int call_align ( int argc, char ** argv )
{
time_t start_t, stop_t, time_bef, time_aft;
time ( &start_t );
initenv ( argc, argv );
overlaplen = getMinOverlap ( graphfile );
printf ( "K = %d\n", overlaplen );
time ( &time_bef );
ctg_short = overlaplen + 2;
printf ( "contig len cutoff: %d\n", ctg_short );
prlContig2nodes ( graphfile, ctg_short );
time ( &time_aft );
printf ( "time spent on De bruijn graph construction: %ds\n\n",
( int ) ( time_aft - time_bef ) );
//map long read to edge one by one
time ( &time_bef );
prlLongRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on mapping long reads: %ds\n\n", ( int ) ( time_aft - time_bef ) );
//map read to edge one by one
time ( &time_bef );
prlRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on mapping reads: %ds\n\n", ( int ) ( time_aft - time_bef ) );
free_Sets ( KmerSets, thrd_num );
time ( &stop_t );
printf ( "overall time for alignment: %dm\n\n", ( int ) ( stop_t - start_t ) / 60 );
return 0;
}
int do_initenv (cmd_tbl_t *cmdtp, int flag, int argc, char *argv[])
{
extern char * env_name_spec;
printf ("Clear Environment to %s...\n", env_name_spec);
return (initenv() ? 1 : 0);
}
int call_scaffold (int argc, char **argv)
{
time_t start_t, stop_t, time_bef, time_aft;
time (&start_t);
initenv (argc, argv);
loadPEgrads (graphfile);
time (&time_bef);
loadUpdatedEdges (graphfile);
time (&time_aft);
printf ("time spent on loading edges %ds\n", (int) (time_aft - time_bef));
if (!SCAFF)
{
time (&time_bef);
PE2Links (graphfile);
time (&time_aft);
printf ("time spent on loading pair end info %ds\n\n", (int) (time_aft - time_bef));
time (&time_bef);
Links2Scaf (graphfile);
time (&time_aft);
printf ("time spent on creating scaffolds %ds\n\n", (int) (time_aft - time_bef));
time(&time_bef);
transcriptome(graphfile);
time(&time_aft);
printf("time spent on creating transcriptome %ds\n",(int)(time_aft-time_bef));
// scaffolding (100, graphfile);
}
prlReadsCloseGap (graphfile);
// locateReadOnScaf(graphfile);
ScafStat (100, graphfile);
if(read_trace)
{
getReadOnScaf(graphfile);
if(RPKM) //Must add '-R' parameter RPKMStat(graphfile);
RPKMStat(graphfile);
}
free_pe_mem ();
if (index_array)
{
free ((void *) index_array);
}
freeContig_array ();
destroyPreArcMem ();
destroyConnectMem ();
deleteCntLookupTable ();
time (&stop_t);
printf ("time elapsed: %dm\n", (int) (stop_t - start_t) / 60);
return 0;
}
main(int argc, char **argv) {
char *aa0;
char libstr[MAX_FN];
char qname[MAX_FN];
int sq0off;
int i, n0;
FILE *fp;
struct pstruct pst, *ppst;
/* stuff from initfa.c/h_init() */
memcpy(qascii,aascii,sizeof(qascii));
/* initialize a pam matrix */
ppst = &pst;
strncpy(ppst->pamfile,"BL50",MAX_FN);
standard_pam(ppst->pamfile,ppst,0,0);
/* this is always protein by default */
ppst->nsq = naa;
ppst->nsqx = naax;
for (i=0; i<=ppst->nsqx; i++) {
ppst->sq[i] = aa[i];
ppst->hsq[i] = haa[i];
ppst->sqx[i]=aax[i]; /* sq = aa */
ppst->hsqx[i]=haax[i]; /* hsq = haa */
}
ppst->sq[ppst->nsqx+1] = ppst->sqx[ppst->nsqx+1] = '\0';
if ((aa0 = calloc(MAXTST,sizeof(char)))==NULL) {
fprintf(stderr,"Cannot allocate aa0\n");
exit(1);
}
initenv(argc, argv, &pst, qname);
alloc_pam(pst.nsq+1,pst.nsq+1, &pst);
initpam2(&pst);
n0 = getseq (qname, qascii, aa0, MAXTST, libstr,&sq0off);
if (!pst.pam_pssm) {
fprintf(stderr," ** ERROR ** No -P PSSM provided\n");
}
else {
ppst->pam2p[0] = alloc_pam2p(n0,pst.nsq);
ppst->pam2p[1] = alloc_pam2p(n0,pst.nsq);
if ((fp = fopen(pst.pgpfile,"rb"))!=NULL) {
read_pssm(aa0, n0, pst.nsq, pst.pamscale,fp,ppst);
}
}
}
int call_align ( int argc, char ** argv )
{
time_t start_t, stop_t, time_bef, time_aft;
time ( &start_t );
fprintf ( stderr, "\n********************\n" );
fprintf ( stderr, "Map\n" );
fprintf ( stderr, "********************\n\n" );
initenv ( argc, argv );
overlaplen = getMinOverlap ( graphfile );
#ifdef MER127
if ( smallKmer > 12 && smallKmer < 128 && smallKmer % 2 == 1 )
{
deltaKmer = overlaplen - smallKmer;
overlaplen = smallKmer;
}
#else
if ( smallKmer > 12 && smallKmer < 64 && smallKmer % 2 == 1 )
{
deltaKmer = overlaplen - smallKmer;
overlaplen = smallKmer;
}
#endif
fprintf ( stderr, "Kmer size: %d.\n", overlaplen );
time ( &time_bef );
ctg_short = overlaplen + 2;
fprintf ( stderr, "Contig length cutoff: %d.\n", ctg_short );
prlContig2nodes ( graphfile, ctg_short );
time ( &time_aft );
fprintf ( stderr, "Time spent on graph construction: %ds.\n\n", ( int ) ( time_aft - time_bef ) );
//map long read (asm_flags=4) to edge one by one
time ( &time_bef );
prlLongRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
fprintf ( stderr, "Time spent on aligning long reads: %ds.\n\n", ( int ) ( time_aft - time_bef ) );
//map read to edge one by one
time ( &time_bef );
prlRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
fprintf ( stderr, "Time spent on aligning reads: %ds.\n\n", ( int ) ( time_aft - time_bef ) );
free_Sets ( KmerSets, thrd_num );
time ( &stop_t );
fprintf ( stderr, "Overall time spent on alignment: %dm.\n\n", ( int ) ( stop_t - start_t ) / 60 );
return 0;
}
extern int main(int argc, char *argv[], char *envp[]) {
char *dashsee[2], *dollarzero, *null[1];
int c;
initprint();
dashsee[0] = dashsee[1] = NULL;
dollarzero = argv[0];
rc_pid = getpid();
dashell = (*argv[0] == '-'); /* Unix tradition */
while ((c = rc_getopt(argc, argv, "c:deiIlnopsvx")) != -1)
switch (c) {
case 'c':
dashsee[0] = rc_optarg;
goto quitopts;
case 'd':
dashdee = TRUE;
break;
case 'e':
dashee = TRUE;
break;
case 'I':
dashEYE = TRUE;
interactive = FALSE;
break;
case 'i':
dasheye = interactive = TRUE;
break;
case 'l':
dashell = TRUE;
break;
case 'n':
dashen = TRUE;
break;
case 'o':
dashoh = TRUE;
break;
case 'p':
dashpee = TRUE;
break;
case 's':
dashess = TRUE;
break;
case 'v':
dashvee = TRUE;
break;
case 'x':
dashex = TRUE;
break;
case '?':
exit(1);
}
quitopts:
argv += rc_optind;
/* use isatty() iff neither -i nor -I is set, and iff the input is not from a script or -c flags */
if (!dasheye && !dashEYE && dashsee[0] == NULL && (dashess || *argv == NULL))
interactive = isatty(0);
if (!dashoh) {
checkfd(0, rFrom);
checkfd(1, rCreate);
checkfd(2, rCreate);
}
initsignal();
inithash();
initparse();
assigndefault("ifs", " ", "\t", "\n", (void *)0);
#ifdef DEFAULTPATH
assigndefault("path", DEFAULTPATH, (void *)0);
#endif
assigndefault("pid", nprint("%d", rc_pid), (void *)0);
assigndefault("prompt", "; ", "", (void *)0);
