void do_sequential_read()
{
int fd;
char *addr;
size_t wsize;
char mypath[PATH_LEN];
if (myrank == 0) {
gio_dbg("Reade: scale: %s, size: %lu", scale, data_size);
}
get_rank_path(mypath);
addr = (char*)gio_malloc(data_size);
fd = gio_open(mypath, O_WRONLY | O_CREAT, 0);
if (fd < 0) {
gio_err("File open failed (%s:%s:%d)", __FILE__, __func__, __LINE__);
}
wsize = gio_write(mypath, fd, addr, data_size);
if (wsize != data_size) {
gio_err("Inputu wirte size is %f, but only %f bytes are written (%s:%s:%d)", data_size, wsize,__FILE__, __func__, __LINE__);
}
gio_close(mypath, fd);
return;
}
/* Debug functions that don't use curses - handy for valgrind testing */
static void test_mode(GapIO *io, contig_t **c, int xpos) {
rangec_t *r;
int nr, i;
r = contig_seqs_in_range(io, c, xpos, xpos+79, CSIR_SORT_BY_X, &nr);
for (i = 0; i < nr; i++) {
seq_t *s = get_seq(io, r[i].rec);
printf("%.*s: range %d..%d seq %d+%d st=%d en=%d %.*s\n",
s->name_len, s->name,
r[i].start, r[i].end,
s->pos, s->len,
s->left, s->right,
ABS(s->len), s->seq);
s = dup_seq(s);
complement_seq_t(s);
printf("%.*s: range %d..%d seq %d+%d st=%d en=%d %.*s\n",
s->name_len, s->name,
r[i].start, r[i].end,
s->pos, s->len,
s->left, s->right,
ABS(s->len), s->seq);
}
gio_close(io);
system("ps lx | grep g_iotest | grep -v grep");
exit(0);
}
static void test_mode2(GapIO *io, contig_t **c, int xpos) {
rangec_t *r;
int nr, i, bpv = 256;
char cons[CONS_LEN+1];
track_t *t;
// r = contig_seqs_in_range(io, c, xpos, xpos+CONS_LEN, &nr);
// qsort(r, nr, sizeof(*r), sort_range);
// calc_cons(io, r, nr, xpos, CONS_LEN, cons);
// printf("Cons=%.*s\n", CONS_LEN, cons);
t = contig_get_track(io, c, xpos, xpos+CONS_LEN, TRACK_READ_DEPTH, bpv);
for (i = 0; i < CONS_LEN/bpv; i++) {
printf("%d\t%d\n", i*bpv, arr(int, t->data, i));
}
cache_flush(io);
gio_close(io);
exit(0);
}
static void benchmark(GapIO *io, contig_t **c) {
int i;
char cons[10000];
srandom(0);
fprintf(stderr, "=== Benchmarking ===\n");
for (i = 0; i < 1000; i++) {
int xpos = random() % 2000000;
int size = random() % 1000;
int nr;
rangec_t *r;
r = contig_seqs_in_range(io, c, xpos, xpos+size, 0, &nr);
calc_cons(io, r, nr, xpos, size, cons);
printf("%.*s\n", size, cons);
fputc('.', stderr);
fflush(stderr);
free(r);
}
gio_close(io);
exit(0);
}
int main(int argc, char **argv) {
GapIO *io;
int xpos = 0;
int opt;
int lp_mode = 0;
int mode = DISPLAY_QUAL | DISPLAY_CUTOFFS;
extern char *optarg;
contig_t *c;
int cnum = 0;
int read_only = 1;
while ((opt = getopt(argc, argv, "hl:dcCx:e")) != -1) {
switch (opt) {
case '?':
case 'h':
usage();
return 0;
case 'd':
mode |= DISPLAY_DIFFS;
break;
case 'c':
mode |= DISPLAY_CUTOFFS;
break;
case 'C':
mode &= ~DISPLAY_CUTOFFS;
break;
case 'l':
lp_mode = atoi(optarg);
break;
case 'x':
cnum = atoi(optarg)-1;
break;
case 'e':
read_only = 0;
break;
default:
if (opt == ':')
fprintf(stderr, "Missing parameter\n");
else
fprintf(stderr, "Unknown option '%c'\n", opt);
usage();
return 1;
}
}
if (optind == argc) {
usage();
return 1;
}
if (NULL == (io = gio_open(argv[optind], read_only, 0))) {
fprintf(stderr, "Unable to open db: %s\n", argv[1]);
return 1;
}
optind++;
if (optind != argc) {
xpos = atoi(argv[optind]);
}
io->contig_num = cnum;
gio_read_contig(io, cnum, &c);
cache_incr(io, c);
#ifdef TEST_MODE
//test_mode(io, &c, xpos);
test_mode2(io, &c, xpos);
//benchmark(io, &c);
//test_mode3(io, arr(GCardinal, io->contig_order, cnum), xpos);
#endif
if (lp_mode) {
print_output(io, &c, xpos, lp_mode, mode);
gio_close(io);
} else {
init_curses();
curses_loop(io, &c, xpos, mode);
endwin();
if (io->cache && io->debug_level > 0) {
fputs("\n=== cache ===", stderr);
HacheTableStats(io->cache, stderr);
}
gio_close(io);
}
if (!lp_mode) {
printf("\n\n\tg_view:\tShort Read Alignment Viewer, version 1.2.11"SVN_VERS"\n");
printf("\n\tAuthor:\tJames Bonfield ([email protected])\n");
printf("\t\t2007-2011, Wellcome Trust Sanger Institute\n\n");
}
return 0;
}
