slow5_aux_get_<primitive_datatype>

NAME

slow5_aux_get_<primitive_datatype> - fetches an auxiliary field (a primitive datatype) from a SLOW5 record

SYNOPSYS

int8_t slow5_aux_get_int8(const slow5_rec_t *read, const char *field, int *err)
int16_t slow5_aux_get_int16(const slow5_rec_t *read, const char *field, int *err)
int32_t slow5_aux_get_int32(const slow5_rec_t *read, const char *field, int *err)
int64_t slow5_aux_get_int64(const slow5_rec_t *read, const char *field, int *err)

uint8_t slow5_aux_get_uint8(const slow5_rec_t *read, const char *field, int *err)
uint16_t slow5_aux_get_uint16(const slow5_rec_t *read, const char *field, int *err)
uint32_t slow5_aux_get_uint32(const slow5_rec_t *read, const char *field, int *err)
uint64_t slow5_aux_get_uint64(const slow5_rec_t *read, const char *field, int *err)

float slow5_aux_get_float(const slow5_rec_t *read, const char *field, int *err)
double slow5_aux_get_double(const slow5_rec_t *read, const char *field, int *err)

char slow5_aux_get_char(const slow5_rec_t *read, const char *field, int *err)

DESCRIPTION

slow5_aux_get_<primitive_datatype>() fetches the value of an auxiliary field of a primitive datatype specified by the field name field from the slow5 record pointed by read. User has to choose the appropriate function so that the returned datatype matches the correct datatype of the stored field, because the data stored in memory as a series of bytes will be reinterpreted as the requested type.

The argument err is an address of an integer which will be set inside the function call to indicate an error. Unless err is NULL, slow5_aux_get_<primitive_datatype>() sets a non zero error code in *err in case of failure.

RETURN VALUE

Upon successful completion, slow5_aux_get_<primitive_datatype>() returns the requested field value. Otherwise, the SLOW5 missing value representation for the particular datatype is returned (SLOW5_INT8_T_NULL, SLOW5_INT16_T_NULL, SLOW5_INT32_T_NULL, SLOW5_INT64_T_NULL, SLOW5_UINT8_T_NULL, SLOW5_UINT16_T_NULL, SLOW5_UINT32_T_NULL, SLOW5_UINT64_T_NULL, SLOW5_FLOAT_NULL, SLOW5_DOUBLE_NULL or SLOW5_CHAR_NULL) and slow5_errno is set to indicate the error. See notes below.

ERRORS

In case of an error, slow5_errno or the non zero error code is set in err (unless err is NULL) are as follows.

• SLOW5_ERR_NOFLD      The requested field was not found.
• SLOW5_ERR_NOAUX      Auxiliary hash map for the record was not found (see notes below).
• SLOW5_ERR_ARG      Invalid argument - read or field is NULL.
• SLOW5_ERR_TYPE      Type conversion was not possible - an array data type field cannot be converted to a primitive type.

NOTES

More error codes may be introduced in future. If the field value has been marked missing for an individual SLOW5 record (“.” in SLOW5 ASCII and as SLOW5_<TYPE>_NULL in BLOW5), the SLOW5 missing value representation for the particular datatype is returned and no error code is set (considered successful as the SLOW5 missing value representation is actually present in the file). This is typically the case when the field name is present in the SLOW5 header, but the field value for the particular record is missing. If the requested field is completely not present (not in the SLOW5 header as well), this is considered an error and SLOW5_ERR_NOAUX code is set.

EXAMPLES

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

#define FILE_PATH "examples/example2.slow5"

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;
    ret = slow5_get_next(&rec,sp);
    if(ret<0){
        fprintf(stderr,"Error in slow5_get_next. Error code %d\n",ret);
        exit(EXIT_FAILURE);
    }

    //------------------------------------------------------------------------
    //              get auxiliary values with primitive datatype
    //------------------------------------------------------------------------

    double median_before = slow5_aux_get_double(rec,"median_before",&ret);
    if(ret!=0){
        fprintf(stderr,"Error in getting auxiliary attribute from the file. Error code %d\n",ret);
        exit(EXIT_FAILURE);
    }
    if(!isnan(median_before)){  //SLOW5_DOUBLE_NULL is the generic NaN value returned by nan("""") and thus median_before != SLOW5_DOUBLE_NULL is not correct
        printf("median_before = %f\n", median_before);
    } else {
        printf("median_before is missing for the record\n");
    }

    uint64_t start_time = slow5_aux_get_uint64(rec, "start_time", &ret);
    if(ret!=0){
        printf("Error in getting auxiliary attribute from the file. Error code %d\n",ret);
        exit(EXIT_FAILURE);
    }
    if(start_time != SLOW5_UINT64_T_NULL){
        printf("start_time = %lu\n", start_time);
    } else{
        printf("start_time is missing for the record\n");
    }

    slow5_rec_free(rec);
    slow5_close(sp);

}

SEE ALSO

slow5_aux_get_<array_datatype>().