assigndefault("version", VERSION, "$Release: @(#)" PACKAGE " " VERSION " " RELDATE " $", (void *)0);
initenv(envp);
initinput();
null[0] = NULL;
starassign(dollarzero, null, FALSE); /* assign $0 to $* */
inithandler();
if (dashell) {
char *rcrc;
int fd;
rcrc = concat(varlookup("home"), word("/.rcrc", NULL))->w;
fd = rc_open(rcrc, rFrom);
if (fd == -1) {
if (errno != ENOENT)
uerror(rcrc);
} else {
bool push_interactive;
pushfd(fd);
push_interactive = interactive;
interactive = FALSE;
doit(TRUE);
interactive = push_interactive;
close(fd);
}
}
if (dashsee[0] != NULL || dashess) { /* input from -c or -s? */
if (*argv != NULL)
starassign(dollarzero, argv, FALSE);
if (dashess)
pushfd(0);
else
pushstring(dashsee, TRUE);
} else if (*argv != NULL) { /* else from a file? */
b_dot(--argv);
rc_exit(getstatus());
} else { /* else stdin */
pushfd(0);
}
dasheye = FALSE;
doit(TRUE);
rc_exit(getstatus());
return 0; /* Never really reached. */
}
void
main(int argc, char **argv)
{
Word *w;
char *s, *temp;
char *files[256], **f = files, **ff;
int sflag = 0;
int i;
int tfd = -1;
Biobuf tb;
Bufblock *buf;
Bufblock *whatif;
/*
* start with a copy of the current environment variables
* instead of sharing them
*/
Binit(&bout, 1, OWRITE);
buf = newbuf();
whatif = 0;
USED(argc);
for(argv++; *argv && (**argv == '-'); argv++)
{
bufcpy(buf, argv[0], strlen(argv[0]));
insert(buf, ' ');
switch(argv[0][1])
{
case 'a':
aflag = 1;
break;
case 'd':
if(*(s = &argv[0][2]))
while(*s) switch(*s++)
{
case 'p': debug |= D_PARSE; break;
case 'g': debug |= D_GRAPH; break;
case 'e': debug |= D_EXEC; break;
}
else
debug = 0xFFFF;
break;
case 'e':
explain = &argv[0][2];
break;
case 'f':
if(*++argv == 0)
badusage();
*f++ = *argv;
bufcpy(buf, argv[0], strlen(argv[0]));
insert(buf, ' ');
break;
case 'i':
iflag = 1;
break;
case 'k':
kflag = 1;
break;
case 'n':
nflag = 1;
break;
case 's':
sflag = 1;
break;
case 't':
tflag = 1;
break;
case 'u':
uflag = 1;
break;
case 'w':
if(whatif == 0)
whatif = newbuf();
else
insert(whatif, ' ');
if(argv[0][2])
bufcpy(whatif, &argv[0][2], strlen(&argv[0][2]));
else {
if(*++argv == 0)
badusage();
bufcpy(whatif, &argv[0][0], strlen(&argv[0][0]));
}
break;
default:
badusage();
}
}
#ifdef PROF
{
extern etext();
monitor(main, etext, buf, sizeof buf, 300);
}
#endif
if(aflag)
iflag = 1;
usage();
syminit();
initenv();
usage();
/*
assignment args become null strings
*/
temp = 0;
for(i = 0; argv[i]; i++) if(utfrune(argv[i], '=')){
bufcpy(buf, argv[i], strlen(argv[i]));
insert(buf, ' ');
if(tfd < 0){
temp = maketmp();
if(temp == 0) {
perror("temp file");
Exit();
}
close(create(temp, OWRITE, 0600));
if((tfd = open(temp, 2)) < 0){
perror(temp);
Exit();
}
Binit(&tb, tfd, OWRITE);
}
Bprint(&tb, "%s\n", argv[i]);
*argv[i] = 0;
}
if(tfd >= 0){
Bflush(&tb);
LSEEK(tfd, 0L, 0);
parse("command line args", tfd, 1);
remove(temp);
}
if (buf->current != buf->start) {
buf->current--;
insert(buf, 0);
}
symlook("MKFLAGS", S_VAR, (void *) stow(buf->start));
buf->current = buf->start;
for(i = 0; argv[i]; i++){
if(*argv[i] == 0) continue;
if(i)
insert(buf, ' ');
bufcpy(buf, argv[i], strlen(argv[i]));
}
insert(buf, 0);
symlook("MKARGS", S_VAR, (void *) stow(buf->start));
freebuf(buf);
if(f == files){
if(access(MKFILE, 4) == 0)
parse(MKFILE, open(MKFILE, 0), 0);
} else
for(ff = files; ff < f; ff++)
parse(*ff, open(*ff, 0), 0);
if(DEBUG(D_PARSE)){
dumpw("default targets", target1);
dumpr("rules", rules);
dumpr("metarules", metarules);
dumpv("variables");
}
if(whatif){
insert(whatif, 0);
timeinit(whatif->start);
freebuf(whatif);
}
execinit();
/* skip assignment args */
while(*argv && (**argv == 0))
argv++;
catchnotes();
if(*argv == 0){
if(target1)
for(w = target1; w; w = w->next)
mk(w->s);
else {
fprint(2, "mk: nothing to mk\n");
Exit();
}
} else {
if(sflag){
for(; *argv; argv++)
if(**argv)
mk(*argv);
} else {
Word *head, *tail, *t;
/* fake a new rule with all the args as prereqs */
tail = 0;
t = 0;
for(; *argv; argv++)
if(**argv){
if(tail == 0)
tail = t = newword(*argv);
else {
t->next = newword(*argv);
t = t->next;
}
}
if(tail->next == 0)
mk(tail->s);
else {
head = newword("command line arguments");
addrules(head, tail, strdup(""), VIR, mkinline, 0);
mk(head->s);
}
}
}
if(uflag)
prusage();
exits(0);
}
main(int argc, char **argv)
{
int i, j, k, l, m, n, centro[200], len_chroseq[100];
int maxi;
int num_seq;
char **chrname, **repnames;
int num_chro;
int *counts, maxc;
SEGMENT *segment;
int num_segment;
int *repeats, num_repeats;
char name[1000], temp[1000], c;
double id;
FILE *fp;
readpar();
initenv(argc, argv);
/* Input chromsomal information */
chrname = alloc_name(100, 100);
fp = ckopen(lenfile, "r");
num_chro = read_chro_centro(chrname, len_chroseq, centro, fp);
fclose(fp);
nchro = findgenname(chriname, chrname, num_chro);
/* input segments */
segment = (SEGMENT *) ckalloc(60000 * sizeof(SEGMENT));
fp = stdin;
num_segment = input_segment(segment, chrname, num_chro, fp);
/* sort the segments */
/*
qsort((void *) segment, num_segment, sizeof(SEGMENT), (void *) segcompar);
*/
/* Define repeats from sub-repeats */
repeats = (int *) ckalloc(num_segment * sizeof(int));
num_repeats = 0;
counts = (int *) ckalloc(10000 * num_segment * sizeof(int));
n = m = 0;
j = 0;
for(i = 0; i < num_segment; i ++) {
if(i == num_segment - 1 || segment[i + 1].pos[0] > segment[i].pos[1] + min_length ||
segment[i + 1].chro != segment[i].chro) {
repeats[num_repeats ++] = i;
if(segment[i].chro == nchro) j ++;
}
if(segment[i].pos[1] - segment[i].pos[0] < min_length) continue;
counts[segment[i].eq_pos[0]] ++;
if(segment[i].eq_pos[0] > n) n = segment[i].eq_pos[0];
}
m += n;
k = maxc = 0;
for(i = 0; i < m; i ++) {
if(counts[i] > 1) k ++;
if(counts[i] > maxc) {
maxi = i;
maxc = counts[i];
}
}
printf("m %d k %d\n", m, k);
printf("%d repeats (%s %d) %d subrepeats %d max_multip subrepeats index %d.\n", num_repeats,
chriname, j, k, maxc, maxi);
free((void *) counts);
chrname = free_name(chrname, 100);
free((void *) repeats);
free((void *) segment);
}
int call_pregraph ( int argc, char ** argv )
{
time_t start_t, stop_t, time_bef, time_aft;
time ( &start_t );
initenv ( argc, argv );
if ( overlaplen % 2 == 0 )
{
overlaplen++;
printf ( "K should be an odd number\n" );
}
if ( overlaplen < 13 )
{
overlaplen = 13;
printf ( "K should not be less than 13\n" );
}
else if ( overlaplen > 31 )
{
overlaplen = 31;
printf ( "K should not be greater than 31\n" );
}
