void benchmark() {
srand(time(NULL));
char key[9], value[13];
int i;
printf("> Benchmarking dispertion with %d buckets and %d entry\n", DISPERS_BENCH_BUCKET, DISPERS_BENCH_ENTRY);
hashtable defaultTable = init_hashtable(DISPERS_BENCH_BUCKET);
hashtable idxTable = init_hashtable(DISPERS_BENCH_BUCKET);
set_hfunc(&idxTable, &idx_hashfunction);
for (i=0; i < DISPERS_BENCH_ENTRY; i++) {
randomString(key, 9);
randomString(value, 13);
/*
printf("%s:%s\n", key, value);
*/
put(&defaultTable, key, value);
put(&idxTable, key, value);
}
/*
printf(":: Default hash function\n");
displayHashTable(defaultTable);
displayStats(get_stats(defaultTable));
printf(":: Idx hash function\n");
displayHashTable(defaultTable);
displayStats(get_stats(idxTable));
*/
}
exchange_t *declare_exchange(int *status,
vhost_t *vhost,
amqp_bytes_t name,
exchange_type_t *type,
amqp_boolean_t durable,
amqp_boolean_t auto_delete,
amqp_table_t arguments)
{
exchange_t *x = internal_lookup_exchange(vhost, name);
if (x == NULL) {
x = malloc(sizeof(exchange_t));
x->name = amqp_bytes_malloc_dup(name);
x->type = type;
x->type_data = NULL;
x->durable = durable;
x->auto_delete = auto_delete;
x->arguments = AMQP_EMPTY_TABLE; /* TODO: copy arguments */
init_hashtable(&x->fanout, 127, NULL, NULL);
init_hashtable(&x->direct, 127, NULL, NULL);
type->init(x);
info("Exchange \"%.*s\" of type %.*s created",
name.len, name.bytes,
type->name.len, type->name.bytes);
hashtable_put(&vhost->exchanges, name, x);
}
return x;
}
void testSuite() {
hashtable table = init_hashtable(7);
printf(":: Table elems: %d\n", table->p);
printf(":: Inserting elements in hashtable\n");
put(&table, "toto", "hey");
put(&table, "lablab", "monk");
put(&table, "blabla", "plop");
put(&table, "toto", "ho!");
put(&table, "tops", "hahah");
put(&table, "pots", "huhuh");
displayHashTable(table);
printf(":: Seeking for hello: %s\n", get(table, "hello"));
printf(":: Seeking for toto: %s\n", get(table, "toto"));
printf(":: Removing elem tops, toto and lablab\n");
rmove(&table, "tops");
rmove(&table, "toto");
rmove(&table, "lablab");
displayHashTable(table);
printf(":: Changing hash function and adding two elems\n");
hashtable table2 = init_hashtable(7);
set_hfunc(&table2, &idx_hashfunction);
put(&table2, "toto", "hey");
put(&table2, "blabla", "plop");
put(&table2, "lablab", "monk");
displayHashTable(table2);
printf(":: Fonction for first hashtable: %p\n", get_hfunc(table));
printf(":: Fonction for second hashtable: %p\n", get_hfunc(table2));
printf(":: Stats for first table\n");
put(&table, "lablab", "monk");
put(&table, "toto", "ho!");
put(&table, "tops", "hahah");
displayStats(get_stats(table));
printf(":: Stats for second table\n");
displayStats(get_stats(table2));
printf(":: Rehash table with 11 buckets\n");
set_hfunc(&table, &idx_hashfunction);
rehash_table(&table, 11);
displayHashTable(table);
}
xsbBucket *search_bucket(Cell name,
xsbHashTable *table,
enum xsbHashSearchOp search_op)
{
xsbBucket *bucket, *prev;
if (! table->initted) init_hashtable(table);
prev = NULL;
bucket = get_top_bucket(table,table_hash(name,table->length));
while (bucket && bucket->name) {
if (bucket->name == name) {
if (search_op == hashtable_delete) {
if (!prev) {
/* if deleting a top bucket, copy the next bucket into the top one
