slow5_get

NAME

slow5_get - fetches a record from a SLOW5 file corresponding to a given read ID

SYNOPSYS

int slow5_get(const char *read_id, slow5_rec_t **read, slow5_file_t *s5p)

DESCRIPTION

slow5_get() fetches a record from a SLOW5 file s5p for a specified read_id into a slow5_rec_t and stores the address of the slow5_rec_t in *read.

The argument read_id points to a read identifier string.

If *read is set to NULL before the call, then slow5_get() 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(), *read can contain a pointer to an allocated slow5_rec_t from a previous slow5_get() call. If the allocated slow5_rec_t is not large enough to hold the record, slow5_get() will resize it internally.

The argument s5p points to a slow5_file_t opened using slow5_open(). slow5_get() requires the SLOW index to be pre-loaded to s5p using slow5_idx_load().

slow5_get() does not affect the file pointer used by slow5_get_next(). slow5_get() can be called by multiple threads in parallel on the same slow5_file_t pointer.

RETURN VALUE

Upon successful completion, slow5_get() 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_NOTFOUND
       Read_id was not found in the index.
• SLOW5_ERR_ARG
       Invalid argument - read_id, read or s5p is NULL.
• SLOW5_ERR_RECPARSE
       Record parsing error.
• SLOW5_ERR_NOIDX
       The index has not been loaded.
• SLOW5_ERR_IO
       I/O error when reading the slow5 file, for instance, pread()failed.
• SLOW5_ERR_MEM
       Memory allocation error.
• SLOW5_ERR_UNK
       Slow5 file format is unknown.
• SLOW5_ERR_PRESS
       Decompression error.

NOTES

slow5_get() internally uses pread().

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;

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

    ret = slow5_get("r3", &rec, sp);
    if(ret < 0){
        fprintf(stderr,"Error when fetching the read\n");
    }
    else{
        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");
    }

    slow5_rec_free(rec);

    slow5_idx_unload(sp);

    slow5_close(sp);

}

SEE ALSO

slow5_get_next()