time ( &time_bef );
prlRead2HashTable ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on pre-graph construction: %ds\n\n", ( int ) ( time_aft - time_bef ) );
printf ( "deLowKmer %d, deLowEdge %d\n", deLowKmer, deLowEdge );
//analyzeTips(hash_table, graphfile);
if ( !deLowKmer && cutTips )
{
time ( &time_bef );
removeSingleTips();
removeMinorTips();
time ( &time_aft );
printf ( "time spent on cutTipe: %ds\n\n", ( int ) ( time_aft - time_bef ) );
}
else
{
time ( &time_bef );
removeMinorTips();
time ( &time_aft );
printf ( "time spent on cutTipe: %ds\n\n", ( int ) ( time_aft - time_bef ) );
}
initKmerSetSize = 0;
//combine each linear part to an edge
time ( &time_bef );
kmer2edges ( graphfile );
time ( &time_aft );
printf ( "time spent on making edges: %ds\n\n", ( int ) ( time_aft - time_bef ) );
//map read to edge one by one
time ( &time_bef );
prlRead2edge ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on mapping reads: %ds\n\n", ( int ) ( time_aft - time_bef ) );
output_vertex ( graphfile );
free_Sets ( KmerSets, thrd_num );
free_Sets ( KmerSetsPatch, thrd_num );
time ( &stop_t );
printf ( "overall time for lightgraph: %dm\n\n", ( int ) ( stop_t - start_t ) / 60 );
return 0;
}
/*ARGSUSED*/ int main (int argc, char **argv)
{
#ifndef USE_PAM
const char *env;
#endif /* !USE_PAM */
char **envp = environ;
TERMIO termio;
int err = 0;
#ifdef USE_TERMIO
ioctl (0, TCGETA, &termio);
termio.c_iflag |= (ICRNL | IXON);
termio.c_oflag |= (OPOST | ONLCR);
termio.c_cflag |= (CREAD);
termio.c_lflag |= (ISIG | ICANON | ECHO | ECHOE | ECHOK);
ioctl (0, TCSETAF, &termio);
#endif
#ifdef USE_TERMIOS
tcgetattr (0, &termio);
termio.c_iflag |= (ICRNL | IXON);
termio.c_oflag |= (CREAD);
termio.c_lflag |= (ECHO | ECHOE | ECHOK | ICANON | ISIG);
tcsetattr (0, TCSANOW, &termio);
#endif
Prog = Basename (argv[0]);
(void) setlocale (LC_ALL, "");
(void) bindtextdomain (PACKAGE, LOCALEDIR);
(void) textdomain (PACKAGE);
#ifdef USE_SYSLOG
OPENLOG ("sulogin");
#endif
initenv ();
if (argc > 1) {
close (0);
close (1);
close (2);
if (open (argv[1], O_RDWR) >= 0) {
dup (0);
dup (0);
} else {
#ifdef USE_SYSLOG
SYSLOG (LOG_WARN, "cannot open %s\n", argv[1]);
closelog ();
#endif
exit (1);
}
}
if (access (PASSWD_FILE, F_OK) == -1) { /* must be a password file! */
(void) puts (_("No password file"));
#ifdef USE_SYSLOG
SYSLOG (LOG_WARN, "No password file\n");
closelog ();
#endif
exit (1);
}
#if !defined(DEBUG) && defined(SULOGIN_ONLY_INIT)
if (getppid () != 1) { /* parent must be INIT */
#ifdef USE_SYSLOG
SYSLOG (LOG_WARN, "Pid == %d, not 1\n", getppid ());
closelog ();
#endif
exit (1);
}
#endif
if ((isatty (0) == 0) || (isatty (1) == 0) || (isatty (2) == 0)) {
#ifdef USE_SYSLOG
closelog ();
#endif
exit (1); /* must be a terminal */
}
/* If we were init, we need to start a new session */
if (getppid() == 1) {
setsid();
if (ioctl(0, TIOCSCTTY, 1) != 0) {
(void) fputs (_("TIOCSCTTY failed"), stderr);
}
}
while (NULL != *envp) { /* add inherited environment, */
addenv (*envp, NULL); /* some variables change later */
envp++;
}
#ifndef USE_PAM
env = getdef_str ("ENV_TZ");
if (NULL != env) {
addenv (('/' == *env) ? tz (env) : env, NULL);
}
env = getdef_str ("ENV_HZ");
if (NULL != env) {
addenv (env, NULL); /* set the default $HZ, if one */
}
#endif /* !USE_PAM */
(void) strcpy (name, "root"); /* KLUDGE!!! */
(void) signal (SIGALRM, catch_signals); /* exit if the timer expires */
(void) alarm (ALARM); /* only wait so long ... */
while (true) { /* repeatedly get login/password pairs */
char *cp;
pw_entry (name, &pwent); /* get entry from password file */
if (pwent.pw_name == (char *) 0) {
/*
* Fail secure
*/
(void) puts (_("No password entry for 'root'"));
#ifdef USE_SYSLOG
SYSLOG (LOG_WARN, "No password entry for 'root'\n");
closelog ();
#endif
exit (1);
}
/*
* Here we prompt for the root password, or if no password
* is given we just exit.
*/
/* get a password for root */
cp = getpass (_(
"\n"
"Type control-d to proceed with normal startup,\n"
"(or give root password for system maintenance):"));
/*
* XXX - can't enter single user mode if root password is
* empty. I think this doesn't happen very often :-). But
* it will work with standard getpass() (no NULL on EOF).
* --marekm
*/
if ((NULL == cp) || ('\0' == *cp)) {
#ifdef USE_SYSLOG
SYSLOG (LOG_INFO, "Normal startup\n");
closelog ();
#endif
(void) puts ("");
#ifdef TELINIT
execl (PATH_TELINIT, "telinit", RUNLEVEL, (char *) 0);
#endif
exit (0);
} else {
STRFCPY (pass, cp);
strzero (cp);
}
if (valid (pass, &pwent)) { /* check encrypted passwords ... */
break; /* ... encrypted passwords matched */
}
#ifdef USE_SYSLOG
SYSLOG (LOG_WARN, "Incorrect root password\n");
#endif
sleep (2);
(void) puts (_("Login incorrect"));
}
strzero (pass);
(void) alarm (0);
(void) signal (SIGALRM, SIG_DFL);
environ = newenvp; /* make new environment active */
(void) puts (_("Entering System Maintenance Mode"));
#ifdef USE_SYSLOG
SYSLOG (LOG_INFO, "System Maintenance Mode\n");
#endif
#ifdef USE_SYSLOG
closelog ();
#endif
/* exec the shell finally. */
err = shell (pwent.pw_shell, (char *) 0, environ);
return ((err == ENOENT) ? E_CMD_NOTFOUND : E_CMD_NOEXEC);
}
/*
* login - create a new login session for a user
*
* login is typically called by getty as the second step of a
* new user session. getty is responsible for setting the line
* characteristics to a reasonable set of values and getting
* the name of the user to be logged in. login may also be
* called to create a new user session on a pty for a variety
* of reasons, such as X servers or network logins.
*
* the flags which login supports are
*
* -p - preserve the environment
* -r - perform autologin protocol for rlogin
* -f - do not perform authentication, user is preauthenticated
* -h - the name of the remote host
*/
int main (int argc, char **argv)
{
const char *tmptty;
char tty[BUFSIZ];
#ifdef RLOGIN
char term[128] = "";
#endif /* RLOGIN */
#if defined(HAVE_STRFTIME) && !defined(USE_PAM)
char ptime[80];
#endif
unsigned int delay;
unsigned int retries;
bool failed;
bool subroot = false;
#ifndef USE_PAM
bool is_console;
#endif
int err;
const char *cp;
char *tmp;
char fromhost[512];
struct passwd *pwd = NULL;
char **envp = environ;
const char *failent_user;
/*@null@*/struct utmp *utent;
#ifdef USE_PAM
int retcode;
pid_t child;
char *pam_user = NULL;
#else
struct spwd *spwd = NULL;
#endif
/*
* Some quick initialization.