and delete that next bucket. If no next, then just nullify name */
prev = bucket;
bucket=bucket->next;
if (bucket) {
/* use memcpy() because client bucket might have extra fields */
memcpy(prev, bucket, table->bucket_size);
free(bucket);
} else {
mark_bucket_free(prev,table->bucket_size);
xsb_dbgmsg((LOG_HASHTABLE,
"SEARCH_BUCKET: Destroying storage handle for %s\n",
string_val(name)));
xsb_dbgmsg((LOG_HASHTABLE,
"SEARCH_BUCKET: Bucket nameptr is %p, next bucket %p\n",
prev->name, prev->next));
}
} else {
/* Not top bucket: rearrange pointers & free space */
prev->next = bucket->next;
free(bucket);
}
return NULL;
} else
return bucket;
}
prev = bucket;
bucket = bucket->next;
}
/* not found */
if (search_op != hashtable_insert) return NULL;
/* else create new bucket */
/* calloc nullifies the allocated space; CLIENTS RELY ON THIS */
if (!bucket) { /* i.e., it is not a top bucket */
bucket = (xsbBucket *)calloc(1,table->bucket_size);
if (!bucket)
xsb_exit("Out of Memory: Can't allocate hash bucket");
prev->next = bucket;
/* NOTE: not necessary to nullify bucket->next because of calloc() */
}
bucket->name = name;
return bucket;
}
void init_node(cmsg_bytes_t container_name) {
if (container_name.len == 0) {
unsigned char buf[CMSG_UUID_BUF_SIZE];
gen_uuid(buf);
_container_name = cmsg_bytes_malloc_dup(CMSG_BYTES(CMSG_UUID_BUF_SIZE, buf));
} else {
_container_name = cmsg_bytes_malloc_dup(container_name);
}
info("Local container name is <<%.*s>>\n", _container_name.len, _container_name.bytes);
init_hashtable(&node_class_table,
31,
NULL,
NULL);
init_hashtable(&directory,
10007,
node_incref,
node_decref);
}
int main(int argc, char **argv)
{
list_node *hashtable[HASHTABLE_SIZE];
init_hashtable(hashtable);
// Determining the file size
struct stat st;
if(stat("names.txt", &st) == -1)
return EXIT_FAILURE;
// Reading all contents to memory
char contents[st.st_size + 1];
FILE *h = fopen("names.txt", "r");
size_t n = fread(contents, sizeof(char), st.st_size, h);
fclose(h);
// Extracting names and inserting in hashtable
int j;
char aux[NAME_LENGTH+1];
for(int i = 0; i < n; i++) {
bzero(aux, NAME_LENGTH);
j = 0;
while(contents[i] != ',' && i < n) {
if(contents[i] != '"')
aux[j++] = contents[i];
i++;
}
aux[j] = '\0';
insert_name(hashtable, aux, strlen(aux));
}
// Reading names
long total = 0;
int pos = 1;
list_node *aux_node;
for(int i = 0; i < HASHTABLE_SIZE; i++) {
if(hashtable[i] != NULL) {
aux_node = hashtable[i];
while(aux_node != NULL) {
total += name_score(
aux_node->name,
strlen(aux_node->name),
pos++);
aux_node = aux_node->next;
}
}
}
printf("%ld\n", total);
return EXIT_SUCCESS;
}
int main()
{
Status status;
char buff[100];
// Setup configuration for validating alphabetic characters
Hashtable *config = init_hashtable();
config->add(config, "min_chars", "4");
config->add(config, "max_chars", "10");
// Instantiate the validation class with configuration and validation type
IOValidate *v = init_validate(config, VALIDATE_ALPHA);
/*
// Setup configuration for validating alphanum characters with specific chars
Hashtable *config = init_hashtable();
config->add(config, "min_chars", "4");
config->add(config, "max_chars", "10");
config->add(config, "allowed_chars", "abcd");
