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# slow5_decode
## NAME
slow5_decode - decodes a slow5 record
## SYNOPSYS
`int slow5_decode(char **mem, size_t *bytes, slow5_rec_t **read, slow5_file_t *s5p);`
## DESCRIPTION
This function decode a raw record pointed by **mem* of size *bytes* (previously fetched using `slow5_get_next_bytes()`) into a *slow5_rec_t* and stores the address of the *slow5_rec_t* in **read*. The argument *s5p* points to a *slow5_file_t* opened using `slow5_open()`.
If **read* is set to NULL before the call, then `slow5_get_next()` will allocate a *slow5_rec_t* for storing the record.
This *slow5_rec_t* should be freed by the user program using `slow5_rec_free()`.
Alternatively, before calling `slow5_get_next()`, **read* can contain a pointer to an allocated *slow5_rec_t* from a previous `slow5_get_next()` call.
If the allocated *slow5_rec_t* is not large enough to hold the record, `slow5_get_next()` will resize it internally.
## RETURN VALUE
Upon successful completion, `slow5_decode()` returns a non negative integer (>=0). Otherwise, a negative value is returned that indicates the error and `slow5_errno` is set to indicate the error.
## ERRORS
* `SLOW5_ERR_RECPARSE`
Record parsing error.
* `SLOW5_ERR_MEM`
Memory allocation error.
* `SLOW5_ERR_PRESS`
Record decompression error.
## NOTES
If the file is compressed binary, the raw record will be first decompressed and before parsing.
This function does NOT free the `*mem` buffer.
## EXAMPLES
```
#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>
#define FILE_PATH "examples/example.slow5"
#define TO_PICOAMPS(RAW_VAL,DIGITISATION,OFFSET,RANGE) (((RAW_VAL)+(OFFSET))*((RANGE)/(DIGITISATION)))
int main(){
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;
int ret=0;
char *mem = NULL;
size_t bytes = 0;
while((ret = slow5_get_next_bytes(&mem,&bytes,sp)) >= 0){
if(slow5_decode(&mem, &bytes, &rec, sp) < 0){
fprintf(stderr,"Error in decoding record\n");
exit(EXIT_FAILURE);
}
free(mem);
printf("%s\t",rec->read_id);
uint64_t len_raw_signal = rec->len_raw_signal;
for(uint64_t i=0;i<len_raw_signal;i++){
double pA = TO_PICOAMPS(rec->raw_signal[i],rec->digitisation,rec->offset,rec->range);
printf("%f ",pA);
}
printf("\n");
}
if(ret != SLOW5_ERR_EOF){ //check if proper end of file has been reached
fprintf(stderr,"Error in slow5_get_next. Error code %d\n",ret);
exit(EXIT_FAILURE);
}
slow5_rec_free(rec);
slow5_close(sp);
}
```
## SEE ALSO
[slow5_get_next_bytes()](slow5_get_next_bytes.md).
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