*/
sanitize_env ();
(void) setlocale (LC_ALL, "");
(void) bindtextdomain (PACKAGE, LOCALEDIR);
(void) textdomain (PACKAGE);
initenv ();
amroot = (getuid () == 0);
Prog = Basename (argv[0]);
if (geteuid() != 0) {
fprintf (stderr, _("%s: Cannot possibly work without effective root\n"), Prog);
exit (1);
}
process_flags (argc, argv);
if ((isatty (0) == 0) || (isatty (1) == 0) || (isatty (2) == 0)) {
exit (1); /* must be a terminal */
}
utent = get_current_utmp ();
/*
* Be picky if run by normal users (possible if installed setuid
* root), but not if run by root. This way it still allows logins
* even if your getty is broken, or if something corrupts utmp,
* but users must "exec login" which will use the existing utmp
* entry (will not overwrite remote hostname). --marekm
*/
if (!amroot && (NULL == utent)) {
(void) puts (_("No utmp entry. You must exec \"login\" from the lowest level \"sh\""));
exit (1);
}
/* NOTE: utent might be NULL afterwards */
tmptty = ttyname (0);
if (NULL == tmptty) {
tmptty = "UNKNOWN";
}
STRFCPY (tty, tmptty);
#ifndef USE_PAM
is_console = console (tty);
#endif
if (rflg || hflg) {
/*
* Add remote hostname to the environment. I think
* (not sure) I saw it once on Irix. --marekm
*/
addenv ("REMOTEHOST", hostname);
}
if (fflg) {
preauth_flag = true;
}
if (hflg) {
reason = PW_RLOGIN;
}
#ifdef RLOGIN
if (rflg) {
assert (NULL == username);
username = xmalloc (USER_NAME_MAX_LENGTH + 1);
username[USER_NAME_MAX_LENGTH] = '\0';
if (do_rlogin (hostname, username, USER_NAME_MAX_LENGTH, term, sizeof term)) {
preauth_flag = true;
} else {
free (username);
username = NULL;
}
}
#endif /* RLOGIN */
OPENLOG ("login");
setup_tty ();
#ifndef USE_PAM
(void) umask (getdef_num ("UMASK", GETDEF_DEFAULT_UMASK));
{
/*
* Use the ULIMIT in the login.defs file, and if
* there isn't one, use the default value. The
* user may have one for themselves, but otherwise,
* just take what you get.
*/
long limit = getdef_long ("ULIMIT", -1L);
if (limit != -1) {
set_filesize_limit (limit);
}
}
#endif
/*
* The entire environment will be preserved if the -p flag
* is used.
*/
if (pflg) {
while (NULL != *envp) { /* add inherited environment, */
addenv (*envp, NULL); /* some variables change later */
envp++;
}
}
#ifdef RLOGIN
if (term[0] != '\0') {
addenv ("TERM", term);
} else
#endif /* RLOGIN */
{
/* preserve TERM from getty */
if (!pflg) {
tmp = getenv ("TERM");
if (NULL != tmp) {
addenv ("TERM", tmp);
}
}
}
init_env ();
if (optind < argc) { /* now set command line variables */
set_env (argc - optind, &argv[optind]);
}
if (rflg || hflg) {
cp = hostname;
#ifdef HAVE_STRUCT_UTMP_UT_HOST
} else if ((NULL != utent) && ('\0' != utent->ut_host[0])) {
cp = utent->ut_host;
#endif /* HAVE_STRUCT_UTMP_UT_HOST */
} else {
cp = "";
}
if ('\0' != *cp) {
snprintf (fromhost, sizeof fromhost,
" on '%.100s' from '%.200s'", tty, cp);
} else {
snprintf (fromhost, sizeof fromhost,
" on '%.100s'", tty);
}
top:
/* only allow ALARM sec. for login */
(void) signal (SIGALRM, alarm_handler);
timeout = getdef_unum ("LOGIN_TIMEOUT", ALARM);
if (timeout > 0) {
(void) alarm (timeout);
}
environ = newenvp; /* make new environment active */
delay = getdef_unum ("FAIL_DELAY", 1);
retries = getdef_unum ("LOGIN_RETRIES", RETRIES);
#ifdef USE_PAM
retcode = pam_start ("login", username, &conv, &pamh);
if (retcode != PAM_SUCCESS) {
fprintf (stderr,
_("login: PAM Failure, aborting: %s\n"),
pam_strerror (pamh, retcode));
SYSLOG ((LOG_ERR, "Couldn't initialize PAM: %s",
pam_strerror (pamh, retcode)));
exit (99);
}
/*
* hostname & tty are either set to NULL or their correct values,
* depending on how much we know. We also set PAM's fail delay to
* ours.
*
* PAM_RHOST and PAM_TTY are used for authentication, only use
* information coming from login or from the caller (e.g. no utmp)
*/
retcode = pam_set_item (pamh, PAM_RHOST, hostname);
PAM_FAIL_CHECK;
retcode = pam_set_item (pamh, PAM_TTY, tty);
PAM_FAIL_CHECK;
#ifdef HAS_PAM_FAIL_DELAY
retcode = pam_fail_delay (pamh, 1000000 * delay);
PAM_FAIL_CHECK;
#endif
/* if fflg, then the user has already been authenticated */
if (!fflg) {
unsigned int failcount = 0;
char hostn[256];
char loginprompt[256]; /* That's one hell of a prompt :) */
/* Make the login prompt look like we want it */
if (gethostname (hostn, sizeof (hostn)) == 0) {
snprintf (loginprompt,
sizeof (loginprompt),
_("%s login: "******"login: "******"TOO MANY LOGIN TRIES (%u)%s FOR '%s'",
failcount, fromhost, failent_user));
fprintf(stderr,
_("Maximum number of tries exceeded (%u)\n"),
failcount);
PAM_END;
exit(0);
} else if (retcode == PAM_ABORT) {
/* Serious problems, quit now */
(void) fputs (_("login: abort requested by PAM\n"), stderr);
SYSLOG ((LOG_ERR,"PAM_ABORT returned from pam_authenticate()"));
PAM_END;
exit(99);
} else if (retcode != PAM_SUCCESS) {
SYSLOG ((LOG_NOTICE,"FAILED LOGIN (%u)%s FOR '%s', %s",
failcount, fromhost, failent_user,
pam_strerror (pamh, retcode)));
failed = true;
}
if (!failed) {
break;
}
#ifdef WITH_AUDIT
audit_fd = audit_open ();
audit_log_acct_message (audit_fd,
AUDIT_USER_LOGIN,
NULL, /* Prog. name */
"login",
failent_user,
AUDIT_NO_ID,
hostname,
NULL, /* addr */
tty,
0); /* result */
close (audit_fd);
#endif /* WITH_AUDIT */
(void) puts ("");
(void) puts (_("Login incorrect"));
if (failcount >= retries) {
SYSLOG ((LOG_NOTICE,
"TOO MANY LOGIN TRIES (%u)%s FOR '%s'",
failcount, fromhost, failent_user));
fprintf(stderr,
_("Maximum number of tries exceeded (%u)\n"),
failcount);
PAM_END;
exit(0);
}
/*
* Let's give it another go around.
* Even if a username was given on the command
* line, prompt again for the username.
*/
retcode = pam_set_item (pamh, PAM_USER, NULL);
PAM_FAIL_CHECK;
}
/* We don't get here unless they were authenticated above */
(void) alarm (0);
}
/* Check the account validity */
retcode = pam_acct_mgmt (pamh, 0);
if (retcode == PAM_NEW_AUTHTOK_REQD) {
retcode = pam_chauthtok (pamh, PAM_CHANGE_EXPIRED_AUTHTOK);
}
PAM_FAIL_CHECK;
/* Open the PAM session */
get_pam_user (&pam_user);
retcode = pam_open_session (pamh, hushed (pam_user) ? PAM_SILENT : 0);
PAM_FAIL_CHECK;
/* Grab the user information out of the password file for future usage
* First get the username that we are actually using, though.
*
* From now on, we will discard changes of the user (PAM_USER) by
* PAM APIs.
*/
get_pam_user (&pam_user);
if (NULL != username) {
free (username);
}
username = pam_user;
failent_user = get_failent_user (username);
pwd = xgetpwnam (username);
if (NULL == pwd) {
SYSLOG ((LOG_ERR, "cannot find user %s", failent_user));
exit (1);
}
/* This set up the process credential (group) and initialize the
* supplementary group access list.
