slow5curl

s5curl_get_batch

NAME

s5curl_get_batch - fetches a list of record from a remote BLOW5 file corresponding to given read IDs

SYNOPSYS

int s5curl_get_batch(s5curl_mt_t *core, slow5_batch_t *db, char **rid, int num_rid)

DESCRIPTION

s5curl_get_batch() fetches and decodes records from a remote BLOW5 file s5c for a specified list of read_ids into db.

The argument rid points to an array of read identifier strings.

The argument num_rid corresponds with the number of read IDs passed in the method.

*records should have the appropriate memory allocated before s5curl_get_batch() is called. Each slow5_rec_t in *records should be freed by the user program using slow5_rec_free().

The argument s5c points to a slow5_file_t opened using s5curl_open(). s5curl_get_batch() requires the SLOW index to be pre-loaded to s5c using s5curl_idx_load() or s5curl_idx_load_with().

The argument core points to an initialised s5curl_mt_t. This is done with s5curl_init_mt.

The argument db points to an initialised slow5_batch_t. This is done with slow5_init_batch.

RETURN VALUE

Upon successful completion, s5curl_get_batch() returns the number of reads passed in. Otherwise, the process will exit and s5curl_errno is set to indicate the error.

EXAMPLES

#include <slow5curl/s5curl.h>

#define N_THREADS 10
#define BATCH_CAPACITY 100

int main () {

    // setup
    
    s5curl_mt_t *core = s5curl_init_mt(N_THREADS, s5c);

    slow5_batch_t *db = slow5_init_batch(BATCH_CAPACITY);

    ret = s5curl_get_batch(core, db, read_ids, num_reads);
    if (ret != num_reads) {
        fprintf(stderr, "Error fetching batch.\n");
        return EXIT_FAILURE;
    }

    slow5_free_batch(db);
    
    s5curl_free_mt(core);

    // cleanup
}