#include "unit_test.h"
#include <slow5/slow5.h>


int slow5_to_blow5_uncomp(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_default.slow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/slow5_to_blow5_uncomp.blow5", "w");
    ASSERT(to != NULL);

    /*
    ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_BINARY, SLOW5_COMPRESS_NONE) != -1);

    struct slow5_rec *read = NULL;
    int ret;
    while ((ret = slow5_get_next(&read, from)) == 0) {
        ASSERT(slow5_rec_fwrite(to, read, SLOW5_FORMAT_BINARY, NULL) != -1);
    }
    slow5_rec_free(read);
    ASSERT(ret == -2);

    ASSERT(slow5_eof_fwrite(to) != -1);
    */
    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    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/one_fast5/exp_1_default.slow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/slow5_to_blow5_gzip.blow5", "w");
    ASSERT(to != NULL);

    /*
    ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_BINARY, SLOW5_COMPRESS_ZLIB) != -1);

    struct slow5_rec *read = NULL;
    int ret;
    struct slow5_press *zlib = slow5_press_init(SLOW5_COMPRESS_ZLIB);
    ASSERT(zlib != NULL);
    while ((ret = slow5_get_next(&read, from)) == 0) {
        ASSERT(slow5_rec_fwrite(to, read, SLOW5_FORMAT_BINARY, zlib) != -1);
    }
    slow5_rec_free(read);
    ASSERT(ret == -2);

    ASSERT(slow5_eof_fwrite(to) != -1);

    slow5_press_free(zlib);
    */
    slow5_press_method_t method = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_uncomp_to_slow5(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_default.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_uncomp_to_slow5.slow5", "w");
    ASSERT(to != NULL);

    /*
    ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_ASCII, SLOW5_COMPRESS_NONE) != -1);

    struct slow5_rec *read = NULL;
    int ret;
    while ((ret = slow5_get_next(&read, from)) == 0) {
        ASSERT(slow5_rec_fwrite(to, read, SLOW5_FORMAT_ASCII, NULL) != -1);
    }
    slow5_rec_free(read);
    ASSERT(ret == -2);
    */

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_ASCII, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_zlib_to_slow5(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_default_gzip.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_gzip_to_slow5.slow5", "w");
    ASSERT(to != NULL);

    /*
    ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_ASCII, SLOW5_COMPRESS_NONE) != -1);

    struct slow5_rec *read = NULL;
    int ret;
    while ((ret = slow5_get_next(&read, from)) == 0) {
        ASSERT(slow5_rec_fwrite(to, read, SLOW5_FORMAT_ASCII, NULL) != -1);
    }
    slow5_rec_free(read);
    ASSERT(ret == -2);
    */
    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_ASCII, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_zlib_to_blow5_uncomp(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_default_gzip.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_gzip_to_blow5_uncomp.blow5", "w");
    ASSERT(to != NULL);

    /*
    ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_BINARY, SLOW5_COMPRESS_NONE) != -1);

    struct slow5_rec *read = NULL;
    int ret;
    while ((ret = slow5_get_next(&read, from)) == 0) {
        ASSERT(slow5_rec_fwrite(to, read, SLOW5_FORMAT_BINARY, NULL) != -1);
    }
    slow5_rec_free(read);
    ASSERT(ret == -2);

    ASSERT(slow5_eof_fwrite(to) != -1);
    */
    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_uncomp_to_blow5_zlib(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_default.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_uncomp_to_blow5_gzip.blow5", "w");
    ASSERT(to != NULL);

    /*
    ASSERT(slow5_hdr_fwrite(to, from->header, SLOW5_FORMAT_BINARY, SLOW5_COMPRESS_ZLIB) != -1);

    struct slow5_rec *read = NULL;
    int ret;
    struct slow5_press *zlib = slow5_press_init(SLOW5_COMPRESS_ZLIB);
    ASSERT(zlib != NULL);
    while ((ret = slow5_get_next(&read, from)) == 0) {
        ASSERT(slow5_rec_fwrite(to, read, SLOW5_FORMAT_BINARY, zlib) != -1);
    }
    slow5_rec_free(read);
    ASSERT(ret == -2);

