struct task_t* task_dispatcher_enqueue_task(struct task_dispatcher_t* td, task_callback_pf callback, void* ctx, long delay, long interval)
{
struct task_t task =
{
.callback = callback,
.ctx = ctx,
.interval = interval,
};
timestamp_set(&task.enqueue_time);
timestamp_offset(&task.enqueue_time, &task.activate_time, delay);
pthread_mutex_lock(&td->lock);
struct task_t* queued_task = pool_get_next(td->tasks, NULL);
struct task_t* after = NULL;
while (queued_task != NULL && timestamp_diff(&queued_task->activate_time, &task.activate_time) <= 0)
{
after = queued_task;
queued_task = pool_get_next(td->tasks, queued_task);
}
struct task_t* p = pool_insert(td->tasks, &task, after);
LOGD("Enqueued task %p after %p", p, after);
if (after == NULL)
{
pthread_cond_broadcast(&td->event);
}
pthread_mutex_unlock(&td->lock);
return p;
}
static void
frametimes_init_base(GH_frametimes *ft)
{
/* get the base timestamp */
if (ft->mode > GH_FRAMETIME_NONE) {
GH_timestamp base;
unsigned int i;
GH_frametime *last=&ft->frametime[ft->num_results * ft->num_timestamps];
timestamp_init(&base);
timestamp_set(&base, &last[0], ft->mode);
timestamp_set(&base, &last[0], ft->mode);
for (i=1; i<ft->num_timestamps; i++) {
last[i]=last[0];
}
timestamp_cleanup(&base);
}
}
static void
frametimes_before_swap(GH_frametimes *ft)
{
unsigned int ts_idx;
unsigned int rs_idx;
if (ft->mode == GH_FRAMETIME_NONE)
return;
ts_idx=ft->cur_pos * ft->num_timestamps + GH_FRAMETIME_BEFORE_SWAPBUFFERS;
rs_idx=ft->cur_result * ft->num_timestamps + GH_FRAMETIME_BEFORE_SWAPBUFFERS;
timestamp_set(&ft->timestamp[ts_idx], &ft->frametime[rs_idx], ft->mode);
}
static void
frametimes_after_swap(GH_frametimes *ft)
{
unsigned int ts_idx;
unsigned int rs_idx;
if (ft->mode == GH_FRAMETIME_NONE)
return;
ts_idx=ft->cur_pos * ft->num_timestamps + GH_FRAMETIME_AFTER_SWAPBUFFERS;
rs_idx=ft->cur_result * ft->num_timestamps + GH_FRAMETIME_AFTER_SWAPBUFFERS;
timestamp_set(&ft->timestamp[ts_idx], &ft->frametime[rs_idx], ft->mode);
frametimes_finish_frame(ft);
}
int am_update_achievements(achievement_manager_t* am, void* context)
{
timestamp_t current_time = {0};
timestamp_set(¤t_time);
uint32_t i = 0;
achievement_state_t* state = &am->states[0];
for (; i < am->nachievements; ++i, ++state)
{
const achievement_info_t* info = am->achievements[i];
achievement_status_t* status = &state->status;
if (status->unlocked)
{
continue;
}
int32_t progress = (*info->get_progress)(info, ¤t_time, &state->data, context);
if (progress != status->progress)
{
status->last_change = current_time;
status->prev_progress = status->progress;
status->progress = progress;
if (status->progress >= info->target_progress)
{
LOGI("Achievement '%s' unlocked", info->id);
status->unlocked = 1;
status->unlocked_at = current_time;
// notify about achievement unlocked
if (am->unlocked)
{
(*am->unlocked)(info);
}
}
else if ((int)(status->prev_progress / info->notification_step) < (int)(status->progress / info->notification_step))
{
