int find_status(struct cv_list cur_cv, struct cv_list *cv, int num_cv, char *name1, char *name2)
{
int i = 0;
struct I src1, dst1, src2, dst2;
int res = -1;
char name[50];
src1 = assign_I(cur_cv.a1, cur_cv.a2);
dst1 = assign_I(cur_cv.b1, cur_cv.b2);
for( i = 0; i < num_cv; i++ ) {
src2 = assign_I(cv[i].a1, cv[i].a2);
dst2 = assign_I(cv[i].b1, cv[i].b2);
if( (strcmp( cv[i].name2, "NAN" ) != 0) && (strcmp( cv[i].name3, "NAN") != 0) ) {
strcpy( name, cv[i].name2 );
}
else if( (strcmp( cv[i].name2, "NAN" ) == 0) && (strcmp( cv[i].name3, "NAN") != 0) ) {
strcpy( name, cv[i].name3 );
}
else if( (strcmp( cv[i].name3, "NAN" ) == 0) && (strcmp( cv[i].name2, "NAN") != 0) ) {
strcpy( name, cv[i].name2 );
}
else {
fatalf("both out-species not found %s %s\n", cv[i].name2, cv[i].name3);
}
if( (cur_cv.fid == cv[i].fid) && ( ((strict_almost_equal(src1, src2) == true) && (strict_almost_equal(dst1, dst2) == true)) || ( (strict_almost_equal(src1, dst2) == true) && (strict_almost_equal(dst1, src2) == true) )) && (strcmp(name1, cv[i].name1) == 0) && (strcmp(name2, name) == 0)) {
res = i;
}
}
if( res == -1 ) {
fatalf("status not found %d\n", cur_cv.fid);
}
return(res);
}
void get_spename(char *configfile) {
FILE *fp;
char buf[500], sn[20];
int tag, die, r, i;
fp = ckopen(configfile, "r");
die = 0;
while(fgets(buf, 500, fp)) {
if (buf[0] == '>' && strstr(buf, "species") != NULL) {
die = 1;
while(fgets(buf, 500, fp)) {
if (buf[0] == '\n')
break;
if (sscanf(buf, "%s %d", sn, &tag) != 2)
fatalf("cannot parse species %s", buf);
strcpy(Spename[Spesz], sn);
Spetag[Spesz] = tag;
++Spesz;
}
}
if (die == 1)
break;
}
fclose(fp);
if (Spesz > MAXSPE)
fatalf("MAXSPE %d too small (%d)", MAXSPE, Spesz);
for (i = r = 0; i < Spesz; i++)
if (Spetag[i] == 0)
++r;
if (r == 0)
fatal("ref species not specified");
if (r > 1)
fatal("ref speices more than one");
}
void get_args (int argc, char **argv, int *output_mode, struct mafFile **file, char **id,
struct MOTIF **motif, int *do_order, int *nrow, float *cutoff, int *misses_allowed)
{
int i;
if (argc < 5 || argc > 12)
fatalf (SYNTAX);
if (strcmp (argv[1], "-verbose") == 0)
*output_mode = VERBOSE;
else if (strcmp (argv[1], "-gala") == 0)
*output_mode = GALA;
else if (strcmp (argv[1], "-hgb") == 0)
*output_mode = HGB;
else
fatalf (SYNTAX);
*file = mafOpen (argv[2]);
strcpy (*id, argv[4]);
i = 5;
argc -= 5;
while (argc)
{
if (strcmp (argv[i], "-order") == 0)
*do_order = 1;
else if (strcmp (argv[i], "-nseq") == 0) {
i++;
argc--;
if (argc == 0)
fatal (SYNTAX);
*nrow = atoi (argv[i]);
if (*nrow < 2)
fatal ("Number of sequences must be at least 2.\n");
} else if (strcmp (argv[i], "-cut") == 0) {
i++;
argc--;
if (argc == 0)
fatal (SYNTAX);
*cutoff = atof (argv[i]);
if (*cutoff < 0.0 || *cutoff > 1.0)
fatal ("Cutoff value must be between 0 and 1.\n");
} else if (strcmp (argv[i], "-nm") == 0) {
i++;
argc--;
if (argc == 0)
fatal (SYNTAX);
*misses_allowed = atoi (argv[i]);
if (*misses_allowed < 0)
fatal ("Number of misses cannot be negative.\n");
} else
fatalf (SYNTAX);
argc--;
i++;
}
init_motif (motif, argv[3], *cutoff, *id);
}
/* ckargs -- check that only certain parameters are set on the command line */
void ckargs(const char *options, int argcx, char **argvx, int non_options)
{
int i;
argc = argcx;
argv = argvx;
argv0 = argv0 ? argv0 : argv[0];
for (i = non_options+1; i < argc; ++i)
if (argv[i][1] != '=')
fatalf("Improper command option: '%s'.", argv[i]);
else if (!strchr(options, argv[i][0]))
fatalf("Available options: %s\n", options);
}
