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 stderr redirect
kstring_t res = { 0, 0, NULL };
FILE* orig_stderr = fdopen(dup(STDERR_FILENO), "a"); // Save stderr
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", stderr); // Redirect stderr to pipe
bam_translate(b, &tbl1);
fclose(stderr);
if (verbose) printf("END RUN test 1\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
res.l = 0;
if (kgetline(&res, (kgets_func *)fgets, check) < 0 &&
(feof(check) || res.l == 0) ) {
++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", stderr); // Redirect stderr to pipe
bam_translate(b, &tbl2);
fclose(stderr);
if (verbose) printf("END RUN test 2\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
res.l = 0;
if (kgetline(&res, (kgets_func *)fgets, check) < 0 &&
(feof(check) || res.l == 0) ) {
++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", stderr); // Redirect stderr to pipe
bam_translate(b, &tbl3);
fclose(stderr);
if (verbose) printf("END RUN test 3\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
res.l = 0;
if (kgetline(&res, (kgets_func *)fgets, check) < 0 &&
(feof(check) || res.l == 0)) {
++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", stderr); // Redirect stderr to pipe
bam_translate(b, &tbl4);
fclose(stderr);
if (verbose) printf("END RUN test 4\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
res.l = 0;
if (kgetline(&res, (kgets_func *)fgets, check) >= 0 &&
strcmp("[bam_translate] RG tag \"rg4hello\" on read \"123456789\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.",res.s) == 0) {
++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", stderr); // Redirect stderr to pipe
bam_translate(b, &tbl5);
fclose(stderr);
if (verbose) printf("END RUN test 5\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
res.l = 0;
if (kgetline(&res, (kgets_func *)fgets, check) >= 0 &&
strcmp("[bam_translate] PG tag \"pg5hello\" on read \"123456789\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.",res.s) == 0) {
++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", stderr); // Redirect stderr to pipe
bam_translate(b, &tbl6);
fclose(stderr);
if (verbose) printf("END RUN test 6\n");
if (verbose > 1) {
printf("b\n");
dump_read(b);
}
// check result
check = fopen(tempfname, "r");
res.l = 0;
if (kgetline(&res, (kgets_func *)fgets, check) < 0 &&
(feof(check) || res.l == 0) ) {
++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.s);
remove(tempfname);
if (failure > 0)
fprintf(orig_stderr, "%d failures %d successes\n", failure, success);
fclose(orig_stderr);
return (success == NUM_TESTS)? EXIT_SUCCESS : EXIT_FAILURE;
}
int main(int argc, char**argv)
{
// test state
int verbose = 0;
int getopt_char;
while ((getopt_char = getopt(argc, argv, "v")) != -1) {
switch (getopt_char) {
case 'v': ++verbose;
break;
default: printf("usage: test_parse_args [-v]\n\n"
" -v verbose output\n"
);
break;
}
}
// Cleanup getopt
optind = 1;
// test checkBarcodeQuality()
char *newBarcode = checkBarcodeQuality("CAGATCTG", "%#144=D@",0);
if (strcmp(newBarcode, "NNGATCTG") == 0) {
success++;
} else {
failure++;
fprintf(stderr, "checkBarcodeQuality() failed: expecting 'NNGATCTG', got '%s'\n", newBarcode);
}
// test isNoCall()
if (!isNoCall('A')) success++;
else { failure++; fprintf(stderr, "isNoCall('A') returned True\n"); }
if (isNoCall('N')) success++;
else { failure++; fprintf(stderr, "isNoCall('N') returned False\n"); }
if (isNoCall('n')) success++;