// Instantiate the validation class with configuration and validation type
IOValidate *v = init_validate(config, VALIDATE_ALPHANUM);
*/
/*
// Setup configuration for validating numbers
Hashtable *config = init_hashtable();
config->add(config, "min_num", "10");
config->add(config, "max_num", "1000");
// Instantiate the validation class with configuration and validation type
IOValidate *v = init_validate(config, VALIDATE_NUM);
*/
// Get user input
fgets(buff, sizeof(buff), stdin);
// Test the user provided input with our validation
if (v->isvalid(v, &status, buff)) {
printf("Validated!\n");
}
else {
printf("Status code: %d\n", status.code);
printf("Status msg: %s\n", status.msg);
}
release(v);
free_hashtable(config);
return 0;
}
int main(int argc, char *argv[])
{
struct hash_functions funcs;
struct hashtable table;
INIT_HASH_FUNCTIONS(&funcs, init_hash_descriptor,
resize_hash_modulus, hash);
init_hashtable(&table, &funcs, 1, 2);
dealloc_hashtable(&table);
}
//read kmer file, the first line of the kmer file contains the number of (distinct) kmers as kmer_index (Note the total number of kmers would be (2*kmer_index) including reverse complementary pairs)
//for a pair of reverse complementary kmers kmer1 and kmer2, if kmer1 < kmer2 (dictionary order) then (the index of kmer2) = (the index of kmer1) + kmer_index
int read_kmer_file(char * kmer_file, struct kmer_state ** kmer, int* hashtable, int kmerlength, int * kmer_index1){
FILE * fr_kmer;
int file_end_tag;
int temp_kmer_index, kmer_index, temp_hash_index, i;
char temp_char[1000];
char line[Length];
fr_kmer = fopen(kmer_file, "r");
if (fr_kmer != NULL){
file_end_tag = 1;
init_hashtable(hashtable);
fgets(line, Length, fr_kmer);
sscanf(line, "%s %d", temp_char, &kmer_index);
(*kmer) = (struct kmer_state *) malloc((kmer_index*2+2)*sizeof(struct kmer_state));
init_kmer((*kmer), kmer_index);
temp_kmer_index = 1;
while((file_end_tag!=0)){ // read the reads file
line[0] = 'X';
if (fgets(line, Length, fr_kmer) == NULL){
file_end_tag = 0;
};
if (line[0] == 'X')
file_end_tag = 0;
if (file_end_tag != 0){
sscanf(line, "%s %d", (*kmer)[temp_kmer_index].seq, &(*kmer)[temp_kmer_index].cov);
(*kmer)[temp_kmer_index].seq[kmerlength] = '\0';
temp_hash_index = get_hash_index((*kmer)[temp_kmer_index].seq);
if (hashtable[temp_hash_index] == -1){
hashtable[temp_hash_index] = temp_kmer_index;
}
for (i=0;i<kmerlength;i++){
if ((*kmer)[temp_kmer_index].seq[kmerlength-1-i] == 'A') (*kmer)[temp_kmer_index+kmer_index].seq[i] = 'T';
if ((*kmer)[temp_kmer_index].seq[kmerlength-1-i] == 'T') (*kmer)[temp_kmer_index+kmer_index].seq[i] = 'A';
if ((*kmer)[temp_kmer_index].seq[kmerlength-1-i] == 'C') (*kmer)[temp_kmer_index+kmer_index].seq[i] = 'G';
if ((*kmer)[temp_kmer_index].seq[kmerlength-1-i] == 'G') (*kmer)[temp_kmer_index+kmer_index].seq[i] = 'C';
}
(*kmer)[temp_kmer_index+kmer_index].seq[kmerlength] = '\0';
(*kmer)[temp_kmer_index+kmer_index].cov = (*kmer)[temp_kmer_index].cov;
temp_kmer_index++;
if (temp_kmer_index % 10000 == -1)
printf("Kmer %d %s count %d\n", temp_kmer_index-1, (*kmer)[temp_kmer_index-1].seq, (*kmer)[temp_kmer_index-1].cov);
}
}
hashtable[1048576] = kmer_index-1;
fclose(fr_kmer);
}
(*kmer_index1) = kmer_index;
}
/*
* Funzione di inizializzazione del superpeer.