int add_one_ops(struct ops_list *ops, int id, char *buf, struct n_pair *contigs, int num_contigs, int *len_sum, int sp_mode)
{
int ctg_id = -1;
char sp_name[LEN_NAME], ctg_name[LEN_NAME];
char name1[LEN_NAME], name2[LEN_NAME];
int count = id;
int mode = -1;
sscanf(buf, "%*s %*s %*s %*s %*s %*s %*s %d %*s", &mode);
if( mode == sp_mode ) {
sscanf(buf, "%c %s %d %d %s %d %d %d %d %f", &ops[count].sign, name1, &ops[count].srcStart, &ops[count].srcEnd, name2, &ops[count].dstStart, &ops[count].dstEnd, &ops[count].sp_id, &ops[count].dir, &ops[count].pid);
ops[count].ctg_id1 = -1;
ops[count].ctg_id2 = -1;
if( num_contigs > 0 ) {
concat_ctg_name(name1, sp_name, ctg_name);
ctg_id = get_ctg_id(sp_name, ctg_name, contigs, num_contigs);
if( ctg_id >= num_contigs ) {
fatalf("contig id %d exceeds %d in util_ops.c\n", ctg_id, num_contigs);
}
else if( ctg_id != -1 ) {
ops[count].srcStart = ops[count].srcStart + len_sum[ctg_id];
ops[count].srcEnd = ops[count].srcEnd + len_sum[ctg_id];
ops[count].ctg_id1 = ctg_id;
}
if( ops[count].sign != 'd' ) {
concat_ctg_name(name2, sp_name, ctg_name);
ctg_id = get_ctg_id(sp_name, ctg_name, contigs, num_contigs);
}
else {
ctg_id = -1;
}
if( (ops[count].sign != 'd') && ((ctg_id >= num_contigs) || (ctg_id < 0) ) ) {
fatalf("contig id %d exceeds %d in util_ops.c\n", ctg_id, num_contigs);
}
else if( ctg_id != -1 ) {
ops[count].dstStart = ops[count].dstStart + len_sum[ctg_id];
ops[count].dstEnd = ops[count].dstEnd + len_sum[ctg_id];
ops[count].ctg_id2 = ctg_id;
}
else {
ops[count].ctg_id2 = ctg_id;
}
}
count = count + 1;
}
return(count);
}
static void split_args(struct entry *e, char *buf)
{
char *p = buf, *q;
char *key, *value;
for (;;) {
/* skip whitespace before arg */
while (Uisspace(*p))
p++;
if (!*p)
return;
key = p;
/* parse the key */
for (q = p ; Uisalnum(*q) ; q++)
;
if (*q != '=')
fatalf(EX_CONFIG, "configuration file %s: "
"bad character '%c' in argument on line %d",
MASTER_CONFIG_FILENAME, *q, e->lineno);
*q++ = '\0';
/* parse the value */
if (*q == '"') {
/* quoted string */
value = ++q;
q = strchr(q, '"');
if (!q)
fatalf(EX_CONFIG, "configuration file %s: missing \" on line %d",
MASTER_CONFIG_FILENAME, e->lineno);
*q++ = '\0';
}
else {
/* simple word */
value = q;
while (*q && !Uisspace(*q))
q++;
if (*q)
*q++ = '\0';
}
if (e->nargs == MAXARGS)
fatalf(EX_CONFIG, "configuration file %s: too many arguments on line %d",
MASTER_CONFIG_FILENAME, e->lineno);
e->args[e->nargs].key = key;
e->args[e->nargs].value = value;
e->nargs++;
p = q;
}
}
double mafScoreRange(struct mafAli *maf, int start, int size) {
uchar ai, ar, bi, br;
int i;
double score;
struct mafComp *c1, *c2;
if (start < 0 || size <= 0 || start+size > maf->textSize)
fatalf("mafScoreRange: start = %d, size = %d, textSize = %d\n",
start, size, maf->textSize);
if (ss == NULL)
fatal("mafScoreRange: scores not initialized");
score = 0.0;
for (i = start; i < start+size; ++i) {
for (c1 = maf->components; c1 != NULL; c1 = c1->next) {
br = c1->text[i];
for (c2 = c1->next; c2 != NULL; c2 = c2->next) {
bi = c2->text[i];
score += SS(br,bi);
if (i > 0) {
ar = c1->text[i-1];
ai = c2->text[i-1];
score -= GAP2(ar,ai,br,bi);
}
}
}
}
return score;
}
void
_cgo_sys_thread_start(ThreadStart *ts)
{
pthread_attr_t attr;
sigset_t ign, oset;
pthread_t p;
size_t size;
int err;
sigfillset(&ign);
pthread_sigmask(SIG_SETMASK, &ign, &oset);
// Not sure why the memset is necessary here,
// but without it, we get a bogus stack size
// out of pthread_attr_getstacksize. C'est la Linux.
