slow5_get_next

NAME

slow5_get_next - fetches the record at the current file pointer of a slow5 file

SYNOPSYS

int slow5_get_next(slow5_rec_t **read, slow5_file_t *s5p)

DESCRIPTION

slow5_get_next() fetches a record from a SLOW5 file s5p at the current file pointer into a slow5_rec_t and stores the address of the slow5_rec_t in *read.

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.

The argument s5p points to a slow5_file_t opened using slow5_open().

RETURN VALUE

Upon successful completion, slow5_get_next() returns a non negative integer (>=0). Otherwise (including the end of file), a negative value is returned that indicates the error and slow5_errno is set to indicate the error.

ERRORS

• SLOW5_ERR_EOF
       End of file (EOF) (if blow5, EOF marker was properly found at the end).
• SLOW5_ERR_ARG
       Invalid argument - Read or s5p is NULL.
• SLOW5_ERR_RECPARSE
       Record parsing error.
• SLOW5_ERR_IO
       I/O error (except EOF) when reading the slow5 file, for instance, getline() or fread() failed.
• SLOW5_ERR_MEM
       Memory allocation error.
• SLOW5_ERR_PRESS
       Record decompression error.
• SLOW5_ERR_TRUNC
       Truncated blow5 file - EOF reached without seeing the blow5 EOF marker.
• SLOW5_ERR_UNK
       Slow5 format is unknown.

NOTES

slow5_get_next does not require an index to be pre-loaded, as opposed to slow5_get() which so.

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;

    while((ret = slow5_get_next(&rec,sp)) >= 0){
        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()