*/
int init_superpeer(const struct sockaddr_in *sp_addr_list, int list_len) {
int rc, ret = 0;
is_sp = 0;
nsock = 0;
curr_p_count = 0;
have_child = 0;
child_miss_pong = 0;
curr_child_redirect = 0;
join_ov_try = 0;
max_tcp_sock = MAX_TCP_SOCKET;
if (near_str != NULL) {
free(near_str);
}
near_str = (char *)malloc(max_tcp_sock * ADDR_STR_LEN);
memset(near_str, 0, max_tcp_sock * ADDR_STR_LEN);
//inizializzo socket di ascolto
if (set_listen_socket(conf.udp_port) < 0) {
fprintf(stderr, "init_superpeer error - set_listen_socket failed\n");
return -1;
}
if ((rc = pthread_mutex_init(&NEAR_LIST_LOCK, NULL)) != 0) {
fprintf(stderr, "init_superpeer error - can't initialize lock: %s\n", strerror(rc));
return -1;
}
if (sp_addr_list != NULL) {
//provo a connettermi agli altri superpeer
if ((ret = join_overlay(sp_addr_list, list_len)) < 0) {
fprintf(stderr, "init_superpeer error - join_overlay failed\n");
return -1;
}
myaddr.sin_port = conf.udp_port;
printf("MIO INDIRIZZO: %s:%d\n", inet_ntoa(myaddr.sin_addr), ntohs(myaddr.sin_port));
}
init_hashtable();
return ret;
}
__init int init_devfs( void ) {
int error;
error = init_hashtable(
&devfs_node_table, 256,
devfs_node_key, hash_int64,
compare_int64
);
if ( error < 0 ) {
goto error1;
}
devfs_mutex = mutex_create( "devfs mutex", MUTEX_NONE );
if ( devfs_mutex < 0 ) {
error = devfs_mutex;
goto error2;
}
error = register_filesystem( "devfs", &devfs_calls );
if ( error < 0 ) {
goto error3;
}
return 0;
error3:
mutex_destroy( devfs_mutex );
error2:
destroy_hashtable( &devfs_node_table );
error1:
return error;
}
int main(int argc,char **argv) {
INFO(char *dbg="Main(init): ");
native_startup(argc, argv);
/*** init modules ***/
INFO(printf("%sSharedMemory\n",dbg));
init_sharedmem(&dope);
INFO(printf("%sTimer\n",dbg));
init_timer(&dope);
INFO(printf("%sTick\n",dbg));
init_tick(&dope);
INFO(printf("%sRelax\n",dbg));
init_relax(&dope);
INFO(printf("%sKeymap\n",dbg));
init_keymap(&dope);
INFO(printf("%sThread\n",dbg));
init_thread(&dope);
INFO(printf("%sCache\n",dbg));
init_cache(&dope);
INFO(printf("%sHashTable\n",dbg));
init_hashtable(&dope);
INFO(printf("%sApplication Manager\n",dbg));
init_appman(&dope);
INFO(printf("%sTokenizer\n",dbg));
init_tokenizer(&dope);
INFO(printf("%sMessenger\n",dbg));
init_messenger(&dope);
INFO(printf("%sScript\n",dbg));
init_script(&dope);
INFO(printf("%sClipping\n",dbg));
init_clipping(&dope);
INFO(printf("%sScreen Driver\n",dbg));
init_scrdrv(&dope);
INFO(printf("%sInput\n",dbg));
init_input(&dope);
INFO(printf("%sViewManager\n",dbg));
init_viewman(&dope);
INFO(printf("%sConvertFNT\n",dbg));
init_conv_fnt(&dope);
INFO(printf("%sFontManager\n",dbg));
init_fontman(&dope);
INFO(printf("%sGfxScreen16\n",dbg));
init_gfxscr16(&dope);
INFO(printf("%sGfxImage16\n",dbg));
init_gfximg16(&dope);
INFO(printf("%sGfxImage32\n",dbg));