memset(&attr, 0, sizeof attr);
pthread_attr_init(&attr);
size = 0;
pthread_attr_getstacksize(&attr, &size);
// Leave stacklo=0 and set stackhi=size; mstack will do the rest.
ts->g->stackhi = size;
err = pthread_create(&p, &attr, threadentry, ts);
pthread_sigmask(SIG_SETMASK, &oset, nil);
if (err != 0) {
fatalf("pthread_create failed: %s", strerror(err));
}
}
void get_numchr(char *configfile) {
FILE *fp;
char buf[500];
fp = ckopen(configfile, "r");
while(fgets(buf, 500, fp)) {
if (buf[0] == '>' && strstr(buf, "numchr") != NULL) {
if (fgets(buf, 500, fp) && sscanf(buf, "%d", &HSACHR) != 1)
fatalf("missing numchr string in config file.");
break;
}
}
fclose(fp);
if (HSACHR == 0)
fatalf("missing numchr string in config file.");
}
void get_minlen(char *configfile) {
FILE *fp;
char buf[500];
fp = ckopen(configfile, "r");
while(fgets(buf, 500, fp)) {
if (buf[0] == '>' && strstr(buf, "resolution") != NULL) {
if (fgets(buf, 500, fp) && sscanf(buf, "%d", &MINLEN) != 1)
fatalf("missing resolution string in config file.");
break;
}
}
fclose(fp);
if (MINLEN == 0)
fatalf("missing resolution string in config file.");
}
bool is_repeats(struct exons_list *exons, int num_exons, char *name, int from, int to) // exons assume to be already sorted by genomic positions
{
int i = 0;
int mid = 0;
bool res = false;
struct I reg;
if( to > from ) {
reg = assign_I(from, to);
}
else {
fatalf("unexpected interval: %d-%d\n", from, to);
}
mid = quick_search_close_exons(exons, 0, num_exons-1, from);
i = mid;
while( (res == false) && (i < num_exons) && (exons[i].reg.lower <= to)) {
if( width(reg) <= SHORT_LEN_TH ) {
// (strcmp(reg, exons[i].reg) == 0) && (almost_subset(reg, exons[i].reg) == true) ) {
// printf("%d-%d too short\n", from, to);
res = true;
}
else if( (strcmp(name, exons[i].chr) == 0) && subset(reg, exons[i].reg) ) {
// printf("%d-%d belongs to %s %d-%d\n", from, to, exons[i].chr, exons[i].reg.lower, exons[i].reg.upper);
res = true;
}
i++;
}
return(res);
}
void get_netdir(char *configfile) {
FILE *fp;
char buf[500];
fp = ckopen(configfile, "r");
while(fgets(buf, 500, fp)) {
if (buf[0] == '>' && strstr(buf, "netdir") != NULL) {
if (fgets(buf, 500, fp) && sscanf(buf, "%s", Netdir) != 1)
fatalf("missing netdir string in config file.");
break;
}
}
fclose(fp);
if (Netdir[0] == '\0')
fatalf("missing netdir string in config file.");
}
int width(struct I temp)
{
if( temp.lower > temp.upper ) {
fatalf("empty interval in (%d,%d)", temp.lower, temp.upper);
}
else return(temp.upper - temp.lower);
}
void get_treestr2(char *configfile) {
FILE *fp;
char buf[500];
fp = ckopen(configfile, "r");
while(fgets(buf, 500, fp)) {
if (buf[0] == '>' && strstr(buf, "tree2") != NULL) {
if (fgets(buf, 500, fp) && sscanf(buf, "%s", Treestr2) != 1)
fatalf("missing tree string in config file.");
break;
}
}
fclose(fp);
if (Treestr2[0] == '\0')
fatalf("missing tree string in config file.");
}
/* ckopen -------------------------------------- open file; check for success */
FILE *ckopen(const char *name, const char *mode)
{
FILE *fp;
if ((fp = fopen(name, mode)) == NULL)
fatalf("Cannot open %s.", name);
return fp;
}
