slow5_write_bytes

NAME

slow5_write_bytes - writes an encoded SLOW5 record to a SLOW5 file

SYNOPSYS

int slow5_write_bytes(char *mem, size_t bytes, slow5_file_t *s5p)

DESCRIPTION

slow5_write_bytes() writes a serialised SLOW5 record pointed by mem to a SLOW5 file pointed by s5p.

The argument s5p points to a slow5_file_t opened using slow5_open() for writing or appending.

RETURN VALUE

Upon successful completion, slow5_write_bytes() returns a non negative integer (>=0). Otherwise a negative value is returned.

ERRORS

TODO

EXAMPLES

```

#include #include #include <slow5/slow5.h>

#define FILE_PATH “test.slow5”

int main(){

slow5_file_t *sp = slow5_open(FILE_PATH, "w");
if(sp==NULL){
    fprintf(stderr,"Error opening file!\n");
    exit(EXIT_FAILURE);
}
slow5_hdr_t* header = sp->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);
}

if(slow5_hdr_write(sp) < 0){
    fprintf(stderr,"Error writing header!\n");
    exit(EXIT_FAILURE);
}

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);
}

char *read_id = "read_1";
int16_t raw_signal[10] = {0,1,2,3,4,5,6,7,8,9}; //a raw signal of length 10

//set the field
slow5_record -> read_id = read_id;
slow5_record -> read_id_len = strlen(read_id);
slow5_record -> read_group = 0;
slow5_record -> digitisation = 4096.0;
slow5_record -> offset = 4.0;
slow5_record -> range = 12.0;
slow5_record -> sampling_rate = 4000.0;
slow5_record -> len_raw_signal = 10;
slow5_record -> raw_signal = raw_signal;

//encode to a buffer
char *mem = NULL;
size_t bytes = 0;
if (slow5_encode(&mem, &bytes, slow5_record, sp) != 0){
    fprintf(stderr,"Error encoding record\n");
    exit(EXIT_FAILURE);
}

//write the buffer
if (slow5_write_bytes(mem, bytes, sp) < 0){
    fprintf(stderr,"Error writing buffer!\n");
    exit(EXIT_FAILURE);
}

//free memory
//slow5_rec_free will attempt to free read_id and raw_signal arrays.
//As we allocated them on the stack and thus they must not be freed, we must set them to NULL before calling slow5_rec_free.
slow5_record -> read_id = NULL;
slow5_record -> raw_signal = NULL;
slow5_rec_free(slow5_record);

free(mem);

//close the file
slow5_close(sp);

return 0;

}```

SEE ALSO

slow5_encode()