int samtools_test_trans_tbl_init_main(int argc, char**argv)
{
const int NUM_TESTS = 6;
int verbose = 0;
int success = 0;
int failure = 0;
int getopt_char;
while ((getopt_char = getopt(argc, argv, "v")) != -1) {
switch (getopt_char) {
case 'v':
++verbose;
break;
default:
break;
}
}
// Set the seed to a fixed value so that calls to lrand48 within functions return predictable values
const long GIMMICK_SEED = 0x1234330e;
srand48(GIMMICK_SEED);
bam_hdr_t* out;
bam_hdr_t* translate;
if (verbose) fprintf(pysam_stdout, "BEGIN test 1\n");
// setup
trans_tbl_t tbl_1;
merged_header_t *merged_hdr = init_merged_header();
translate = setup_test_1(merged_hdr);
assert(translate);
// test
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 1\n");
trans_tbl_init(merged_hdr, translate, &tbl_1, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 1\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_1(translate, out, &tbl_1)) {
if (verbose) fprintf(pysam_stdout, "Test 1 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 1 : FAIL\n");
fprintf(pysam_stderr, "Test 1 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_1);
if (verbose) fprintf(pysam_stdout, "END test 1\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 2\n");
// reinit
trans_tbl_t tbl_2;
merged_hdr = init_merged_header();
translate = setup_test_2(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 2\n");
trans_tbl_init(merged_hdr, translate, &tbl_2, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 2\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_2(translate, out, &tbl_2)) {
if (verbose) fprintf(pysam_stdout, "Test 2 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 2 : FAIL\n");
fprintf(pysam_stderr, "Test 2 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_2);
if (verbose) fprintf(pysam_stdout, "END test 2\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 3\n");
// reinit
trans_tbl_t tbl_3;
merged_hdr = init_merged_header();
translate = setup_test_3(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 3\n");
trans_tbl_init(merged_hdr, translate, &tbl_3, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 3\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_3(translate, out, &tbl_3)) {
if (verbose) fprintf(pysam_stdout, "Test 3 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 3 : FAIL\n");
fprintf(pysam_stderr, "Test 3 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_3);
if (verbose) fprintf(pysam_stdout, "END test 3\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 4\n");
// reinit
trans_tbl_t tbl_4;
merged_hdr = init_merged_header();
translate = setup_test_4(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 4\n");
trans_tbl_init(merged_hdr, translate, &tbl_4, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 4\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_4(translate, out, &tbl_4)) {
if (verbose) fprintf(pysam_stdout, "Test 4 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 4 : FAIL\n");
fprintf(pysam_stderr, "Test 4 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_4);
if (verbose) fprintf(pysam_stdout, "END test 4\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 5\n");
// reinit
trans_tbl_t tbl_5;
merged_hdr = init_merged_header();
translate = setup_test_5(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 5\n");
trans_tbl_init(merged_hdr, translate, &tbl_5, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 5\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_5(translate, out, &tbl_5)) {
if (verbose) fprintf(pysam_stdout, "Test 5 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 5 : FAIL\n");
fprintf(pysam_stderr, "Test 5 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_5);
if (verbose) fprintf(pysam_stdout, "END test 5\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 6\n");
// reinit
trans_tbl_t tbl_6;
merged_hdr = init_merged_header();
translate = setup_test_6(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 6\n");
trans_tbl_init(merged_hdr, translate, &tbl_6, false, false, true, "filename");
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 6\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_6(translate, out, &tbl_6)) {
if (verbose) fprintf(pysam_stdout, "Test 6 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 6 : FAIL\n");
fprintf(pysam_stderr, "Test 6 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_6);
if (verbose) fprintf(pysam_stdout, "END test 6\n");
if (success == NUM_TESTS) {
return 0;
} else {
fprintf(pysam_stderr, "%d failures %d successes\n", failure, success);
return 1;
}
}
int main(int argc, char**argv)
{
// test state
const int NUM_TESTS = 6;
int verbose = 0;
int success = 0;
int failure = 0;