int get_level(char *s) {
int i = 0;
while (s[i] == ' ')
++i;
if (i > MAXDEP)
fatalf("MAXDEP = %d not enough", MAXDEP);
return i;
}
void read_ops_file(char *name, FILE *f, struct ops_list *ops, int num_ops, int sp_mode, struct n_pair *contigs, int num_contigs, char *ref_name)
{
char buf[1000];
bool is_in = false;
char temp_name1[LEN_NAME], temp_name2[LEN_NAME];
int *len_sum;
int count = 0;
if( num_contigs > 0 ) {
len_sum = (int *) ckalloc(sizeof(int) * num_contigs);
cal_length_sum(len_sum, contigs, num_contigs);
}
strcpy(temp_name1, "");
strcpy(temp_name2, "");
fseek(f, 0, SEEK_SET);
while(fgets(buf, 500, f)) {
if( buf[0] == '#' ) {
is_in = false;
sscanf(buf, "%*s %s %s", temp_name1, temp_name2);
if( (strcmp(temp_name1, ref_name) == 0) && (strcmp(temp_name2, name) == 0 )) {
is_in = true;
}
count = 0;
}
else {
if( is_in == true ) {
if( sp_mode == SELF1 ) {
count = add_one_ops(ops, count, buf, contigs, num_contigs, len_sum, sp_mode);
}
else if( sp_mode == SELF2 ) {
count = add_one_ops(ops, count, buf, contigs, num_contigs, len_sum, sp_mode);
}
else {
fatalf("%d: mode must be %d or %d in util_ops.c\n", sp_mode, SELF1, SELF2);
}
}
if( count > num_ops ) {
fatalf("counting events mismatches: %d in %s\n", num_ops, name);
}
}
}
if( num_contigs > 0 ) free(len_sum);
}
Logfile *
logfileOpen(const char *path, size_t bufsz, int fatal_flag)
{
Logfile *lf;
const char *patharg;
int ret;
debug(50, 1) ("logfileOpen: opening log %s\n", path);
CBDATA_INIT_TYPE(Logfile);
lf = cbdataAlloc(Logfile);
xstrncpy(lf->path, path, MAXPATHLEN);
patharg = path;
/* need to call the per-logfile-type code */
if (strncmp(path, "stdio:", 6) == 0)
{
patharg = path + 6;
ret = logfile_mod_stdio_open(lf, patharg, bufsz, fatal_flag);
}
else if (strncmp(path, "daemon:", 7) == 0)
{
patharg = path + 7;
ret = logfile_mod_daemon_open(lf, patharg, bufsz, fatal_flag);
}
else if (strncmp(path, "udp:", 4) == 0)
{
patharg = path + 4;
ret = logfile_mod_udp_open(lf, patharg, bufsz, fatal_flag);
#if HAVE_SYSLOG
}
else if (strncmp(path, "syslog:", 7) == 0)
{
patharg = path + 7;
ret = logfile_mod_syslog_open(lf, patharg, bufsz, fatal_flag);
#endif
}
else
{
ret = logfile_mod_stdio_open(lf, patharg, bufsz, fatal_flag);
}
if (!ret)
{
if (fatal_flag)
fatalf("logfileOpen: path %s: couldn't open!\n", path);
else
debug(50, 1) ("logfileOpen: path %s: couldn't open!\n", path);
lf->f_close(lf);
cbdataFree(lf);
return NULL;
}
assert(lf->data != NULL);
if (fatal_flag)
lf->flags.fatal = 1;
lf->sequence_number = 0;
return lf;
}
int spe_idx(char *sname) {
int i;
for (i = 0; i < Spesz; i++)
if (same_string(Spename[i], sname))
break;
if (i == Spesz)
fatalf("unkonwn species %s", sname);
return i;
}
void get_chaindir(char *configfile) {
FILE *fp;
char buf[500];
fp = ckopen(configfile, "r");
while(fgets(buf, 500, fp)) {
if (buf[0] == '#' || buf[0] == '\n')
continue;
if (buf[0] == '>' && strstr(buf, "chaindir") != NULL) {
if (fgets(buf, 500, fp) && sscanf(buf, "%s", Chaindir) != 1)
fatalf("missing chaindir string in config file.");
break;
}
}
fclose(fp);
if (Chaindir[0] == '\0')
fatalf("missing chaindir string in config file.");
}