    ASSERT(slow5_eof_fwrite(to) != -1);

    slow5_press_free(zlib);
    */
    slow5_press_method_t method = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int slow5_to_blow5_uncomp_lossless(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_lossless.slow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/slow5_to_blow5_uncomp_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int slow5_to_blow5_zlib_lossless(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_lossless.slow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/slow5_to_blow5_gzip_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_uncomp_to_slow5_lossless(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_lossless.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_uncomp_to_slow5_lossless.slow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_ASCII, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_zlib_to_slow5_lossless(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_lossless_gzip.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_gzip_to_slow5_lossless.slow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_ASCII, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_zlib_to_blow5_uncomp_lossless(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_lossless_gzip.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_gzip_to_blow5_uncomp_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_uncomp_to_blow5_zlib_lossless(void) {
    struct slow5_file *from = slow5_open("test/data/exp/one_fast5/exp_1_lossless.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/one_fast5/blow5_uncomp_to_blow5_gzip_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int slow5_to_blow5_uncomp_lossless_aux_array(void) {
    struct slow5_file *from = slow5_open("test/data/exp/aux_array/exp_lossless.slow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/aux_array/slow5_to_blow5_uncomp_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int slow5_to_blow5_zlib_lossless_aux_array(void) {
    struct slow5_file *from = slow5_open("test/data/exp/aux_array/exp_lossless.slow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/aux_array/slow5_to_blow5_gzip_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_uncomp_to_slow5_lossless_aux_array(void) {
    struct slow5_file *from = slow5_open("test/data/exp/aux_array/exp_lossless.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/aux_array/blow5_uncomp_to_slow5_lossless.slow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_ASCII, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_zlib_to_slow5_lossless_aux_array(void) {
    struct slow5_file *from = slow5_open("test/data/exp/aux_array/exp_lossless_gzip.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/aux_array/blow5_gzip_to_slow5_lossless.slow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_ASCII, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_zlib_to_blow5_uncomp_lossless_aux_array(void) {
    struct slow5_file *from = slow5_open("test/data/exp/aux_array/exp_lossless_gzip.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/aux_array/blow5_gzip_to_blow5_uncomp_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 0);

    return EXIT_SUCCESS;
}

int blow5_uncomp_to_blow5_zlib_lossless_aux_array(void) {
    struct slow5_file *from = slow5_open("test/data/exp/aux_array/exp_lossless.blow5", "r");
    ASSERT(from != NULL);

    FILE *to = fopen("test/data/out/aux_array/blow5_uncomp_to_blow5_gzip_lossless.blow5", "w");
    ASSERT(to != NULL);

    slow5_press_method_t method = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_NONE};
    ASSERT(slow5_convert(from, to, SLOW5_FORMAT_BINARY, method) == 0)

    ASSERT(slow5_close(from) == 0);
    ASSERT(fclose(to) == 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_to_blow5_uncomp)
        CMD(slow5_to_blow5_zlib)
        CMD(blow5_uncomp_to_slow5)
        CMD(blow5_zlib_to_slow5)
        CMD(blow5_zlib_to_blow5_uncomp)
        CMD(blow5_uncomp_to_blow5_zlib)

        CMD(slow5_to_blow5_uncomp_lossless)
        CMD(slow5_to_blow5_zlib_lossless)
        CMD(blow5_uncomp_to_slow5_lossless)
        CMD(blow5_zlib_to_slow5_lossless)
        CMD(blow5_zlib_to_blow5_uncomp_lossless)
        CMD(blow5_uncomp_to_blow5_zlib_lossless)

        CMD(slow5_to_blow5_uncomp_lossless_aux_array)
        CMD(slow5_to_blow5_zlib_lossless_aux_array)
        CMD(blow5_uncomp_to_slow5_lossless_aux_array)
        CMD(blow5_zlib_to_slow5_lossless_aux_array)
        CMD(blow5_zlib_to_blow5_uncomp_lossless_aux_array)
        CMD(blow5_uncomp_to_blow5_zlib_lossless_aux_array)
    };

    return RUN_TESTS(tests);
}