void k_debugger(regs *r,uint32 eip, uint32 cs, uint32 eflags)
{
char *line;
uint32 n;
kprintf("OpenBLT Kernel Debugger");
for(;;){
krefresh();
line = kgetline(linebuf,80);
if(!strncmp(line,"pgroup ",7)) { dumppgroup(readnum(line+7)); continue; }
if(!strncmp(line,"resource ", 9)) { dumponersrc(line+9); continue; }
if(!strcmp(line,"resources")) { dumprsrc(&resource_list); continue; }
if(!strncmp(line,"queue ",6)) { dumpqueue(readnum(line+6)); continue; }
if(!strcmp(line,"tasks")) { dumptasks(); continue; }
if(!strcmp(line,"ports")) { dumpports(); continue; }
if(!strcmp(line,"memory")) { memory_status(); continue; }
if(!strcmp(line,"trace")) { trace(r->ebp,eip); continue; }
if(!strcmp(line,"regs")) { print_regs(r,eip,cs,eflags); continue; }
if(!strncmp(line,"dump ",5)) { dump(readnum(line+5),16); continue; }
if(!strncmp(line,"aspace ",7)) { dumpaddr(readnum(line+7)); continue; }
if(!strcmp(line,"reboot")) { reboot(); }
if(!strncmp(line,"checksum ",9)) { checksum(line+9); continue; }
if(!strncmp(line,"team ",5)) { dumpteam(readnum(line+5)); continue; }
if(!strncmp(line,"find ",5)) { findpage(readnum(line+5)); continue; }
if(!strcmp(line,"teams")) { dumpteams(); continue; }
if(!strcmp(line,"exit")) break;
if(!strcmp(line,"x")) break;
if(!strcmp(line,"c")) break;
}
}
static void parse_simple(const char *fname, kstring_t *id, kstring_t *secret)
{
kstring_t text = { 0, 0, NULL };
char *s;
size_t len;
FILE *fp = expand_tilde_open(fname, "r");
if (fp == NULL) return;
while (kgetline(&text, (kgets_func *) fgets, fp) >= 0)
kputc(' ', &text);
fclose(fp);
s = text.s;
while (isspace_c(*s)) s++;
kputsn(s, len = strcspn(s, " \t"), id);
s += len;
while (isspace_c(*s)) s++;
kputsn(s, strcspn(s, " \t"), secret);
free(text.s);
}
static void parse_ini(const char *fname, const char *section, ...)
{
kstring_t line = { 0, 0, NULL };
int active = 1; // Start active, so global properties are accepted
char *s;
FILE *fp = expand_tilde_open(fname, "r");
if (fp == NULL) return;
while (line.l = 0, kgetline(&line, (kgets_func *) fgets, fp) >= 0)
if (line.s[0] == '[' && (s = strchr(line.s, ']')) != NULL) {
*s = '\0';
active = (strcmp(&line.s[1], section) == 0);
}
else if (active && (s = strpbrk(line.s, ":=")) != NULL) {
const char *key = line.s, *value = &s[1], *akey;
va_list args;
while (isspace_c(*key)) key++;
while (s > key && isspace_c(s[-1])) s--;
*s = '\0';
while (isspace_c(*value)) value++;
while (line.l > 0 && isspace_c(line.s[line.l-1]))
line.s[--line.l] = '\0';
va_start(args, section);
while ((akey = va_arg(args, const char *)) != NULL) {
kstring_t *avar = va_arg(args, kstring_t *);
if (strcmp(key, akey) == 0) { kputs(value, avar); break; }
}
va_end(args);
}
fclose(fp);
free(line.s);
}
int main(int argc, char**argv)
{
// test state
const int NUM_TESTS = 1;
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_expand_format_string [-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_expand_format_string.tmp";
FILE* check = NULL;
// setup
if (verbose) printf("BEGIN test 1\n"); // default format string test
const char* format_string_1 = "%*_%#.bam";
const char* basename_1 = "basename";
const char* rg_id_1 = "1#2.3";
const int rg_idx_1 = 4;
if (verbose > 1) {
printf("format_string:%s\n"
"basename:%s\n"
"rg_id:%s\n"
"rg_idx:%d\n", format_string_1, basename_1, rg_id_1, rg_idx_1);
}
if (verbose) printf("RUN test 1\n");
// test
xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe
char* output_1 = expand_format_string(format_string_1, basename_1, rg_id_1, rg_idx_1, NULL);
fclose(pysamerr);
if (verbose) printf("END RUN test 1\n");
if (verbose > 1) {
printf("format_string:%s\n"
"basename:%s\n"
"rg_id:%s\n"
"rg_idx:%d\n", format_string_1, basename_1, rg_id_1, rg_idx_1);
}
// check result
res.l = 0;
check = fopen(tempfname, "r");
if (output_1 != NULL && !strcmp(output_1, "basename_4.bam")
&& 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
free(output_1);
if (verbose) printf("END test 1\n");
// Cleanup test harness
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;
}
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 samtools_test_count_rg_main(int argc, char**argv)
{
// test state
const int NUM_TESTS = 1;
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:
fprintf(pysam_stdout,
"usage: test_count_rg [-v]\n\n"
" -v verbose output\n"
);
break;
}
}
// Setup pysam_stderr redirect
kstring_t res = { 0, 0, NULL };
FILE* orig_pysam_stderr = fdopen(dup(STDERR_FILENO), "a"); // Save pysam_stderr
char* tempfname = (optind < argc)? argv[optind] : "test_count_rg.tmp";
FILE* check = NULL;
// setup
if (verbose) fprintf(pysam_stdout, "BEGIN test 1\n"); // TID test
bam_hdr_t* hdr1;
size_t count;
char** output;
setup_test_1(&hdr1);
if (verbose > 1) {
fprintf(pysam_stdout, "hdr1\n");
dump_hdr(hdr1);
}
if (verbose) fprintf(pysam_stdout, "RUN test 1\n");
// test
xfreopen(tempfname, "w", pysam_stderr); // Redirect pysam_stderr to pipe
bool result_1 = count_RG(hdr1, &count, &output);
fclose(pysam_stderr);
if (verbose) fprintf(pysam_stdout, "END RUN test 1\n");
if (verbose > 1) {
fprintf(pysam_stdout, "b\n");
dump_hdr(hdr1);
}
// check result
check = fopen(tempfname, "r");
if (result_1 && count == 1 && !strcmp(output[0], "fish")
&& kgetline(&res, (kgets_func *)fgets, check) < 0
&& (feof(check) || res.l == 0)) {
++success;
} else {
++failure;
if (verbose) fprintf(pysam_stdout, "FAIL test 1\n");
}
fclose(check);
// teardown
int i;
for (i = 0; i < count; i++){
free(output[i]);
}
free(output);
bam_hdr_destroy(hdr1);
if (verbose) fprintf(pysam_stdout, "END test 1\n");
// Cleanup
free(res.s);
remove(tempfname);
if (failure > 0)
fprintf(orig_pysam_stderr, "%d failures %d successes\n", failure, success);
fclose(orig_pysam_stderr);
return (success == NUM_TESTS)? EXIT_SUCCESS : EXIT_FAILURE;
}
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;
}
