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//get all the read ids and print them to stdout
//make zstd=1
//gcc -Wall -O2 -I include/ -o get_all_read_ids test/bench/get_all_read_ids.c lib/libslow5.a -lm -lz -lzstd
#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>
#include <sys/time.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 != 3) {
fprintf(stderr, "Usage: %s in_file.blow5 out_file.csv\n", argv[0]);
return EXIT_FAILURE;
}
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);
}
int ret=0;
ret = slow5_idx_load(sp);
if(ret<0){
fprintf(stderr,"Error in loading index\n");
exit(EXIT_FAILURE);
}
uint64_t num_reads = 0;
char **read_ids = slow5_get_rids(sp, &num_reads);
tot_time += realtime() - t0;
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\n", fp);
for(int i=0; i<num_reads; i++) {
fputs(read_ids[i],fp);
fputc('\n',fp);
}
fclose(fp);
t0 = realtime();
slow5_idx_unload(sp);
slow5_close(sp);
tot_time += realtime() - t0;
fprintf(stderr,"Time taken for getting read IDs: %f\n", tot_time);
return 0;
}
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