slow5_get_rids

NAME

slow5_get_rids - gets the pointer to the list of read IDs associated with a SLOW5 file

SYNOPSYS

char **slow5_get_rids(const slow5_file_t *s5p, uint64_t *len)

DESCRIPTION

slow5_get_rids() gets the pointer to the list of read IDs associated with a SLOW5 file pointed by s5p. The SLOW5 index should have been already loaded before by calling slow5_idx_load(). The number of reads will be set on the address specified by len.

RETURN VALUE

Upon successful completion, slow5_get_rids() returns a char** pointer. Otherwise, a negative value is returned that indicates the error and slow5_errno is set to indicate the error.

ERRORS

• SLOW5_ERR_NOIDX      SLOW5 index has not been loaded.
• SLOW5_ERR_OTH:      Other error.

NOTES

slow5_get_rids() returns the list of read IDs stored in the index. Thus, returned pointer is from an internal data structure and must NOT be freed by user.

EXAMPLES

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

#define FILE_PATH "examples/example.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);
    }

    int ret=0;
    ret = slow5_idx_load(sp);
    if(ret<0){
        fprintf(stderr,"Error in loading index\n");
        exit(EXIT_FAILURE);
    }

    uint64_t num_reads = 0;
    char **read_ids = slow5_get_rids(sp, &num_reads);
    if(read_ids==NULL){
        fprintf(stderr,"Error in getting list of read IDs\n");
        exit(EXIT_FAILURE);
    }

    for(uint64_t i=0; i<num_reads; i++) {
        printf("%s\n",read_ids[i]);
    }

    slow5_idx_unload(sp);

    slow5_close(sp);

}

SEE ALSO

slow5_idx_load()