* This has to be done before pam_setcred
*/
if (setup_groups (pwd) != 0) {
exit (1);
}
retcode = pam_setcred (pamh, PAM_ESTABLISH_CRED);
PAM_FAIL_CHECK;
/* NOTE: If pam_setcred changes PAM_USER, this will not be taken
* into account.
*/
#else /* ! USE_PAM */
while (true) { /* repeatedly get login/password pairs */
/* user_passwd is always a pointer to this constant string
* or a passwd or shadow password that will be memzero by
* pw_free / spw_free.
* Do not free() user_passwd. */
const char *user_passwd = "!";
/* Do some cleanup to avoid keeping entries we do not need
* anymore. */
if (NULL != pwd) {
pw_free (pwd);
pwd = NULL;
}
if (NULL != spwd) {
spw_free (spwd);
spwd = NULL;
}
failed = false; /* haven't failed authentication yet */
if (NULL == username) { /* need to get a login id */
if (subroot) {
closelog ();
exit (1);
}
preauth_flag = false;
username = xmalloc (USER_NAME_MAX_LENGTH + 1);
username[USER_NAME_MAX_LENGTH] = '\0';
login_prompt (_("\n%s login: "******"!",
* the account is locked and the user cannot
* login, even if they have been
* "pre-authenticated."
*/
if ( ('!' == user_passwd[0])
|| ('*' == user_passwd[0])) {
failed = true;
}
}
if (strcmp (user_passwd, SHADOW_PASSWD_STRING) == 0) {
spwd = xgetspnam (username);
if (NULL != spwd) {
user_passwd = spwd->sp_pwdp;
} else {
/* The user exists in passwd, but not in
* shadow. SHADOW_PASSWD_STRING indicates
* that the password shall be in shadow.
*/
SYSLOG ((LOG_WARN,
"no shadow password for '%s'%s",
username, fromhost));
}
}
/*
* The -r and -f flags provide a name which has already
* been authenticated by some server.
*/
if (preauth_flag) {
goto auth_ok;
}
if (pw_auth (user_passwd, username, reason, (char *) 0) == 0) {
goto auth_ok;
}
SYSLOG ((LOG_WARN, "invalid password for '%s' %s",
failent_user, fromhost));
failed = true;
auth_ok:
/*
* This is the point where all authenticated users wind up.
* If you reach this far, your password has been
* authenticated and so on.
*/
if ( !failed
&& (NULL != pwd)
&& (0 == pwd->pw_uid)
&& !is_console) {
SYSLOG ((LOG_CRIT, "ILLEGAL ROOT LOGIN %s", fromhost));
failed = true;
}
if ( !failed
&& !login_access (username, ('\0' != *hostname) ? hostname : tty)) {
SYSLOG ((LOG_WARN, "LOGIN '%s' REFUSED %s",
username, fromhost));
failed = true;
}
if ( (NULL != pwd)
&& getdef_bool ("FAILLOG_ENAB")
&& !failcheck (pwd->pw_uid, &faillog, failed)) {
SYSLOG ((LOG_CRIT,
"exceeded failure limit for '%s' %s",
username, fromhost));
failed = true;
}
if (!failed) {
break;
}
/* don't log non-existent users */
if ((NULL != pwd) && getdef_bool ("FAILLOG_ENAB")) {
failure (pwd->pw_uid, tty, &faillog);
}
if (getdef_str ("FTMP_FILE") != NULL) {
#ifdef USE_UTMPX
struct utmpx *failent =
prepare_utmpx (failent_user,
tty,
/* FIXME: or fromhost? */hostname,
utent);
#else /* !USE_UTMPX */
struct utmp *failent =
prepare_utmp (failent_user,
tty,
hostname,
utent);
#endif /* !USE_UTMPX */
failtmp (failent_user, failent);
free (failent);
}
retries--;
if (retries <= 0) {
SYSLOG ((LOG_CRIT, "REPEATED login failures%s",
fromhost));
}
/*
* If this was a passwordless account and we get here, login
* was denied (securetty, faillog, etc.). There was no
* password prompt, so do it now (will always fail - the bad
* guys won't see that the passwordless account exists at
* all). --marekm
*/
if (user_passwd[0] == '\0') {
pw_auth ("!", username, reason, (char *) 0);
}
/*
* Authentication of this user failed.
* The username must be confirmed in the next try.
*/
free (username);
username = NULL;
/*
* Wait a while (a la SVR4 /usr/bin/login) before attempting
* to login the user again. If the earlier alarm occurs
* before the sleep() below completes, login will exit.
*/
if (delay > 0) {
(void) sleep (delay);
}
(void) puts (_("Login incorrect"));
/* allow only one attempt with -r or -f */
if (rflg || fflg || (retries <= 0)) {
closelog ();
exit (1);
}
} /* while (true) */
#endif /* ! USE_PAM */
assert (NULL != username);
assert (NULL != pwd);
(void) alarm (0); /* turn off alarm clock */
#ifndef USE_PAM /* PAM does this */
/*
* porttime checks moved here, after the user has been
* authenticated. now prints a message, as suggested
* by Ivan Nejgebauer <*****@*****.**>. --marekm
*/
if ( getdef_bool ("PORTTIME_CHECKS_ENAB")
&& !isttytime (username, tty, time ((time_t *) 0))) {
SYSLOG ((LOG_WARN, "invalid login time for '%s'%s",
username, fromhost));
closelog ();
bad_time_notify ();
exit (1);
}
check_nologin (pwd->pw_uid == 0);
#endif
if (getenv ("IFS")) { /* don't export user IFS ... */
addenv ("IFS= \t\n", NULL); /* ... instead, set a safe IFS */
}
if (pwd->pw_shell[0] == '*') { /* subsystem root */
pwd->pw_shell++; /* skip the '*' */
subsystem (pwd); /* figure out what to execute */
subroot = true; /* say I was here again */
endpwent (); /* close all of the file which were */
endgrent (); /* open in the original rooted file */
endspent (); /* system. they will be re-opened */
#ifdef SHADOWGRP
endsgent (); /* in the new rooted file system */
#endif
goto top; /* go do all this all over again */
}
#ifdef WITH_AUDIT
audit_fd = audit_open ();
audit_log_acct_message (audit_fd,
AUDIT_USER_LOGIN,
NULL, /* Prog. name */
"login",
username,
AUDIT_NO_ID,
hostname,
NULL, /* addr */
tty,
1); /* result */
close (audit_fd);
#endif /* WITH_AUDIT */
#ifndef USE_PAM /* pam_lastlog handles this */
if (getdef_bool ("LASTLOG_ENAB")) { /* give last login and log this one */
dolastlog (&ll, pwd, tty, hostname);
}
#endif
#ifndef USE_PAM /* PAM handles this as well */
/*
* Have to do this while we still have root privileges, otherwise we
* don't have access to /etc/shadow.
*/
if (NULL != spwd) { /* check for age of password */
if (expire (pwd, spwd)) {
/* The user updated her password, get the new
* entries.
* Use the x variants because we need to keep the
* entry for a long time, and there might be other
* getxxyy in between.
*/
pw_free (pwd);
pwd = xgetpwnam (username);
if (NULL == pwd) {
SYSLOG ((LOG_ERR,
"cannot find user %s after update of expired password",
username));
exit (1);
}
spw_free (spwd);
spwd = xgetspnam (username);
}
}
setup_limits (pwd); /* nice, ulimit etc. */
#endif /* ! USE_PAM */
chown_tty (pwd);
#ifdef USE_PAM
/*
* We must fork before setuid() because we need to call
* pam_close_session() as root.
*/
(void) signal (SIGINT, SIG_IGN);
child = fork ();
if (child < 0) {
/* error in fork() */
fprintf (stderr, _("%s: failure forking: %s"),
Prog, strerror (errno));
PAM_END;
exit (0);
} else if (child != 0) {
/*
* parent - wait for child to finish, then cleanup
* session
*/
wait (NULL);
PAM_END;
exit (0);
}
/* child */
#endif
/* If we were init, we need to start a new session */
if (getppid() == 1) {
setsid();
if (ioctl(0, TIOCSCTTY, 1) != 0) {
fprintf (stderr, _("TIOCSCTTY failed on %s"), tty);
}
}
/*
* The utmp entry needs to be updated to indicate the new status
* of the session, the new PID and SID.
*/
update_utmp (username, tty, hostname, utent);
/* The pwd and spwd entries for the user have been copied.
