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#include "unit_test.h"
#include <slow5/slow5.h>
#include "slow5_extra.h"
int slow5_open_valid(void) {
struct slow5_file *s5p = slow5_open("test/data/exp/two_rg/exp_default.slow5", "r");
ASSERT(s5p != NULL);
ASSERT(s5p->format == SLOW5_FORMAT_ASCII);
ASSERT(s5p->header != NULL);
ASSERT(s5p->header->version.major == 0);
ASSERT(s5p->header->version.minor == 1);
ASSERT(s5p->header->version.patch == 0);
ASSERT(s5p->header->num_read_groups == 2);
ASSERT(s5p->header->data.num_attrs == 32);
ASSERT(strcmp(slow5_hdr_get("asic_id", 1, s5p->header), "420170566") == 0);
ASSERT(strcmp(slow5_hdr_get("experiment_type", 1, s5p->header), "") == 0);
ASSERT(strcmp(slow5_hdr_get("file_version", 1, s5p->header), "0.6") == 0);
ASSERT(slow5_close(s5p) == 0);
return EXIT_SUCCESS;
}
int slow5_get_valid(void) {
struct slow5_file *s5p = slow5_open("test/data/exp/two_rg/exp_default.slow5", "r");
ASSERT(s5p != NULL);
ASSERT(slow5_idx_load(s5p) == 0);
struct slow5_rec *read = NULL;
ASSERT(slow5_get("40aac17d-56a6-44db-934d-c0dbb853e2cd", &read, s5p) == 0);
ASSERT(strcmp(read->read_id, "40aac17d-56a6-44db-934d-c0dbb853e2cd") == 0);
ASSERT(read->read_group == 1);
ASSERT(read->digitisation == 8192);
ASSERT(read->offset == 26);
ASSERT(read->range == 1444.86);
ASSERT(read->sampling_rate == 4000);
ASSERT(read->len_raw_signal == 46971);
ASSERT(read->raw_signal[0] == 1233);
ASSERT(read->raw_signal[read->len_raw_signal - 1] == 390);
slow5_rec_free(read);
ASSERT(slow5_close(s5p) == 0);
return EXIT_SUCCESS;
}
int slow5_to_blow5_uncomp(void) {
struct slow5_file *from = slow5_open("test/data/exp/two_rg/exp_default.slow5", "r");
ASSERT(from != NULL);
FILE *to = fopen("test/data/out/two_rg/out_default.blow5", "w");
ASSERT(to != NULL);
slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_BINARY, method) != -1);
struct slow5_rec *read = NULL;
int ret;
while ((ret = slow5_get_next(&read, from)) == 0) {
ASSERT(slow5_rec_fwrite(to, read, from->header->aux_meta, SLOW5_FORMAT_BINARY, NULL) != -1);
}
slow5_rec_free(read);
ASSERT(ret == SLOW5_ERR_EOF);
ASSERT(slow5_eof_fwrite(to) != -1);
ASSERT(slow5_close(from) == 0);
ASSERT(fclose(to) == 0);
return EXIT_SUCCESS;
}
int slow5_to_blow5_zlib(void) {
struct slow5_file *from = slow5_open("test/data/exp/two_rg/exp_default.slow5", "r");
ASSERT(from != NULL);
FILE *to = fopen("test/data/out/two_rg/out_default_gzip.blow5", "w");
ASSERT(to != NULL);
slow5_press_method_t method = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_NONE};
ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_BINARY, method) != -1);
struct slow5_rec *read = NULL;
int ret;
struct slow5_press *zlib = slow5_press_init(method);
ASSERT(zlib != NULL);
while ((ret = slow5_get_next(&read, from)) == 0) {
ASSERT(slow5_rec_fwrite(to, read, from->header->aux_meta, SLOW5_FORMAT_BINARY, zlib) != -1);
}
slow5_rec_free(read);
ASSERT(ret == SLOW5_ERR_EOF);
ASSERT(slow5_eof_fwrite(to) != -1);
slow5_press_free(zlib);
ASSERT(slow5_close(from) == 0);
ASSERT(fclose(to) == 0);
return EXIT_SUCCESS;
}
int slow5_add_rg_data_valid(void) {
struct slow5_file *s5p = slow5_open("test/data/exp/one_fast5/exp_1_default.slow5", "r");
ASSERT(s5p != NULL);
struct slow5_file *s5p_two = slow5_open("test/data/exp/two_rg/exp_default.slow5", "r");
ASSERT(s5p_two != NULL);
khash_t(slow5_s2s) *rg_two = slow5_hdr_get_data(1, s5p_two->header);
ASSERT(rg_two != NULL);
ASSERT(slow5_hdr_add_rg_data(s5p->header, rg_two) == 1);
ASSERT(s5p->header->num_read_groups == 2);
slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
slow5_hdr_print(s5p->header, SLOW5_FORMAT_ASCII, method);
ASSERT(slow5_close(s5p) == 0);
ASSERT(slow5_close(s5p_two) == 0);
return EXIT_SUCCESS;
}
int main(void) {
slow5_set_log_level(SLOW5_LOG_OFF);
slow5_set_exit_condition(SLOW5_EXIT_OFF);
struct command tests[] = {
CMD(slow5_open_valid)
CMD(slow5_get_valid)
CMD(slow5_to_blow5_uncomp)
CMD(slow5_to_blow5_zlib)
CMD(slow5_add_rg_data_valid)
};
return RUN_TESTS(tests);
}
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