = strdup(tmp);
}
int num_rid = i;
t0 = realtime();
ret = slow5_get_batch(&rec, sp, rid, num_rid, num_thread);
tot_time += realtime() - t0;
if(ret!=num_rid){
fprintf(stderr,"Error in getting batch\n");
exit(EXIT_FAILURE);
}
fprintf(stderr,"batch loaded with %d reads\n",ret);
for(int i=0;i<ret;i++){
t0 = realtime();
int err = 0;
int32_t rn = slow5_aux_get_int32(rec[i],"read_number",&err);
if(err!=0){
fprintf(stderr,"Error in getting auxiliary attribute from the file. Error code %d\n",ret);
exit(EXIT_FAILURE);
}
tot_time += realtime() - t0;
fprintf(fpw,"%s,%d\n",rec[i]->read_id, rn);
}
fprintf(stderr,"batch printed with %d reads\n",ret);
t0 = realtime();
slow5_free_batch(&rec,ret);
tot_time += realtime() - t0;
for(int i=0; i<num_rid; i++){
free(rid[i]);
}
if(num_rid<batch_size){ //this indicates nothing left to read
break;
}
}
t0 = realtime();
slow5_idx_unload(sp);
slow5_close(sp);
tot_time += realtime() - t0;
free(sums);
fclose(fpr);
fclose(fpw);
free(rid);
fprintf(stderr,"Time for getting samples %f\n", tot_time);
return 0;
}
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