int FreePM_session::InitDevice(int _dev_type, FreePM_DeskTop *pDesktop)
{
int rc,id,idd,nx,ny, bytes_PerPixel;
static int params[4];
PBYTE pBmpBuffer = NULL;
static int LbmpBuffOld = 0;
int LbmpBuff;
switch(_dev_type)
{
case FPM_DEV_PMWIN: /* */
debug(7, 0) ("FreePM_session::InitDevice PMWIN: %d \n", _dev_type);
pDesktop->GetPar(nx, ny, bytes_PerPixel);
debug(7, 0)("nx=%u, ny=%u, bpp=%u\n", nx, ny, bytes_PerPixel);
if(pBmpBuffer)
{
LbmpBuff = bytes_PerPixel * nx * (ny+2)+4;
if(LbmpBuff != LbmpBuffOld)
pBmpBuffer = (BYTE *) realloc(pBmpBuffer,LbmpBuff);
} else {
LbmpBuff = bytes_PerPixel * nx * (ny+2)+4;
pBmpBuffer = (BYTE *)malloc(LbmpBuff);
}
LbmpBuffOld = LbmpBuff;
debug(7, 0) ("pDesktop=%lx\n", pDesktop);
//pDesktop->pVBuffmem = (int *) initGD(nx, ny);
pDesktop->pVBuffmem = pBmpBuffer;
/* start separate thread for PM window */
params[0] = (int)pDesktop;
params[1] = (int)pDesktop->pVBuffmem;
params[2] = (int)(&_DeskTopSendQueue);
params[3] = 0;
id = _beginthread(_FPM_PMWinStart,NULL, THREAD_STACK_SIZE * 16, (void *)params);
break;
case FPM_DEV_PMWIN_DIR:
debug(7, 0) ("WARNING:FreePM_session::InitDevice device PMWIN_DIR not yet supported\n");
break;
case FPM_DEV_SERVERMEM:
debug(7, 0) ("FreePM_session::InitDevice SERVERMEM\n", _dev_type);
pDesktop->GetPar(nx, ny, bytes_PerPixel);
/*rc = initGD( nx, ny);*/
pDesktop->pVBuffmem = (int *) initGD(nx, ny);
debug(7, 0) ("WARNING:FreePM_session::InitDevice device SERVERMEM not yet supported\n");
break;
default:
debug(7, 0) ("WARNING:FreePM_session::InitDevice device %i not supported\n", _dev_type);
fatalf("Device not supported");
break;
}
return rc;
}
void ctx_load_program(struct context *ctx, const char *name, const char *vertpath, const char *fragpath)
{
struct program *p = program_load(name, vertpath, fragpath);
if (! p) fatalf("ctx", "failed to load program '%s'", name);
ctx_setup_program(ctx, p);
list_push(&ctx->programs, p);
}
static void
do_select_init()
{
kdpfd = epoll_create(Squid_MaxFD);
if (kdpfd < 0)
fatalf("comm_select_init: epoll_create(): %s\n", xstrerror());
fd_open(kdpfd, FD_UNKNOWN, "epoll ctl");
commSetCloseOnExec(kdpfd);
epoll_state = xcalloc(Squid_MaxFD, sizeof(*epoll_state));
}
// inittls allocates a thread-local storage slot for g.
//
// It finds the first available slot using pthread_key_create and uses
// it as the offset value for runtime.tlsg.
static void
inittls(void **tlsg, void **tlsbase)
{
pthread_key_t k;
int i, err;
err = pthread_key_create(&k, nil);
if(err != 0) {
fatalf("pthread_key_create failed: %d", err);
}
pthread_setspecific(k, (void*)magic1);
for (i=0; i<PTHREAD_KEYS_MAX; i++) {
if (*(tlsbase+i) == (void*)magic1) {
*tlsg = (void*)(i*sizeof(void *));
pthread_setspecific(k, 0);
return;
}
}
fatalf("could not find pthread key");
}
/* find a value in the hashtable or die if the key does not exist in the hash*/
void* must_find_hashtable(hashtable* const hash,
const char* const name,
const int len)
{
pre(name != NULL);
bin* bin = lookup_hashtable(hash, name, len);
if(bin == NULL){
fatalf("did not find %s in the hash", name);
}
return bin->val;
}
// inittls allocates a thread-local storage slot for g.