init_gfximg32(&dope);
INFO(printf("%sGfxImageYUV420\n",dbg));
init_gfximgyuv420(&dope);
INFO(printf("%sGfx\n",dbg));
init_gfx(&dope);
INFO(printf("%sRedrawManager\n",dbg));
init_redraw(&dope);
INFO(printf("%sUserState\n",dbg));
init_userstate(&dope);
INFO(printf("%sWidgetManager\n",dbg));
init_widman(&dope);
INFO(printf("%sScope\n",dbg));
init_scope(&dope);
INFO(printf("%sButton\n",dbg));
init_button(&dope);
INFO(printf("%sEntry\n",dbg));
init_entry(&dope);
INFO(printf("%sVariable\n",dbg));
init_variable(&dope);
INFO(printf("%sLabel\n",dbg));
init_label(&dope);
INFO(printf("%sLoadDisplay\n",dbg));
init_loaddisplay(&dope);
INFO(printf("%sBackground\n",dbg));
init_background(&dope);
INFO(printf("%sScrollbar\n",dbg));
init_scrollbar(&dope);
INFO(printf("%sScale\n",dbg));
init_scale(&dope);
INFO(printf("%sFrame\n",dbg));
init_frame(&dope);
INFO(printf("%sContainer\n",dbg));
init_container(&dope);
INFO(printf("%sGrid\n",dbg));
init_grid(&dope);
INFO(printf("%sWinLayout\n",dbg));
init_winlayout(&dope);
INFO(printf("%sWindow\n",dbg));
init_window(&dope);
INFO(printf("%sScreen\n",dbg));
init_screen(&dope);
INFO(printf("%sScheduler\n",dbg));
if (config_don_scheduler)
{
// init_don_scheduler(&dope);
printf("NOOOOOOOOOOOOOOOOOOO\n");
}
else
init_simple_scheduler(&dope);
INFO(printf("%sVScreenServer\n",dbg));
init_vscr_server(&dope);
INFO(printf("%sVScreen\n",dbg));
init_vscreen(&dope);
INFO(printf("%sVTextScreen\n",dbg));
init_vtextscreen(&dope);
INFO(printf("%sServer\n",dbg));
init_server(&dope);
INFO(printf("%screate screen\n",dbg));
{
static GFX_CONTAINER *scr_ds;
gfx = pool_get("Gfx 1.0");
screen = pool_get("Screen 1.0");
userstate = pool_get("UserState 1.0");
scr_ds = gfx->alloc_scr("default");
curr_scr = screen->create();
curr_scr->scr->set_gfx(curr_scr, scr_ds);
userstate->set_max_mx(gfx->get_width(scr_ds));
userstate->set_max_my(gfx->get_height(scr_ds));
}
INFO(printf("%sstarting server\n",dbg));
if ((server = pool_get("Server 1.0")))
server->start();
INFO(printf("%sstarting scheduler\n",dbg));
if ((sched = pool_get("Scheduler 1.0")))
sched->process_mainloop();
return 0;
}
static void init_node_names(node_t *n) {
init_hashtable(&n->names, 5, NULL, NULL);
}
int main (int argc, char** argv)
{
char samfile[1024]; char bamfile[1024]; char variantfile[1024]; char fastafile[1024]; char maskfile[1024];
strcpy(samfile,"None"); strcpy(bamfile,"None"); strcpy(variantfile,"None"); strcpy(fastafile,"None"); strcpy(maskfile,"None");
GROUPNAME = NULL;
int readsorted = 0;
char* sampleid = (char*)malloc(1024); sampleid[0] = '-'; sampleid[1] = '\0';
int samplecol=10; // default if there is a single sample in the VCF file
int i=0,variants=0,hetvariants=0;
char** bamfilelist = NULL; int bamfiles =0;
logfile = NULL; fragment_file = stdout; // write fragments to this file if it is present