LOGI("Achievement '%s' progress [%d of %d]", info->id, status->progress, info->target_progress);
// notify about achievement progress
if (am->progress)
{
(*am->progress)(info, status);
}
}
}
}
return 0;
}
void SensorConditionItem::getStruct(shf_condition_item_t* item) const
{
memset(item, 0, sizeof(shf_condition_item_t));
item->dindex1 = mIndex1;
item->dindex2 = mIndex2;
item->op = mOperation;
item->combine = mCombine;
switch (mDataType) {
case DATA_TYPE_UINT32: {
item->value.duint32 = mIntValue;
}
break;
case DATA_TYPE_UINT64: {
ALOGV("getStruct: value=%lld", mLongValue);
timestamp_set(&item->value.dtime, mLongValue);
}
break;
case DATA_TYPE_FLOAT: {
uint32_t temp = mFloatValue * FLOAT_MULTIPLY_FACTOR;
ALOGV("getStruct: float(%f) -> int(%u)", mFloatValue, temp);
item->value.duint32 = temp;
}
break;
default:
break;
}
if (mIsLast1) {
item->op |= SHF_OPERATION_MASK_OLD1;
}
if (mIsLast2) {
item->op |= SHF_OPERATION_MASK_OLD2;
}
if (mConditionType == CONDITION_TYPE_CMP) {
item->op |= SHF_OPERATION_MASK_CMP;
} else if (mConditionType == CONDITION_TYPE_DIF) {
item->op |= SHF_OPERATION_MASK_DIF;
}
if (mBracketLeft) {
item->combine |= SHF_COMBINE_MASK_BRACKET_LEFT;
}
}
int am_init(struct achievement_manager_t** pam, const achievement_info_t* const* achievements, uint32_t nachievements, am_achievement_progress progress, am_achievement_unlocked unlocked)
{
uint32_t i = 0;
uint32_t size = sizeof(achievement_manager_t) + nachievements * (sizeof(achievement_state_t) + sizeof(achievement_index_t));
achievement_manager_t* am = malloc(size);
memset(am, 0, size);
am->nachievements = nachievements;
am->achievements = achievements;
am->progress = progress;
am->unlocked = unlocked;
am->states = (achievement_state_t*)((uint8_t*)am + sizeof(achievement_manager_t));
am->indices = (achievement_index_t*)((uint8_t*)am->states + nachievements * sizeof(achievement_state_t));
timestamp_t current_time = {0};
timestamp_set(¤t_time);
achievement_state_t* state = &am->states[0];
achievement_index_t* index = &am->indices[0];
for (; i < am->nachievements; ++i, ++state, ++index)
{
const achievement_info_t* info = am->achievements[i];
strcpy(state->achievement_id, info->id);
state->status.unlocked = 0;
state->status.last_change = current_time;
strcpy(index->achievement_id, info->id);
index->index = i;
}
qsort(am->indices, am->nachievements, sizeof(achievement_index_t), cmp_achievement_index);
(*pam) = am;
return 0;
}
int main(int argc, char** argv) {
char buff[MAXBUFFLENGTH];
char aux[MAXBUFFLENGTH];
dictionary<ATOMIC>* dict_f[MAXSPECIES];
dictionary<ATOMIC>* dict_r[MAXSPECIES];
dictionary<PAIR<ATOMIC> >* dict_bp[MAXSPECIES];
dictionary<ATOMIC>* filter;
conservation_table* cons_f[MAXSPECIES];
conservation_table* cons_r[MAXSPECIES];
char right_file_name[MAXBUFFLENGTH]="";
char left_file_name[MAXBUFFLENGTH]="";
char right_sbs_file_name[MAXBUFFLENGTH]="";
char left_sbs_file_name[MAXBUFFLENGTH]="";
char rel_binary_file_name[MAXBUFFLENGTH]="";
char rel_tabdel_file_name[MAXBUFFLENGTH]="";
