/*
* Main code
*/
static int seqchksum(opts_t* opts)
{
int retcode = 0;
BAMit_t *bam_in = NULL;
bam1_t *rec = NULL;
/*
* Open input BAM file
*/
bam_in = BAMit_open(opts->input_name, 'r', opts->input_fmt, 0, NULL);
if (!bam_in) return 1;
// Initialise results structure
chksum_results_t *results = chksum_init_results(opts->hash);
// Read and process each record in the input BAM
while ( (rec = BAMit_next(bam_in)) ) {
// ignore secondary and supplementary records
if (!(rec->core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY))) {
if (seqchksum_processRecord(rec, opts->hash, results)) { retcode = 1; break; }
}
}
hFILE *f = hdopen(fileno(stdout),"w");
if (!f) die("Can't open stdout");
chksum_print_results(f, results);
if (hclose(f)) die("Can't close stdout");
// tidy up after us
BAMit_free(bam_in);
chksum_free_results(results);
return retcode;
}
static hFILE *hopen_fd_stdinout(const char *mode)
{
int fd = (strchr(mode, 'r') != NULL)? STDIN_FILENO : STDOUT_FILENO;
#if defined HAVE_SETMODE && defined O_BINARY
if (setmode(fd, O_BINARY) < 0) return NULL;
#endif
return hdopen(fd, mode);
}
htsFile * sam_popen(char *cmd) {
htsFile *fp = (htsFile*)calloc(1, sizeof(htsFile));
int fid, fid2;
assert(fp);
popen_fd = popen(cmd, "r"); //Global
fid = fileno(popen_fd);
fid2 = dup(fid); //otherwise, the file descriptor is closed by zlib and pclose() won't work!!
if(popen_fd == NULL) return 0;
if(fp == NULL) return 0;
hFILE *hfile = hdopen(fid2, "r"); //does this exist?
if(hfile == NULL) return 0;
fp->is_be = ed_is_big();
BGZF *gzfp = bgzf_hopen(hfile, "r");
fp->fp.voidp = ks_init(gzfp);
fp->format.format = sam;
return(fp);
}
static hFILE *hopen_fd_stdinout(const char *mode)
{
int fd = (strchr(mode, 'r') != NULL)? STDIN_FILENO : STDOUT_FILENO;
// TODO Set binary mode (for Windows)
return hdopen(fd, mode);
}
static htsFile *dup_stdout(const char *mode)
{
int fd = dup(STDOUT_FILENO);
hFILE *hfp = (fd >= 0)? hdopen(fd, mode) : NULL;
return hfp? hts_hopen(hfp, "-", mode) : NULL;
}
/*
* Find all disks through /sys/block.
*/
static char *list_disks(DIR* blk, unsigned int* flags)
{
struct dirent *d;
while ((d = readdir(blk))) {
(*flags) = 0;
if (d->d_name[1] == 'd' && (d->d_name[0] == 'h' || d->d_name[0] == 's')) {
char buf[NAME_MAX+1], lnk[NAME_MAX+1], *ptr;
FILE *fp;
int ret;
fp = hdopen(SYS_BLK "/%s/removable", d->d_name);
if (0 == (long)fp || -1 == (long)fp) {
if (-1 == (long)fp)
goto empty; /* error */
continue; /* no entry `removable' */
}
ret = getc(fp);
fclose(fp);
if (ret != '0')
(*flags) |= DISK_REMOVABLE;
if (d->d_name[0] == 'h') {
if ((*flags) & DISK_REMOVABLE)
continue; /* not a hard disk */
(*flags) |= DISK_IS_IDE;
if ((ret = flush_cache_ext(d->d_name))) {
if (ret < 0)
goto empty;
(*flags) |= DISK_EXTFLUSH;
}
break; /* old IDE disk not managed by kernel, out here */
}
ret = snprintf(buf, sizeof(buf), SYS_BLK "/%s/device", d->d_name);