*
* Close all the files so that unauthorized access won't occur.
*/
endpwent (); /* stop access to password file */
endgrent (); /* stop access to group file */
endspent (); /* stop access to shadow passwd file */
#ifdef SHADOWGRP
endsgent (); /* stop access to shadow group file */
#endif
/* Drop root privileges */
#ifndef USE_PAM
if (setup_uid_gid (pwd, is_console))
#else
/* The group privileges were already dropped.
* See setup_groups() above.
*/
if (change_uid (pwd))
#endif
{
exit (1);
}
setup_env (pwd); /* set env vars, cd to the home dir */
#ifdef USE_PAM
{
const char *const *env;
env = (const char *const *) pam_getenvlist (pamh);
while ((NULL != env) && (NULL != *env)) {
addenv (*env, NULL);
env++;
}
}
#endif
(void) setlocale (LC_ALL, "");
(void) bindtextdomain (PACKAGE, LOCALEDIR);
(void) textdomain (PACKAGE);
if (!hushed (username)) {
addenv ("HUSHLOGIN=FALSE", NULL);
/*
* pam_unix, pam_mail and pam_lastlog should take care of
* this
*/
#ifndef USE_PAM
motd (); /* print the message of the day */
if ( getdef_bool ("FAILLOG_ENAB")
&& (0 != faillog.fail_cnt)) {
failprint (&faillog);
/* Reset the lockout times if logged in */
if ( (0 != faillog.fail_max)
&& (faillog.fail_cnt >= faillog.fail_max)) {
(void) puts (_("Warning: login re-enabled after temporary lockout."));
SYSLOG ((LOG_WARN,
"login '%s' re-enabled after temporary lockout (%d failures)",
username, (int) faillog.fail_cnt));
}
}
if ( getdef_bool ("LASTLOG_ENAB")
&& (ll.ll_time != 0)) {
time_t ll_time = ll.ll_time;
#ifdef HAVE_STRFTIME
(void) strftime (ptime, sizeof (ptime),
"%a %b %e %H:%M:%S %z %Y",
localtime (&ll_time));
printf (_("Last login: %s on %s"),
ptime, ll.ll_line);
#else
printf (_("Last login: %.19s on %s"),
ctime (&ll_time), ll.ll_line);
#endif
#ifdef HAVE_LL_HOST /* __linux__ || SUN4 */
if ('\0' != ll.ll_host[0]) {
printf (_(" from %.*s"),
(int) sizeof ll.ll_host, ll.ll_host);
}
#endif
printf (".\n");
}
agecheck (spwd);
mailcheck (); /* report on the status of mail */
#endif /* !USE_PAM */
} else {
addenv ("HUSHLOGIN=TRUE", NULL);
}
ttytype (tty);
(void) signal (SIGQUIT, SIG_DFL); /* default quit signal */
(void) signal (SIGTERM, SIG_DFL); /* default terminate signal */
(void) signal (SIGALRM, SIG_DFL); /* default alarm signal */
(void) signal (SIGHUP, SIG_DFL); /* added this. --marekm */
(void) signal (SIGINT, SIG_DFL); /* default interrupt signal */
if (0 == pwd->pw_uid) {
SYSLOG ((LOG_NOTICE, "ROOT LOGIN %s", fromhost));
} else if (getdef_bool ("LOG_OK_LOGINS")) {
SYSLOG ((LOG_INFO, "'%s' logged in %s", username, fromhost));
}
closelog ();
tmp = getdef_str ("FAKE_SHELL");
if (NULL != tmp) {
err = shell (tmp, pwd->pw_shell, newenvp); /* fake shell */
} else {
/* exec the shell finally */
err = shell (pwd->pw_shell, (char *) 0, newenvp);
}
return ((err == ENOENT) ? E_CMD_NOTFOUND : E_CMD_NOEXEC);
}
/*************************************************
Function:
call_heavygraph
Description:
The main function for contig step . its processes are as below:
1. Solve repeat
2. Merge bubble(clean bubble is optional for multikmer)
3. Remove weak edge and low coverage edge
4. Cut tips
5. Iterate multikmer(optional)
Input:
@see display_contig_usage ()
Output:
The files below:
1. *.contig
2. *.ContigIndex
3. *.update.edge
4. *.Arc
5. *.read [optional]
6. *.preGraphBasic [optional]
Return:
None.
*************************************************/
int call_heavygraph ( int argc, char ** argv )
{
time_t start_t, stop_t, time_bef, time_aft;
time ( &start_t );
boolean ret;
fprintf ( stderr, "\n********************\n" );
fprintf ( stderr, "Contig\n" );
fprintf ( stderr, "********************\n\n" );
initenv ( argc, argv );
loadVertex ( graphfile );
loadEdge ( graphfile );
if ( repeatSolve )
{
ret = loadPathBin ( graphfile );
}
swapedge();
sortedge();
freshArc();
if ( repeatSolve )
{
time ( &time_bef );
// ret = loadPathBin (graphfile);
if ( ret )
{
solveReps ();
}
else
{
fprintf ( stderr, "Repeat solving can't be done...\n" );
}
time ( &time_aft );
fprintf ( stderr, "Time spent on solving repeat: %ds.\n", ( int ) ( time_aft - time_bef ) );
}
//edgecvg_bar(edge_array,num_ed,graphfile,100);
if ( !iter && M > 0 )
{
time ( &time_bef );
bubblePinch ( 0.90, graphfile, M, 0, 1 );
time ( &time_aft );
fprintf ( stderr, "Time spent on pinching bubbles: %ds.\n", ( int ) ( time_aft - time_bef ) );
}
if ( iter && cleanBubble && M > 0 )
{
time ( &time_bef );
clean = 1;
long long oldpinCounter = 0;
long long min = 10;
int times = 0;
while ( min >= 10 )
{
times++;
if ( times >= 4 ) { break; }
bubblePinch ( 0.90, graphfile, M, 1, 0 );
min = pinCounter;
fprintf ( stderr, "%lld clean bubbles merged.\n", pinCounter );
}
time ( &time_aft );
fprintf ( stderr, "Time spent on pinching clean bubbles: %ds.\n", ( int ) ( time_aft - time_bef ) );
clean = 0;
}
if ( deLowEdge )
{
removeWeakEdges ( 2 * overlaplen, 1 );
removeLowCovEdges ( 2 * overlaplen, deLowEdge, !iter );
}
cutTipsInGraph ( 0, 0, !iter );
if ( iter )
{
Iterate ( shortrdsfile, graphfile, maxk, M ); //keepReadFile,
if ( M > 0 )
{
time ( &time_bef );
bubblePinch ( 0.90, graphfile, M, 1, 0 );
time ( &time_aft );
fprintf ( stderr, "Time spent on pinching bubbles: %ds.\n", ( int ) ( time_aft - time_bef ) );
}
freshpreGraphBasic ( iter, maxk, graphfile );
}
//output_graph(graphfile);
output_contig ( edge_array, num_ed, graphfile, overlaplen + 1 );
output_updated_edges ( graphfile );
output_heavyArcs ( graphfile );
if ( vt_array )
{
free ( ( void * ) vt_array );
vt_array = NULL;
}
if ( edge_array )
{
free_edge_array ( edge_array, num_ed_limit );
edge_array = NULL;
}
destroyArcMem ();
time ( &stop_t );
fprintf ( stderr, "\nTime spent on constructing contig: %dm.\n\n", ( int ) ( stop_t - start_t ) / 60 );
return 0;
}
main(int argc, char **argv)
{
int i, j, k, l, m, n;
int dist[20];
int reads;
int num_vertex, num_class, num_edge;
int *len_seq, num_seq, num_remain;
int **num_pa;
char **src_seq, **src_name;
char temp[100];
ALIGN **eq_class, *align;
EDGE **edge, *edge1, *edge2, *bal_edge1, *bal_edge2;
PATH *path;
int num_path;
NODES **vertex, *begin, *node, *node_next, **start_node;
LIST **list;
READINTERVAL *readinterval;
POSITION *position;
FILE *fp, *fp1;
readpar();
random1(&idum);
initenv(argc, argv);
printf("%d %d %d\n", sizeof(POSITION), sizeof(NODES), sizeof(LIST));
/* Input the length of the genome (required) */
len_seq = (int *) ckalloc(2 * MAX_NUM * sizeof(int));
src_name = alloc_name(MAX_NUM, 100);
fp = ckopen(lenfile, "r");
num_seq = readlen(fp, len_seq, src_name);
fclose(fp);