relation* rel=NULL;
FILE *right_file, *left_file, *rel_file, *outfile;
char* specie_name[MAXSPECIES];
double weight[MAXSPECIES];
char filename[MAXBUFFLENGTH];
char outfilename[MAXBUFFLENGTH];
double threshold, threshold1, threshold2;
int halfsize,gap,n_species;
int halfsize1,gap1,n_species1;
double tot_weight=0;
int redundant_pairs = 2;
const char RED_P[3][24]={"strictly not allowed", "not allowed", "allowed"};
double min_cons = 0;
int min_length = 0;
int joint_fold = 1;
int number_of_gt_basepairs=0;
index_t p,q,r,s;
word_t a,b;
int i,j;
int repeat_length=1;
int min_gc=0;
char *pc;
word_t aux_array[GT_ARRAY_CAPACITY];
int aux_array_length;
int n,m;
subset *left_restriction=NULL;
subset *right_restriction=NULL;
if(argc==1) {
fprintf(stderr, "BInary Search for COnserved RNa Structures\n");
fprintf(stderr, "Usage: %s -l [left_metacalc] -r [right_metacalc] -o [output_tabular file]\n",argv[0]);
fprintf(stderr, " -v suppress verbose output\n -t threshold for intersection\n -u redundant pairs (0=strict no, 1=no, 2=allowed)\n -L min length\n");
fprintf(stderr, " -B binary relation file\n -b tab-delimited relation file\n -j suppress joint fold (fold species separately)\n");
exit(0);
}
timestamp_set();
rel_binary_file_name[0] = rel_tabdel_file_name[0] = 0;
for(i=1;i<argc;i++) {
pc = argv[i];
if(*pc == '-') {
if(strcmp(pc+1,"v") == 0) verbose=0;
if(strcmp(pc+1,"l") == 0) sscanf(argv[++i], "%s", &left_file_name[0]);
if(strcmp(pc+1,"r") == 0) sscanf(argv[++i], "%s", &right_file_name[0]);
if(strcmp(pc+1,"lr")== 0) sscanf(argv[++i], "%s", &left_sbs_file_name[0]);
if(strcmp(pc+1,"rr")== 0) sscanf(argv[++i], "%s", &right_sbs_file_name[0]);
if(strcmp(pc+1,"B") == 0) sscanf(argv[++i], "%s", &rel_binary_file_name[0]);
if(strcmp(pc+1,"b") == 0) sscanf(argv[++i], "%s", &rel_tabdel_file_name[0]);
if(strcmp(pc+1,"o") == 0) sscanf(argv[++i], "%s", &outfilename[0]);
if(strcmp(pc+1,"t") == 0) sscanf(argv[++i], "%lf", &threshold);
if(strcmp(pc+1,"L") == 0) sscanf(argv[++i], "%i", &min_length);
if(strcmp(pc+1,"C") == 0) sscanf(argv[++i], "%lf", &min_cons);
if(strcmp(pc+1,"u") == 0) sscanf(argv[++i], "%i", &redundant_pairs);
if(strcmp(pc+1,"g") == 0) sscanf(argv[++i], "%i", &number_of_gt_basepairs);
if(strcmp(pc+1,"j") == 0) joint_fold = 0;
}
}
outfile = fopen(outfilename,"w");
if(outfile==NULL) {
if(verbose) fprintf(logfile,"Cannot open outfile, exiting\n");
exit(1);
}
if(left_sbs_file_name[0]!=0) left_restriction = new subset(left_sbs_file_name);
if(right_sbs_file_name[0]!=0) right_restriction = new subset(right_sbs_file_name);
if(redundant_pairs>2) redundant_pairs=2;
if(verbose) fprintf(logfile,"[Params: max_gt=%i, threshold=%2.1lf%%, min_length=%i, min_cons_score=%2.1lf, redundant_pairs=%s, joint_fold=%s]\n",
number_of_gt_basepairs, threshold*100, min_length, min_cons, RED_P[redundant_pairs], yesno(joint_fold));
if(rel_binary_file_name[0]!=0) {
rel = new relation();
rel->get_from_bin_file(rel_binary_file_name);
}
if(rel_tabdel_file_name[0]!=0) {
rel = new relation();
