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// an example programme that uses slow5lib to obtain auxiliary field from a slow5/blow5 file
#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>
#define FILE_PATH "examples/example2.slow5"
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);
}
slow5_rec_t *rec = NULL; //slow5 record to be read
int ret=0; //for return value
//get the very first record
ret = slow5_get_next(&rec,sp);
if(ret<0){
fprintf(stderr,"Error in slow5_get_next. Error code %d\n",ret);
exit(EXIT_FAILURE);
}
//------------------------------------------------------------------------
// getting auxiliary fields whose values are primitive datatypes
//------------------------------------------------------------------------
//median_before auxiliary field - double data type
double median_before = slow5_aux_get_double(rec,"median_before",&ret);
if(ret!=0){
fprintf(stderr,"Error in getting auxiliary attribute from the file. Error code %d\n",ret);
exit(EXIT_FAILURE);
}
if(!isnan(median_before)){ //SLOW5_DOUBLE_NULL is the generic NaN value returned by nan("""") and thus median_before != SLOW5_DOUBLE_NULL is not correct
printf("median_before = %f\n", median_before);
} else {
printf("median_before is missing for the record\n");
}
//start_time auxiliary field - uint64 data type
uint64_t start_time = slow5_aux_get_uint64(rec, "start_time", &ret);
if(ret!=0){
fprintf(stderr,"Error in getting auxiliary attribute from the file. Error code %d\n",ret);
exit(EXIT_FAILURE);
}
if(start_time != SLOW5_UINT64_T_NULL){ //check if the field value is marked missing and print the value
printf("start_time = %lu\n", start_time);
} else{
printf("start_time is missing for the record\n");
}
//------------------------------------------------------------------------
// getting auxiliary fields whose values are array datatypes
//------------------------------------------------------------------------
//channel_number auxiliary field - string (char *) datatype
uint64_t len; //length of the array
char* channel_number = slow5_aux_get_string(rec, "channel_number", &len, &ret);
if(ret!=0){
fprintf(stderr,"Error in getting auxiliary attribute from the file. Error code %d\n",ret);
exit(EXIT_FAILURE);
}
if (channel_number != NULL){ //check if the field value exists and print the value
printf("channel_number = %s\n", channel_number);
} else{
printf("channel_number is missing for the record\n");
}
//free the SLOW5 record
slow5_rec_free(rec);
//close the SLOW5 file
slow5_close(sp);
return 0;
}
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