src_seq = (char **) ckalloc(2 * num_seq * sizeof(char *));
l = 0;
printf("Genome length: ");
for(i = 0; i < num_seq; i ++) {
l += len_seq[i];
printf("%d ", len_seq[i]);
}
printf("\n");
printf("Total length: %d\n", l);
/* Make reverse complements of input sequences rev(i) --> i + num_seq */
for(i = 0; i < num_seq; i ++) {
len_seq[i + num_seq] = len_seq[i];
src_seq[i] = (char *) ckalloc(len_seq[i] * sizeof(char));
src_seq[i + num_seq] = (char *) ckalloc(len_seq[i] * sizeof(char));
for(j = 0; j < len_seq[i]; j ++) {
src_seq[num_seq + i][j] = rev(src_seq[i][len_seq[i] - j - 1]);
}
}
/* Input equivalent readintervales between reads --
see the format of the equivalent readinterval files */
printf("Read equivalent readintervales...\n");
eq_class = (ALIGN **) ckalloc(2 * num_seq * sizeof(ALIGN *));
fp = ckopen(inpfile, "r");
num_class = readclass(eq_class, num_seq, fp);
fclose(fp);
printf("# equivalent readintervales input: %d\n", num_class);
/*
for(i = 0; i < 2 * num_seq; i ++) {
align = eq_class[i];
while(align) {
printf("See: \n");
output_align(align, src_name, src_seq, len_seq, num_seq);
getchar();
align = align -> next;
}
}
*/
/* Initialize the nodes: each position in each read is assigned
as a new node. An array of "list" is set up for each read */
list = (LIST **) ckalloc(2 * num_seq * sizeof(LIST *));
for(i = 0; i < 2 * num_seq; i ++) {
list[i] = (LIST *) ckalloc(len_seq[i] * sizeof(LIST));
}
printf("intitialize nodes...\n");
initialize(list, len_seq, num_seq);
printf("done.\n");
n = countnode(list, len_seq, 2 * num_seq);
printf("# of nodes before merge: %d\n", n);
/* Glue together two nodes if their corresponding positions are defined
as equivalent in a pairwise alignment */
printf("Merge...\n");
merge(num_seq, len_seq, eq_class, num_class, list);
printf("done.\n");
for(i = 0; i < num_seq; i ++) {
while(eq_class[i]) {
eq_class[i] = free_align(eq_class[i]);
}
}
free((void **) eq_class);
/* Compute the width of each node */
for(i = 0; i < 2 * num_seq; i ++) {
for(j = 0; j < len_seq[i]; j ++) {
if(!list[i][j].node -> visit) {
list[i][j].node -> num_path = countthickness(list[i][j].node);
list[i][j].node -> visit = 1;
}
}
}
cleannode(list, len_seq, 2 * num_seq);
n = countnode(list, len_seq, 2 * num_seq);
printf("# of nodes after merge: %d\n", n);
/* Add edges to the graph */
edge = (EDGE **) ckalloc(n * sizeof(EDGE *));
num_edge = graph(num_seq, len_seq, list, edge);
printf("# edges: %d\n", num_edge);
start_node = (NODES **) ckalloc(num_seq * sizeof(NODES *));
for(i = 0; i < num_seq; i ++) {
if(len_seq[i] > 0) {
start_node[i] = list[i][0].node;
} else {
start_node[i] = (NODES *) NULL;
}
}
for(i = 0; i < 2 * num_seq; i ++) {
free((void *) list[i]);
}
free((void **) list);
vertex = (NODES **) ckalloc(2 * num_edge * sizeof(NODES *));
num_vertex = count_vertex(edge, num_edge, vertex);
free((void **) edge);
num_pa = (int **) ckalloc(MAX_BRA * sizeof(int *));
for(i = 0; i < MAX_BRA; i ++) {
num_pa[i] = (int *) ckalloc(MAX_BRA * sizeof(int));
}
num_edge = count_edge_simp(vertex, num_vertex, num_pa);
printf("%d vertices %d edges (%d source %d sinks) remained.\n", num_vertex, num_edge,
num_pa[0][1], num_pa[1][0]);
/* Assign the complementary edges of each edge */
for(i = 0; i < num_vertex; i ++) {
for(j = 0; j < vertex[i] -> num_nextedge; j ++) {
edge1 = vertex[i] -> nextedge[j];
edge1 -> bal_edge = find_bal_edge(edge1, len_seq, num_seq, i);
}
}
/* Remove bulges in the graph */
printf("Shave...\n");
num_vertex = shave_graph(vertex, num_vertex);
printf("done.\n");
/* Remove cycles shorter than some threshold in the graph */
/*
printf("Shaving graph...\n");
num_vertex = rem_cycle(vertex, num_vertex);
printf("done.\n%d vertices remained.\n", num_vertex);
*/
/* remove short edges */
/*
printf("Remove shortedges...\n");
num_vertex = rem_short_edge(vertex, num_vertex, len_seq);
printf("done.\n%d vertices remained.\n", num_vertex);
fflush(stdout);
*/
num_edge = count_edge_simp(vertex, num_vertex, num_pa);
printf("%d vertices %d edges (%d source %d sinks) remained.\n", num_vertex, num_edge,
num_pa[0][1], num_pa[1][0]);
fflush(stdout);
/* Allocate the spaces for paths */
printf("Allocating paths...\n");
for(i = 0; i < num_vertex; i ++) {
vertex[i] -> num_path = 0;
}
/* Build sequence paths */
printf("Define paths...\n");
m = 0;
for(i = 0; i < num_vertex; i ++) {
for(j = 0; j < vertex[i] -> num_nextedge; j ++) {
m += vertex[i] -> nextedge[j] -> multip;
}
}
path = (PATH *) ckalloc(2 * num_seq * sizeof(PATH));
for(i = 0; i < 2 * num_seq; i ++) {
path[i].edge = (EDGE **) ckalloc(m * sizeof(EDGE *));
}
num_path = readpath(start_node, path, num_seq);
free((void **) start_node);
num_edge = count_edge_simp(vertex, num_vertex, num_pa);
m = l = 0;
for(i = 0; i < num_vertex; i ++) {
for(j = 0; j < vertex[i] -> num_nextedge; j ++) {
l += vertex[i] -> nextedge[j] -> length;
if(vertex[i] -> nextedge[j] -> length > m) {
m = vertex[i] -> nextedge[j] -> length;
}
}
}
printf("%d vertics %d edges (%d source %d sinks) remained: total length %d (maximal %d).\n", num_vertex, num_edge,
num_pa[0][1], num_pa[1][0], l, m);
fflush(stdout);
/* Make consensus of edges */
initial_edge(vertex, num_vertex, src_seq, num_seq);
printf("edge initialed\n");
/* Output sequence path */
n = 0;
for(i = 0; i < num_vertex; i ++) {
vertex[i] -> visit = i;
for(j = 0; j < vertex[i] -> num_nextedge; j ++) {
vertex[i] -> nextedge[j] -> start_cover = n;
n ++;
}
}
for(m = 0; m < num_seq; m ++) {
printf("len_path %d\n", path[m].len_path);
printf("Sequence%d: ", m + 1);
for(i = 0; i < path[m].len_path; i ++) {
printf("%d -- %d(%d,%d) --> ", path[m].edge[i] -> begin -> visit,
path[m].edge[i] -> start_cover, path[m].edge[i] -> multip,
path[m].edge[i] -> length);
if(i % 5 == 4) {
printf("\n");
}
}
if(path[m].len_path > 0) {
printf("%d\n", path[m].edge[i - 1] -> end -> visit);
} else {
printf("\n");
}
fflush(stdout);
}
/* Output graph & contigs */
sprintf(temp, "%s.edge", seqfile);
fp = ckopen(temp, "w");
sprintf(temp, "%s.graph", seqfile);
fp1 = ckopen(temp, "w");
write_graph(vertex, num_vertex, fp, fp1);
fclose(fp);
fclose(fp1);
/* Output read intervals in each edge */
sprintf(temp, "%s.intv", seqfile);
fp = ckopen(temp, "w");
write_interval(vertex, num_vertex, fp);
fclose(fp);
/* Output graphviz format graph */
sprintf(temp, "%s", outfile);
fp = ckopen(temp, "w");
output_graph(vertex, num_vertex, fp);
fclose(fp);
for(i = 0; i < MAX_BRA; i ++) {
free((void *) num_pa[i]);
}
free((void **) num_pa);
for(i = 0; i < 2 * num_seq; i ++) {