//
// It finds the first available slot using pthread_key_create and uses
// it as the offset value for runtime.tls_g.
static void
inittls(void **tlsg, void **tlsbase)
{
pthread_key_t k;
int i, err;
void *handle, *get_ver;
// Check for Android Q where we can use the free TLS_SLOT_APP slot.
handle = dlopen("libc.so", RTLD_LAZY);
if (handle == NULL) {
fatalf("inittls: failed to dlopen main program");
return;
}
// android_get_device_api_level is introduced in Android Q, so its mere presence
// is enough.
get_ver = dlsym(handle, "android_get_device_api_level");
dlclose(handle);
if (get_ver != NULL) {
*tlsg = (void *)(TLS_SLOT_APP*sizeof(void *));
return;
}
err = pthread_key_create(&k, nil);
if(err != 0) {
fatalf("pthread_key_create failed: %d", err);
}
pthread_setspecific(k, (void*)magic1);
// If thread local slots are laid out as we expect, our magic word will
// be located at some low offset from tlsbase. However, just in case something went
// wrong, the search is limited to sensible offsets. PTHREAD_KEYS_MAX was the
// original limit, but issue 19472 made a higher limit necessary.
for (i=0; i<384; i++) {
if (*(tlsbase+i) == (void*)magic1) {
*tlsg = (void*)(i*sizeof(void *));
pthread_setspecific(k, 0);
return;
}
}
fatalf("inittls: could not find pthread key");
}
void read_configuration(const char* const filename,
hashtable* const id2chroms,
hashtable* insertlengths,
uint* const averagecoverage)
{
size_t n = 1;
char* fptr = ckalloc(n + 1);
char rgname[128]; // name of the library
uint minsize; // minimum size in a proper pair
uint maxsize; // maximum size in a proper pair
char chrom[128]; // chromosome
uint meancov; // mean coverage on that chromosome
FILE* fp = ckopen(filename,"r");
while(getline(&fptr, &n, fp) != -1){
if(strncmp(fptr, "IL", 2) == 0){
if(sscanf(fptr, "IL %s %u %u\n", rgname, &minsize, &maxsize) != 3){
fatalf("error in reading the insert length range: %s", fptr);
}
int32_t* range = ckalloc(2*sizeof(int32_t));
range[0] = minsize;
range[1] = maxsize;
add_hashtable(insertlengths,rgname,strlen(rgname),range);
} else if(averagecoverage && (strncmp(fptr, "RC", 2) == 0)){
if(sscanf(fptr, "RC %s %u\n", chrom, &meancov) != 2){
fatalf("error in reading the mean coverage: %s", fptr);
}
averagecoverage[must_find_hashtable_int(id2chroms,
chrom,
strlen(chrom))] = meancov;
} else {
fatalf("unknown tag in configuration: %s", fptr);
}
}
ckfree(fptr);
fclose(fp);
}
/* ckalloc -------------------------------- allocate space; check for success */
void *ckalloc(size_t amount)
{
void *p;
if ((long)amount < 0) /* was "<= 0" -CR */
fatal("ckalloc: request for negative space.");
if (amount == 0)
amount = 1; /* ANSI portability hack */
if ((p = malloc(amount)) == NULL)
fatalf("Ran out of memory trying to allocate %lu.",
(unsigned long)amount);
return p;
}
struct mafFile *mafOpen(char *fileName, int verbose) {
struct mafFile *mf;
FILE *fp;
char buf[500], *s;
mf = ckalloc(sizeof(struct mafFile));
mf->next = NULL;
fp = mf->fp = ckopen(fileName, "r");
if (fgets(buf, 500, fp) == NULL)
fatalf("empty file %s", fileName);
if (sscanf(buf, "##maf version=%d", &(mf->version)) != 1)
fatalf("improper maf header line: %s", buf);
if ((s = strstr(buf, "scoring=")) != NULL)
mf->scoring = copy_string(s+8);
else
mf->scoring = NULL;
mf->alignments = NULL;
mf->fileName = copy_string(fileName);
mf->line_nbr = 0;
mf->verbose = verbose;
return mf;
}
int get_id_in_list(char *name, struct sp_list *list, int num_sp)
{
int i;
i = 0;
while( ( i < num_sp) && (strcmp(name, list[i].name) != 0) ) i++;
if( i >= num_sp ) {
fatalf("error: no species name exist in %s\n", name);
return(num_sp);
}
else return(list[i].id);
}