else { failure++; fprintf(stderr, "isNoCall('n') returned False\n"); }
if (isNoCall('.')) success++;
else { failure++; fprintf(stderr, "isNoCall('.') returned False\n"); }
// test noCalls()
test_noCalls("ABC",0);
test_noCalls("ABCN",1);
test_noCalls("NABCN",2);
// test countMismatches()
test_countMismatches("ABC","AXC",1);
test_countMismatches("ABC","XYZ",3);
test_countMismatches("ABC","ABC",0);
test_countMismatches("ABCNXYZ","ABCxXYZ",0);
test_countMismatches("ABCiXYZ","ABCNXYZ",0);
test_countMismatches("NBCiXYZ",".BCNXYz",1);
test_countMismatches("AGCACGTT","AxCACGTTXXXXXX",1);
//
// Now test the actual decoding
//
// minimal options
int argc_1;
char** argv_1;
setup_test_1(&argc_1, &argv_1);
main_decode(argc_1-1, argv_1+1);
int result = system("diff test/decode/out/xxx.sam test/decode/out/6383_9_nosplit_nochange.sam");
if (result) {
fprintf(stderr, "test 1 failed\n");
failure++;
} else {
success++;
}
// --convert_low_quality option
int argc_2;
char** argv_2;
setup_test_2(&argc_2, &argv_2);
main_decode(argc_2-1, argv_2+1);
result = system("diff test/decode/out/xxx.sam test/decode/out/6383_8_nosplitN.sam");
if (result) {
fprintf(stderr, "test 2 failed\n");
failure++;
} else {
success++;
}
printf("decode tests: %s\n", failure ? "FAILED" : "Passed");
return failure ? EXIT_FAILURE : EXIT_SUCCESS;
}
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 = 2;
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:
printf(
"usage: test_filter_header_rg [-v]\n\n"
" -v verbose output\n"
);
break;
}
}
// Setup pysamerr redirect
kstring_t res = { 0, 0, NULL };
FILE* orig_pysamerr = fdopen(dup(STDERR_FILENO), "a"); // Save pysamerr
char* tempfname = (optind < argc)? argv[optind] : "test_count_rg.tmp";
FILE* check = NULL;
// setup
if (verbose) printf("BEGIN test 1\n"); // test eliminating a tag that isn't there
bam_hdr_t* hdr1;
const char* id_to_keep_1 = "1#2.3";
setup_test_1(&hdr1);
if (verbose > 1) {
printf("hdr1\n");
dump_hdr(hdr1);
}
if (verbose) printf("RUN test 1\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bool result_1 = filter_header_rg(hdr1, id_to_keep_1);
fclose(pysamerr);
if (verbose) printf("END RUN test 1\n");
if (verbose > 1) {
printf("hdr1\n");
dump_hdr(hdr1);
}
// check result
res.l = 0;
check = fopen(tempfname, "r");
if ( result_1
&& check_test_1(hdr1)
&& kgetline(&res, (kgets_func *)fgets, check) < 0
&& (feof(check) || res.l == 0)) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 1\n");
}
fclose(check);
// teardown
bam_hdr_destroy(hdr1);
if (verbose) printf("END test 1\n");
if (verbose) printf("BEGIN test 2\n"); // test eliminating a tag that is there
bam_hdr_t* hdr2;
const char* id_to_keep_2 = "fish";
setup_test_2(&hdr2);
if (verbose > 1) {
printf("hdr2\n");
dump_hdr(hdr2);
}
if (verbose) printf("RUN test 2\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
bool result_2 = filter_header_rg(hdr2, id_to_keep_2);
fclose(pysamerr);
if (verbose) printf("END RUN test 2\n");
if (verbose > 1) {
printf("hdr2\n");
dump_hdr(hdr2);
}
// check result
res.l = 0;
check = fopen(tempfname, "r");
if ( result_2
&& check_test_2(hdr2)
&& kgetline(&res, (kgets_func *)fgets, check) < 0
&& (feof(check) || res.l == 0)) {
++success;
} else {
++failure;
if (verbose) printf("FAIL test 2\n");
}
fclose(check);
// teardown
bam_hdr_destroy(hdr2);
if (verbose) printf("END test 2\n");
// Cleanup
free(res.s);
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;
}
