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// an example programme that uses slow5lib to write a SLOW5 file with an enum data type
/*
A BLOW5 file with following content will be written in this example
#num_read_groups 1
@run_id run_0
#char* uint32_t double double double double uint64_t int16_t* enum{unknown,partial,mux_change,unblock_mux_change,signal_positive,signal_negative}
#read_id read_group digitisation offset range sampling_rate len_raw_signal raw_signal end_reason
read_0 0 4096 3 10 4000 10 0,1,2,3,4,5,6,7,8,9 1
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <slow5/slow5.h>
#define FILE_PATH "test.blow5"
int main(){
//open the SLOW5 file for writing
slow5_file_t *sp = slow5_open(FILE_PATH, "w");
if(sp==NULL){
fprintf(stderr,"Error opening file!\n");
exit(EXIT_FAILURE);
}
// //This section can be optionally uncommented to set non-default compression methods for blow5 (the recommended default is zlib+svb-zd)
// if(slow5_set_press(sp, SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE) < 0){ // no record compression, no signal compression
// fprintf(stderr,"Error setting compression method!\n");
// exit(EXIT_FAILURE);
// }
/*********************** Header ******************/
/*
@run_id run_id_0
*/
slow5_hdr_t *header=sp->header; //pointer to the SLOW5 header
//add a header group attribute called run_id
if (slow5_hdr_add("run_id", header) < 0){
fprintf(stderr,"Error adding run_id attribute\n");
exit(EXIT_FAILURE);
}
//set the run_id attribute to "run_0" for read group 0
if (slow5_hdr_set("run_id", "run_0", 0, header) < 0){
fprintf(stderr,"Error setting run_id attribute in read group 0\n");
exit(EXIT_FAILURE);
}
/*
enum{unknown,partial,mux_change,unblock_mux_change,signal_positive,signal_negative}
end_reason
*/
const char *enum_labels[] = {"unknown", "partial", "mux_change", "unblock_mux_change", "signal_positive", "signal_negative"};
uint8_t num_labels = 6;
if (slow5_aux_add_enum("end_reason", enum_labels, num_labels, sp->header) < 0){
fprintf(stderr,"Error adding end_reason auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_hdr_write(sp) < 0){
fprintf(stderr,"Error writing header!\n");
exit(EXIT_FAILURE);
}
/******************* A SLOW5 record ************************/
slow5_rec_t *slow5_record = slow5_rec_init();
if(slow5_record == NULL){
fprintf(stderr,"Could not allocate space for a slow5 record.");
exit(EXIT_FAILURE);
}
/* primary fields
#read_id read_group digitisation offset range sampling_rate len_raw_signal raw_signal
read_0 0 4096 3 10 4000 10 0,1,2,3,4,5,6,7,8,9
*/
slow5_record -> read_id = strdup("read_0");
if(slow5_record->read_id == NULL){
fprintf(stderr,"Could not do strdup.");
exit(EXIT_FAILURE);
}
slow5_record-> read_id_len = strlen(slow5_record -> read_id);
slow5_record -> read_group = 0;
slow5_record -> digitisation = 4096.0;
slow5_record -> offset = 3.0;
slow5_record -> range = 10.0;
slow5_record -> sampling_rate = 4000.0;
slow5_record -> len_raw_signal = 10;
slow5_record -> raw_signal = (int16_t *)malloc(sizeof(int16_t) * slow5_record->len_raw_signal);
if(slow5_record->raw_signal == NULL){
fprintf(stderr,"Could not allocate space for raw signal.");
exit(EXIT_FAILURE);
}
for(int i=0; i<slow5_record->len_raw_signal; i++){
slow5_record->raw_signal[i] = i;
}
/* auxiliary fileds
end_reason
1
*/
uint8_t end_reason = 1;
if(slow5_aux_set(slow5_record, "end_reason", &end_reason, sp->header) < 0){
fprintf(stderr,"Error setting end_reason auxilliary field\n");
exit(EXIT_FAILURE);
}
//write to file
if(slow5_write(slow5_record, sp) < 0){
fprintf(stderr,"Error writing record!\n");
exit(EXIT_FAILURE);
}
//free the slow5 record
slow5_rec_free(slow5_record);
//close the SLOW5 file
slow5_close(sp);
return 0;
}
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