if(path[i].len_path > 0) {
free((void **) path[i].edge);
}
}
free((void *) path);
free_graph(vertex, num_vertex);
for(i = 0; i < 2 * num_seq; i ++) {
free((void *) src_seq[i]);
}
free((void **) src_seq);
free_name(src_name, MAX_NUM);
free((void *) len_seq);
}
main(int argc, char **argv)
{
int i, j, k, l, m, n;
char **src_seq, **src_name;
int *len_seq, num_seq;
char temp[100];
ALIGN **align, *aln, *aln0;
FILE *fp;
readpar();
random1(&idum);
initenv(argc, argv);
/* Input the length of the reads (required) */
len_seq = (int *) ckalloc(2 * sizeof(int));
src_seq = (char **) ckalloc(2 * sizeof(char *));
src_name = (char **) ckalloc(1 * sizeof(char *));
src_name[0] = (char *) ckalloc(100 * sizeof(char));
fp = ckopen(seqfile, "r");
num_seq = readseq1by1(src_seq, src_name, len_seq, fp);
fclose(fp);
printf("Genome length: %d\n", len_seq[0]);
/* Make reverse complements of input sequences rev(i) --> i + num_seq */
len_seq[1] = len_seq[0];
src_seq[1] = (char *) ckalloc(len_seq[0] * sizeof(char));
for(j = 0; j < len_seq[0]; j ++) {
src_seq[1][j] = rev(src_seq[0][len_seq[0] - j - 1]);
}
/* read in pairwise alignments by Reputer */
align = (ALIGN **) ckalloc(2 * sizeof(ALIGN *));
fp = ckopen(inpfile, "r");
n = readph(align, src_seq, len_seq, fp, min_leg, min_id);
fclose(fp);
printf("# alignments input: %d.\n", n);
/* Write alignments */
fp = ckopen(outfile, "w");
for(m = 0; m < 2; m ++) {
n = size_align(align[m]);
fwrite(&n, sizeof(int), 1, fp);
aln = align[m];
while(aln) {
fwrite(&(aln -> reads[1]), sizeof(int), 1, fp);
fwrite(&(aln -> mis_match), sizeof(int), 1, fp);
fwrite(&(aln -> length), sizeof(int), 1, fp);
fwrite(aln -> pos[0], sizeof(int), aln -> length, fp);
fwrite(aln -> pos[1], sizeof(int), aln -> length, fp);
aln0 = aln -> next;
free((void *) aln -> pos[0]);
free((void *) aln -> pos[1]);
free((void *) aln);
aln = aln0;
}
}
fclose(fp);
printf("Done...\n");
free((void **) align);
for(i = 0; i < 2 * num_seq; i ++) {
free((void *) src_seq[i]);
}
for(i = 0; i < num_seq; i ++) {
free((void *) src_name[i]);
}
free((void **) src_seq);
free((void **) src_name);
free((void *) len_seq);
}
/*
* su - switch user id
*
* su changes the user's ids to the values for the specified user. if
* no new user name is specified, "root" or UID 0 is used by default.
*
* Any additional arguments are passed to the user's shell. In
* particular, the argument "-c" will cause the next argument to be
* interpreted as a command by the common shell programs.
*/
int main (int argc, char **argv)
{
const char *cp;
const char *tty = NULL; /* Name of tty SU is run from */
bool doshell = false;
bool fakelogin = false;
bool amroot = false;
uid_t my_uid;
struct passwd *pw = NULL;
char **envp = environ;
char *shellstr = NULL;
char *command = NULL;
#ifdef USE_PAM
char **envcp;
int ret;
#else /* !USE_PAM */
int err = 0;
RETSIGTYPE (*oldsig) (int);
int is_console = 0;
struct spwd *spwd = 0;
#ifdef SU_ACCESS
char *oldpass;
#endif
#endif /* !USE_PAM */
(void) setlocale (LC_ALL, "");
(void) bindtextdomain (PACKAGE, LOCALEDIR);
(void) textdomain (PACKAGE);
change_environment = true;
/*
* Get the program name. The program name is used as a prefix to
* most error messages.
*/
Prog = Basename (argv[0]);
OPENLOG ("su");
/*
* Process the command line arguments.
*/
{
/*
* Parse the command line options.
*/
int option_index = 0;
int c;
static struct option long_options[] = {
{"command", required_argument, NULL, 'c'},
{"help", no_argument, NULL, 'h'},
{"login", no_argument, NULL, 'l'},
{"preserve-environment", no_argument, NULL, 'p'},
{"shell", required_argument, NULL, 's'},
{NULL, 0, NULL, '\0'}
};
while ((c =
getopt_long (argc, argv, "c:hlmps:", long_options,
&option_index)) != -1) {
switch (c) {
case 'c':
command = optarg;
break;
case 'h':
usage (E_SUCCESS);
break;
case 'l':
fakelogin = true;
break;
case 'm':
case 'p':
/* This will only have an effect if the target
* user do not have a restricted shell, or if
* su is called by root.
*/
change_environment = false;
break;
case 's':
shellstr = optarg;
break;
default:
usage (E_USAGE); /* NOT REACHED */
}
}
if ((optind < argc) && (strcmp (argv[optind], "-") == 0)) {
fakelogin = true;
optind++;
if ( (optind < argc)
&& (strcmp (argv[optind], "--") == 0)) {
optind++;
}
}
}
initenv ();
my_uid = getuid ();
amroot = (my_uid == 0);
/*
* Get the tty name. Entries will be logged indicating that the user
* tried to change to the named new user from the current terminal.
*/
tty = ttyname (0);
if ((isatty (0) != 0) && (NULL != tty)) {
#ifndef USE_PAM
is_console = console (tty);
#endif
} else {
/*
* Be more paranoid, like su from SimplePAMApps. --marekm
*/
if (!amroot) {
fprintf (stderr,
_("%s: must be run from a terminal\n"),
Prog);
exit (1);
}
tty = "???";
}
/*
* The next argument must be either a user ID, or some flag to a
* subshell. Pretty sticky since you can't have an argument which
* doesn't start with a "-" unless you specify the new user name.
* Any remaining arguments will be passed to the user's login shell.
*/
if ((optind < argc) && ('-' != argv[optind][0])) {
STRFCPY (name, argv[optind++]); /* use this login id */
if ((optind < argc) && (strcmp (argv[optind], "--") == 0)) {
optind++;
}
}
if ('\0' == name[0]) { /* use default user */
struct passwd *root_pw = getpwnam ("root");
if ((NULL != root_pw) && (0 == root_pw->pw_uid)) {
(void) strcpy (name, "root");
} else {
root_pw = getpwuid (0);
if (NULL == root_pw) {
SYSLOG ((LOG_CRIT, "There is no UID 0 user."));
su_failure (tty);
}
(void) strcpy (name, root_pw->pw_name);
}
}
doshell = (argc == optind); /* any arguments remaining? */
if (NULL != command) {
doshell = false;
}
/*
* Get the user's real name. The current UID is used to determine
* who has executed su. That user ID must exist.
*/
pw = get_my_pwent ();
if (NULL == pw) {
fprintf (stderr,
_("%s: Cannot determine your user name.\n"),
Prog);
SYSLOG ((LOG_WARN, "Cannot determine the user name of the caller (UID %lu)",
(unsigned long) my_uid));
su_failure (tty);
}
STRFCPY (oldname, pw->pw_name);
#ifndef USE_PAM
#ifdef SU_ACCESS
/*
* Sort out the password of user calling su, in case needed later
* -- chris
*/
spwd = getspnam (oldname); /* !USE_PAM, no need for xgetspnam */
if (NULL != spwd) {
pw->pw_passwd = spwd->sp_pwdp;
}
oldpass = xstrdup (pw->pw_passwd);
#endif /* SU_ACCESS */
#else /* USE_PAM */
ret = pam_start ("su", name, &conv, &pamh);
if (PAM_SUCCESS != ret) {
SYSLOG ((LOG_ERR, "pam_start: error %d", ret);
fprintf (stderr,
_("%s: pam_start: error %d\n"),
Prog, ret));
exit (1);
}
