static void *read_det_cov(void *vd)
{
int i,err;
FILE *fptr;
string *s;
tokens *tok;
void *tbuf;
char *p,*p1,cc,*fname;
struct contig *c,*ctg;
struct tdc_par *tp;
count *ct,ct1,ct2;
struct lk_compress *lkc;
u_int32_t x;
tp=vd;
ctg=tp->ctg;
lkc=tp->lkc;
while((fname=get_input_file())) {
s=0;
tok=0;
tbuf=0;
err=0;
fptr=open_readfile(fname,&i,lkc);
if(!fptr) return 0;
printf("Reading detailed coverage file '%s'\n",fname);
c=0;
ct=0;
x=0;
while(!err) {
s=fget_string(fptr,s,&tbuf);
if(!s->len) break;
tok=tokenize(get_cstring(s),'\t',tok);
if(tok->n_tok==2) {
p=tok->toks[0];
if(*p=='>') {
if(!c || strcmp(c->name,p+1)) {
HASH_FIND_STR(ctg,p+1,c);
}
if(c) {
p=tok->toks[1];
x=strtoul(p,&p1,10)-1;
if(p==p1 || *p1) {
err=10;
fprintf(stderr,"(a) Bad file format\n");
}
ct=c->counts;
}
}
} else if(c) {
if(tok->n_tok!=1) {
fprintf(stderr,"(b) Bad file format\n");
err=-1;
}
p=tok->toks[0];
while(x<c->size && (cc=*p++)) {
if(cc>=33 && cc<=125) {
cc-=33;
ct1=(count)cc;
} else if(cc==126) {
ct1=(count)strtoul(p,&p1,16);
p=p1+1;
} else {
fprintf(stderr,"(c) Bad file format (%d) '%s'\n",cc,tok->toks[0]);
err=-1;
}
if(!err) {
pthread_mutex_lock(&c->mut);
ct2=ct[x];
if(ct2<MAX_COUNT) {
if(MAX_COUNT-ct2<ct1) ct[x]=MAX_COUNT;
else ct[x]=ct2+ct1;
}
pthread_mutex_unlock(&c->mut);
x++;
}
}
}
}
fclose(fptr);
if(s) free_string(s);
if(tok) free_tokens(tok);
if(tbuf) free_fget_buffer(&tbuf);
signal(SIGCHLD,SIG_DFL);
while(waitpid(-1,&i,WNOHANG)>0);
}
return 0;
}
void get_input_file(int& optind, int argc, char** argv, function<void(istream&)> callback) {
// Just combine the two operations below in the way they're supposed to be used together
get_input_file(get_input_file_name(optind, argc, argv), callback);
}
int run_test(int argc, char **argv,
unsigned int test_num, Test *test, char **fifos) {
char *in_file = NULL;
int in_fd = -1;
char **out_files = NULL;
int *out_fds = NULL;
int fifo_fds[MAX_READERS];
pid_t child = 0;
int i, res = 0, wres;
/* Write some information about the test to the log */
print_test_info(test_num, test);
assert(test->npipes <= MAX_READERS);
for (i = 0; i < MAX_READERS; i++) fifo_fds[i] = -1;
/* Open any output files needed */
if (test->nfiles > 0) {
if (0 != get_output_files(test, &out_files, &out_fds)) goto BAIL;
}
/* Create an input file if the test needs one */
if (test->in_type == IN_FILE) {
if (NULL == (in_file = get_input_file(test))) goto BAIL;
}
/* Start the program under test */
child = start_prog(argc, argv, test, &in_fd, in_file, fifos, out_files);
if (child < 0) goto BAIL;
/* Open any named pipes required */
if (test->npipes > 0) {
if (0 != open_fifos(test->npipes, fifos, fifo_fds)) goto BAIL;
}
if (test->npipes) {
/* reading from pipes, run the full poll loop */
res = run_poll_loop(test, in_fd, fifo_fds, fifos);
/* Close any pipes that are still open */
if (0 != close_fifos(test->npipes, fifos, fifo_fds)) {
res = -1;
}
} else if (test->in_type == IN_PIPE || test->in_type == IN_SLOW_PIPE) {
/* only sending to a pipe, so just shove the data down it */
size_t offset = 0;
if (gen_data("pipe", in_fd, test->in_len, &offset, 0, 0) != test->in_len) {
res = -1;
}
if (0 != close(in_fd)) {
perror("Closing pipe");
res = -1;
}
}
/* Wait for the program to finish and check the exit status */
wres = wait_child(child);
if (-99 == wres) goto BAIL;
if (wres < 0) res = -1;
/* Check the contents of any regular files that were created */
if (test->nfiles > 0) {
if (0 != check_output_files(test, out_fds, out_files)) res = -1;
}
/* Clean up */
if (NULL != in_file) remove_files(&in_file, 1);
if (test->nfiles > 0) {
remove_files(out_files, test->nfiles);
}
return res;
BAIL:
/* Something went wrong, clean up and return 99 */
if (NULL != in_file) remove_files(&in_file, 1);
if (test->nfiles > 0 && NULL != out_files) {
remove_files(out_files, test->nfiles);
}
if (test->npipes > 0) {
close_fifos(test->npipes, fifos, fifo_fds);
}
return 99;
}