for (i=1;i<argc;i+=2)
{
if (strcmp(argv[i],"--bam") ==0 || strcmp(argv[i],"--bamfile") ==0) bamfiles++;
else if (strcmp(argv[i],"--variants") ==0) strcpy(variantfile,argv[i+1]);
else if (strcmp(argv[i],"--reffile") ==0 || strcmp(argv[i],"--ref") ==0) strcpy(fastafile,argv[i+1]);
else if (strcmp(argv[i],"--mask") ==0 || strcmp(argv[i],"--mappability") ==0) strcpy(maskfile,argv[i+1]);
else if (strcmp(argv[i],"--VCF") ==0 || strcmp(argv[i],"--vcf") ==0) { strcpy(variantfile,argv[i+1]); VCFformat =1; }
else if (strcmp(argv[i],"--sorted") ==0) readsorted = atoi(argv[i+1]);
else if (strcmp(argv[i],"--mbq") ==0) MINQ = atoi(argv[i+1]);
else if (strcmp(argv[i],"--mmq") ==0) MIN_MQ = atoi(argv[i+1]);
else if (strcmp(argv[i],"--maxIS") ==0) MAX_IS = atoi(argv[i+1]);
else if (strcmp(argv[i],"--minIS") ==0) MIN_IS = atoi(argv[i+1]);
else if (strcmp(argv[i],"--PEonly") ==0) PEONLY = 1; // discard single end mapped reads
else if (strcmp(argv[i],"--indels") ==0) PARSEINDELS = atoi(argv[i+1]); // allow indels in hairs
else if (strcmp(argv[i],"--pflag") ==0) IFLAG = atoi(argv[i+1]); // allow indels in hairs
else if (strcmp(argv[i],"--qvoffset") ==0) QVoffset = atoi(argv[i+1]);
else if (strcmp(argv[i],"--out") == 0 || strcmp(argv[i],"-o") ==0) fragment_file = fopen(argv[i+1],"w");
else if (strcmp(argv[i],"--logfile")==0 || strcmp(argv[i],"--log") ==0) logfile = fopen(argv[i+1],"w");
else if (strcmp(argv[i],"--singlereads")==0) SINGLEREADS = atoi(argv[i+1]);
else if (strcmp(argv[i],"--maxfragments")==0) MAXFRAG = atoi(argv[i+1]);
else if (strcmp(argv[i],"--noquality")==0) MISSING_QV = atoi(argv[i+1]);
else if (strcmp(argv[i],"--triallelic")==0) TRI_ALLELIC = atoi(argv[i+1]);
//else if (strcmp(argv[i],"--fosmids") == 0 || strcmp(argv[i],"--fosmid") ==0) FOSMIDS = 1;
//else if (strcmp(argv[i],"--prior") == 0) PRIOR = atoi(argv[i+1]);
//else if (strcmp(argv[i],"--comparephase") == 0 || strcmp(argv[i],"--compare") ==0) COMPARE_PHASE = atoi(argv[i+1]);
else if (strcmp(argv[i],"--groupname") == 0)
{
GROUPNAME = (char*)malloc(1024); strcpy(GROUPNAME,argv[i+1]);
}
}
if (bamfiles > 0 && strcmp(variantfile,"None") !=0)
{
bamfilelist = (char**)malloc(sizeof(char*)*bamfiles);
for (i=0;i<bamfiles;i++) bamfilelist[i] = (char*)malloc(1024);
bamfiles=0;
for (i=1;i<argc;i+=2)
{
if (strcmp(argv[i],"--bam") ==0 || strcmp(argv[i],"--bamfile") ==0) strcpy(bamfilelist[bamfiles++],argv[i+1]);
}
fprintf(stderr,"\n extracting haplotype informative reads from bamfiles %s minQV %d minMQ %d maxIS %d \n\n",bamfilelist[0],MINQ,MIN_MQ,MAX_IS);
}
else
{
print_options(); return -1;
}
HASHTABLE ht; ht.htsize = 7919; init_hashtable(&ht);
VARIANT* varlist;
int chromosomes=0;
if (VCFformat ==1)
{
variants = count_variants(variantfile,sampleid,&samplecol);
if (variants < 0) return -1;
varlist = (VARIANT*)malloc(sizeof(VARIANT)*variants);
