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// an example programme that uses slow5lib to write a SLOW5 file
// gcc -Wall examples/write.c -I include/ lib/libslow5.a -lm -lz -O2 -g
/*
A BLOW5 file with following content will be written in this example
#num_read_groups 1
@asic_id asic_id_0
@run_id run_0
#char* uint32_t double double double double uint64_t int16_t* char* double int32_t uint8_t uint64_t
#read_id read_group digitisation offset range sampling_rate len_raw_signal raw_signal channel_number median_before read_number start_mux start_time
read_0 0 4096 3 10 4000 10 0,1,2,3,4,5,6,7,8,9 0 0.1 10 1 100
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <slow5/slow5.h>
#define FILE_PATH "test.blow5"
void set_header_attributes(slow5_file_t *sp);
void set_header_aux_fields(slow5_file_t *sp);
void set_record_primary_fields(slow5_rec_t *slow5_record, slow5_file_t *sp);
void set_record_aux_fields(slow5_rec_t *slow5_record, slow5_file_t *sp);
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 ******************/
/*
@asic_id asic_id_0
@run_id run_0
*/
set_header_attributes(sp);
/*
char* double int32_t uint8_t uint64_t
channel_number median_before read_number start_mux start_time
*/
set_header_aux_fields(sp);
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
*/
set_record_primary_fields(slow5_record, sp);
/* auxiliary fileds
channel_number median_before read_number start_mux start_time
0 0.1 10 1 100
*/
set_record_aux_fields(slow5_record, sp);
//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;
}
void set_header_attributes(slow5_file_t *sp){
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);
}
//add another header group attribute called asic_id
if (slow5_hdr_add("asic_id", header) < 0){
fprintf(stderr,"Error adding asic_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);
}
//set the asic_id attribute to "asic_0" for read group 0
if (slow5_hdr_set("asic_id", "asic_id_0", 0, header) < 0){
fprintf(stderr,"Error setting asic_id attribute in read group 0\n");
exit(EXIT_FAILURE);
}
}
void set_header_aux_fields(slow5_file_t *sp){
//add auxilliary field: channel number
if (slow5_aux_add("channel_number", SLOW5_STRING, sp->header) < 0){
fprintf(stderr,"Error adding channel_number auxilliary field\n");
exit(EXIT_FAILURE);
}
//add auxilliary field: median_before
if (slow5_aux_add("median_before", SLOW5_DOUBLE, sp->header) < 0) {
fprintf(stderr,"Error adding median_before auxilliary field\n");
exit(EXIT_FAILURE);
}
//add auxilliary field: read_number
if(slow5_aux_add("read_number", SLOW5_INT32_T, sp->header) < 0){
fprintf(stderr,"Error adding read_number auxilliary field\n");
exit(EXIT_FAILURE);
}
//add auxilliary field: start_mux
if(slow5_aux_add("start_mux", SLOW5_UINT8_T, sp->header) < 0){
fprintf(stderr,"Error adding start_mux auxilliary field\n");
exit(EXIT_FAILURE);
}
//add auxilliary field: start_time
if(slow5_aux_add("start_time", SLOW5_UINT64_T, sp->header) < 0){
fprintf(stderr,"Error adding start_time auxilliary field\n");
exit(EXIT_FAILURE);
}
}
void set_record_primary_fields(slow5_rec_t *slow5_record, slow5_file_t *sp){
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;
}
}
void set_record_aux_fields(slow5_rec_t *slow5_record, slow5_file_t *sp){
char *channel_number = "0";
double median_before = 0.1;
int32_t read_number = 10;
uint8_t start_mux = 1;
uint64_t start_time = 100;
if(slow5_aux_set_string(slow5_record, "channel_number", channel_number, sp->header) < 0){
fprintf(stderr,"Error setting channel_number auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "median_before", &median_before, sp->header) < 0){
fprintf(stderr,"Error setting median_before auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "read_number", &read_number, sp->header) < 0){
fprintf(stderr,"Error setting read_number auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "start_mux", &start_mux, sp->header) < 0){
fprintf(stderr,"Error setting start_mux auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "start_time", &start_time, sp->header) < 0){
fprintf(stderr,"Error setting start_time auxilliary field\n");
exit(EXIT_FAILURE);
}
}
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