if ((ret >= (int)sizeof(buf)) || (ret < 0))
goto empty; /* error */
ret = readlink(buf, lnk, sizeof(lnk));
if (ret >= (int)sizeof(lnk))
goto empty; /* error */
if (ret < 0) {
if (errno != ENOENT)
goto empty; /* error */
continue; /* no entry `device' */
}
lnk[ret] = '\0';
ptr = basename(lnk);
if (!ptr || !*ptr)
continue; /* should not happen */
fp = hdopen(SYS_CLASS "/%s/manage_start_stop", ptr);
if (0 == (long)fp || -1 == (long)fp) {
if (-1 == (long)fp)
goto empty; /* error */
} else {
ret = getc(fp);
fclose(fp);
if (ret != '0') {
(*flags) |= DISK_MANAGED;
continue;
}
}
fp = hdopen(SYS_BLK "/%s/device/vendor", d->d_name);
if (0 == (long)fp || -1 == (long)fp) {
if (-1 == (long)fp)
goto empty; /* error */
continue; /* no entry `device/vendor' */
}
ptr = fgets(buf, sizeof(buf), fp);
fclose(fp);
if (ptr == (char*)0)
continue; /* should not happen */
ptr = strstrip(buf);
if (*ptr == '\0')
continue; /* should not happen */
if (strncmp(buf, "ATA", sizeof(buf)) == 0) {
if ((*flags) & DISK_REMOVABLE)
continue; /* not a hard disk */
(*flags) |= (DISK_IS_IDE|DISK_IS_SATA);
if ((ret = flush_cache_ext(d->d_name))) {
if (ret < 0)
goto empty;
(*flags) |= DISK_EXTFLUSH;
}
break; /* new SATA disk to shutdown, out here */
}
if (((*flags) & DISK_REMOVABLE) == 0)
continue; /* Seems to be a real SCSI disk */
if ((ret = flush_cache_ext(d->d_name))) {
if (ret < 0)
goto empty;
(*flags) |= DISK_EXTFLUSH;
}
break; /* Removable disk like USB stick to shutdown */
}
}
if (d == (struct dirent*)0)
goto empty;
return d->d_name;
empty:
return (char*)0;
}
/*
* Check IDE/(S)ATA hard disk identity for
* the FLUSH CACHE EXT bit set.
*/
static int flush_cache_ext(const char *device)
{
#ifndef WIN_IDENTIFY
#define WIN_IDENTIFY 0xEC
#endif
unsigned char args[4+IDBYTES];
unsigned short *id = (unsigned short*)(&args[4]);
char buf[NAME_MAX+1], *ptr;
int fd = -1, ret = 0;
FILE *fp;
fp = hdopen(SYS_BLK "/%s/size", device);
if (0 == (long)fp || -1 == (long)fp) {
if (-1 == (long)fp)
return -1; /* error */
goto out; /* no entry `size' */
}
ptr = fgets(buf, sizeof(buf), fp);
fclose(fp);
if (ptr == (char*)0)
goto out; /* should not happen */
ptr = strstrip(buf);
if (*ptr == '\0')
goto out; /* should not happen */
if ((size_t)atoll(buf) < (1<<28))
goto out; /* small disk */
ret = snprintf(buf, sizeof(buf), DEV_BASE "/%s", device);
if ((ret >= (int)sizeof(buf)) || (ret < 0))
return -1; /* error */
if ((fd = open(buf, O_RDONLY|O_NONBLOCK)) < 0)
goto out;
memset(&args[0], 0, sizeof(args));
args[0] = WIN_IDENTIFY;
args[3] = 1;
if (ioctl(fd, HDIO_DRIVE_CMD, &args))
goto out;
#ifdef WORDS_BIGENDIAN
# if 0
{
const unsigned short *end = id + IDBYTES/2;
const unsigned short *from = id;
unsigned short *to = id;
while (from < end)
*to++ = bswap_16(*from++);
}
# else
id[83] = bswap_16(id[83]);
# endif
#endif
if ((id[83] & MASK_EXT) == TEST_EXT)
ret = 1;
out:
if (fd >= 0)
close(fd);
return ret;
}