chromosomes = read_variantfile(variantfile,varlist,&ht,&hetvariants,samplecol);
}
else
{
variants = count_variants_oldformat(variantfile);
if (variants < 0) return -1;
varlist = (VARIANT*)malloc(sizeof(VARIANT)*variants);
chromosomes = read_variantfile_oldformat(variantfile,varlist,&ht,variants);
}
// variants is set to hetvariants only, but this is not correct since
VARIANTS = variants;
// there are two options, we include all variants in the chromvars datastructure but only use heterozygous variants for outputting HAIRS
// variant-id should correspond to line-number in VCF file since that will be used for printing out variants in Hapcut
// fprintf(stderr,"read %d variants from file %s chromosomes %d\n",snps,argv[1],chromosomes);
CHROMVARS* chromvars = (CHROMVARS*)malloc(sizeof(CHROMVARS)*chromosomes);
build_intervalmap(chromvars,chromosomes,varlist,VARIANTS);
// read reference fasta file for INDELS, currently reads entire genome in one go, need to modify to read chromosome by chromosome
REFLIST* reflist = (REFLIST*)malloc(sizeof(REFLIST));
reflist->ns = 0; reflist->names = NULL; reflist->lengths = NULL; reflist->sequences = NULL; reflist->current = -1;
if (strcmp(fastafile,"None") != 0)
{
if (read_fastaheader(fastafile,reflist) > 0)
{
reflist->sequences = calloc(reflist->ns,sizeof(char*)); //(char**)malloc(sizeof(char*)*reflist->ns);
if (FOSMIDS ==0)
{
for (i=0;i<reflist->ns;i++)
{
reflist->sequences[i] = calloc(reflist->lengths[i]+1,sizeof(char));
if (i < 5) fprintf(stderr,"contig %s length %d\n",reflist->names[i],reflist->lengths[i]);
}
read_fasta(fastafile,reflist);
}
else // 10.27.14 new code to read one chromosome at a time
{
fprintf(stderr,"opening fasta file %s \n",fastafile);
reflist->fp = fopen(fastafile,"r");
}
}
}
//return 1;
if (readsorted ==0 && bamfiles > 0)
{
for (i=0;i<bamfiles;i++)
{
if (FOSMIDS ==0) parse_bamfile_sorted(bamfilelist[i],&ht,chromvars,varlist,reflist);
//else parse_bamfile_fosmid(bamfilelist[i],&ht,chromvars,varlist,reflist,maskfile); // fosmid pool bam file
}
}
if (logfile != NULL) fclose(logfile);
if (fragment_file != NULL && fragment_file != stdout) fclose(fragment_file);
// need to free up all memory before we exit the program
/*
int xor = pow(2,16)-1;
for (i=0;i<variants;i++)
{
//if (varlist[i].type ==0) continue;
if (varlist[i].genotype[0] == varlist[i].genotype[2]) continue;
fprintf(stdout,"variant %d %s %d %d %s %s %d:%d %d:%d \n",i+1,varlist[i].genotype,varlist[i].position-1,varlist[i].type,varlist[i].RA,varlist[i].AA,varlist[i].A1>>16,varlist[i].A1 & xor,varlist[i].A2>>16,varlist[i].A2 & xor);
}
*/
return 0;
}
int init_cgi_local()
{
init_hashtable();
return load_funSet_from_web();
}
void init_exchange(void) {
init_hashtable(&all_exchange_types, 53, NULL, NULL);
init_exchange_direct();
init_exchange_fanout();
init_exchange_topic();
}