int getopt_char;
while ((getopt_char = getopt(argc, argv, "v")) != -1) {
switch (getopt_char) {
case 'v':
++verbose;
break;
default:
break;
}
}
bam1_t* b;
// Setup pysamerr redirect
size_t len = 0;
char* res = NULL;
FILE* orig_pysamerr = fdopen(dup(STDERR_FILENO), "a"); // Save pysamerr
char* tempfname = (optind < argc)? argv[optind] : "test_bam_translate.tmp";
FILE* check = NULL;
// setup
if (verbose) printf("BEGIN test 1\n"); // TID test
trans_tbl_t tbl1;
setup_test_1(&b,&tbl1);
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
if (verbose) printf("RUN test 1\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bam_translate(b, &tbl1);
fclose(pysamerr);
if (verbose) printf("END RUN test 1\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
if ( (getline(&res, &len, check) == -1 ) &&
(feof(check) || (res && !strcmp("",res))) ) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 1\n");
}
fclose(check);
// teardown
bam_destroy1(b);
trans_tbl_destroy(&tbl1);
if (verbose) printf("END test 1\n");
// setup
if (verbose) printf("BEGIN test 2\n"); // RG exists and translate test
trans_tbl_t tbl2;
setup_test_2(&b,&tbl2);
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
if (verbose) printf("RUN test 2\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bam_translate(b, &tbl2);
fclose(pysamerr);
if (verbose) printf("END RUN test 2\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
if ( (getline(&res, &len, check) == -1 ) &&
(feof(check) || (res && !strcmp("",res))) ) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 2\n");
}
fclose(check);
// teardown
bam_destroy1(b);
trans_tbl_destroy(&tbl2);
if (verbose) printf("END test 2\n");
if (verbose) printf("BEGIN test 3\n"); // PG exists and translate test
// setup
trans_tbl_t tbl3;
setup_test_3(&b,&tbl3);
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
if (verbose) printf("RUN test 3\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bam_translate(b, &tbl3);
fclose(pysamerr);
if (verbose) printf("END RUN test 3\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
if ( (getline(&res, &len, check) == -1 ) &&
(feof(check) || (res && !strcmp("",res)))) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 3\n");
}
fclose(check);
// teardown
bam_destroy1(b);
trans_tbl_destroy(&tbl3);
if (verbose) printf("END test 3\n");
if (verbose) printf("BEGIN test 4\n"); // RG test non-existent
// setup
trans_tbl_t tbl4;
setup_test_4(&b,&tbl4);
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
if (verbose) printf("RUN test 4\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bam_translate(b, &tbl4);
fclose(pysamerr);
if (verbose) printf("END RUN test 4\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
if ( (getline(&res, &len, check) != -1 ) &&
res && !strcmp("[bam_translate] RG tag \"rg4hello\" on read \"123456789\" encountered with no corresponding entry in header, tag lost\n",res)) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 4\n");
}
fclose(check);
// teardown
bam_destroy1(b);
trans_tbl_destroy(&tbl4);
if (verbose) printf("END test 4\n");
if (verbose) printf("BEGIN test 5\n"); // PG test non-existent
// setup
trans_tbl_t tbl5;
setup_test_5(&b,&tbl5);
if (verbose > 1) {
printf("b\n");
dump_read(b);
printf("RUN test 5\n");
}
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bam_translate(b, &tbl5);
fclose(pysamerr);
if (verbose) printf("END RUN test 5\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
if ( (getline(&res, &len, check) != -1 ) &&
res && !strcmp("[bam_translate] PG tag \"pg5hello\" on read \"123456789\" encountered with no corresponding entry in header, tag lost\n",res)) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 5\n");
}
fclose(check);
// teardown
bam_destroy1(b);
trans_tbl_destroy(&tbl5);
if (verbose) printf("END test 5\n");
if (verbose) printf("BEGIN test 6\n"); // RG and PG exists and translate test
// setup
trans_tbl_t tbl6;
setup_test_6(&b,&tbl6);
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
if (verbose) printf("RUN test 6\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bam_translate(b, &tbl6);
fclose(pysamerr);
if (verbose) printf("END RUN test 6\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
if ( (getline(&res, &len, check) == -1 ) &&
(feof(check) || (res && !strcmp("",res))) ) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 6\n");
}
fclose(check);
// teardown
bam_destroy1(b);
trans_tbl_destroy(&tbl6);
if (verbose) printf("END test 6\n");
// Cleanup
free(res);
remove(tempfname);
if (failure > 0)
fprintf(orig_pysamerr, "%d failures %d successes\n", failure, success);
fclose(orig_pysamerr);
return (success == NUM_TESTS)? EXIT_SUCCESS : EXIT_FAILURE;
}
