int main(int argc, char **argv)
{
static const struct option options[] = {
{ "header-only", no_argument, NULL, 'h' },
{ "no-header", no_argument, NULL, 'H' },
{ "view", no_argument, NULL, 'c' },
{ "help", no_argument, NULL, '?' },
{ NULL, 0, NULL, 0 }
};
int status = EXIT_SUCCESS;
int c, i;
while ((c = getopt_long(argc, argv, "chH", options, NULL)) >= 0)
switch (c) {
case 'c': mode = view_all; break;
case 'h': mode = view_headers; show_headers = 1; break;
case 'H': show_headers = 0; break;
case '?': usage(stdout, EXIT_SUCCESS); break;
default: usage(stderr, EXIT_FAILURE); break;
}
if (optind == argc) usage(stderr, EXIT_FAILURE);
for (i = optind; i < argc; i++) {
htsFormat fmt;
hFILE *fp = hopen(argv[i], "r");
if (fp == NULL) {
fprintf(stderr, "htsfile: can't open \"%s\": %s\n", argv[i], strerror(errno));
status = EXIT_FAILURE;
continue;
}
if (hts_detect_format(fp, &fmt) < 0) {
fprintf(stderr, "htsfile: detecting \"%s\" format failed: %s\n", argv[i], strerror(errno));
hclose_abruptly(fp);
status = EXIT_FAILURE;
continue;
}
if (mode == identify) {
printf("%s:\t%s\n", argv[i], hts_format_description(&fmt));
}
else
switch (fmt.category) {
case sequence_data: if (view_sam(fp, argv[i])) fp = NULL; break;
case variant_data: if (view_vcf(fp, argv[i])) fp = NULL; break;
default:
fprintf(stderr, "htsfile: can't view %s: unknown format\n", argv[i]);
status = EXIT_FAILURE;
break;
}
if (fp && hclose(fp) < 0) {
fprintf(stderr, "htsfile: closing %s failed\n", argv[i]);
status = EXIT_FAILURE;
}
}
return status;
}
// Loads the contents of filename to produced a read-only, in memory,
// immobile hfile. fp is the already opened file. We always close this
// input fp, irrespective of whether we error or whether we return a new
// immobile hfile.
static hFILE *hpreload(hFILE *fp) {
hFILE *mem_fp;
char *buf = NULL;
off_t buf_sz = 0, buf_a = 0, buf_inc = 8192, len;
for (;;) {
if (buf_a - buf_sz < 5000) {
buf_a += buf_inc;
char *t = realloc(buf, buf_a);
if (!t) goto err;
buf = t;
if (buf_inc < 1000000) buf_inc *= 1.3;
}
len = hread(fp, buf+buf_sz, buf_a-buf_sz);
if (len > 0)
buf_sz += len;
else
break;
}
if (len < 0) goto err;
mem_fp = hfile_init_fixed(sizeof(hFILE), "r", buf, buf_sz, buf_a);
if (!mem_fp) goto err;
mem_fp->backend = &mem_backend;
if (hclose(fp) < 0) {
hclose_abruptly(mem_fp);
goto err;
}
return mem_fp;
err:
free(buf);
hclose_abruptly(fp);
return NULL;
}
mFILE *find_file_url(char *file, char *url) {
char buf[8192], *cp;
mFILE *mf = NULL;
int maxlen = 8190 - strlen(file), len;
hFILE *hf;
/* Expand %s for the trace name */
for (cp = buf; *url && cp - buf < maxlen; url++) {
if (*url == '%' && *(url+1) == 's') {
url++;
cp += strlen(strcpy(cp, file));
} else {
*cp++ = *url;
}
}
*cp++ = 0;
if (!(hf = hopen(buf, "r")))
return NULL;
if (NULL == (mf = mfcreate(NULL, 0)))
return NULL;
while ((len = hread(hf, buf, 8192)) > 0) {
if (mfwrite(buf, len, 1, mf) <= 0) {
hclose_abruptly(hf);
mfdestroy(mf);
return NULL;
}
}
if (hclose(hf) < 0 || len < 0) {
mfdestroy(mf);
return NULL;
}
mrewind(mf);
return mf;
}
