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().