rel->get_from_tab_file(rel_tabdel_file_name);
}
if(verbose) fprintf(logfile,"Reading left %s", left_file_name);
left_file = fopen(left_file_name,"r");
if(left_file==NULL) {
fprintf(stderr,"cannot be found, exiting\n");
exit(1);
}
fgets(buff, MAXBUFFLENGTH, left_file);
sscanf(buff,"%i %i %i %lf",&halfsize, &gap, &n_species, &threshold1);
if(verbose) fprintf(logfile,"\n");
for(i=0;i<n_species;i++) {
dict_f[i] = new dictionary<ATOMIC>(halfsize,gap);
fgets(buff, MAXBUFFLENGTH, left_file);
specie_name[i] = (char*)malloc(sizeof(char)*MAXBUFFLENGTH);
sscanf(buff,"%s %lf",&specie_name[i][0],&weight[i]);
tot_weight+=weight[i];
if(verbose) fprintf(logfile,"[Loading %s ",specie_name[i]);
dict_f[i]->load(left_file);
cons_f[i] = new conservation_table();
cons_f[i]->load(left_file);
dict_f[i]->info();
if(left_restriction!=NULL) {
dict_f[i]->subset_on(left_restriction);
}
dict_f[i]->check();
if(verbose) fprintf(logfile,"]\n");
}
if(verbose) fprintf(logfile,"Reading right %s", right_file_name);
right_file = fopen(right_file_name,"r");
if(right_file == NULL) {
fprintf(stderr, "cannot be found, exiting\n");
exit(1);
}
if(verbose) fprintf(logfile,"\n");
fgets(buff, MAXBUFFLENGTH, right_file);
sscanf(buff,"%i %i %i %lf",&halfsize1, &gap1, &n_species1, &threshold2);
if(halfsize!=halfsize1 || gap!=gap1) {
fprintf(logfile,"Dictionaries not compartible (%i %i) and (%i %i), exiting\n", halfsize, gap, halfsize1, gap1);
exit(1);
}
if(n_species!=n_species1) {
fprintf(logfile,"Number of species are different");
exit(1);
}
for(i=0;i<n_species;i++) {
dict_r[i] = new dictionary<ATOMIC>(halfsize,gap);
fgets(buff, MAXBUFFLENGTH, right_file);
sscanf(buff,"%s",&aux[0]);
if(strcmp(aux,specie_name[i])!=0) {
fprintf(logfile,"Species are not the same (%s vs %s), exiting\n", aux, specie_name[i]);
exit(1);
}
if(verbose) fprintf(logfile,"[Loading %s ",specie_name[i]);
dict_r[i]->load(right_file);
cons_r[i] = new conservation_table();
cons_r[i]->load(right_file);
dict_r[i]->info();
if(right_restriction!=NULL) {
dict_r[i]->subset_on(right_restriction);
}
dict_r[i]->check();
if(verbose) fprintf(logfile,"]\n");
}
if(threshold<threshold1 || threshold<threshold2) {
threshold=MAX2(threshold1, threshold2);
if(verbose) fprintf(logfile,"[WARNING: product threshold set to %2.2lf%%]\n",threshold*100);
}
if((threshold1<threshold || threshold2<threshold) && verbose) fprintf(logfile,"Threshold rose to %2.2lf%%, need to trim again\n",threshold*100);
if(threshold1<threshold) dictionary<ATOMIC>::intersect_many(dict_f, n_species, weight, threshold*tot_weight, (char*)"Forward\t");
if(threshold2<threshold) dictionary<ATOMIC>::intersect_many(dict_r, n_species, weight, threshold*tot_weight, (char*)"Reverse\t");
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile,"[%s forward ",specie_name[i]);
dict_f[i]->info();
if(verbose) fprintf(logfile,", reverse: ");
dict_r[i]->info();
if(verbose) fprintf(logfile,", product: ");
/** times procedure **/
dict_bp[i] = new dictionary<PAIR<ATOMIC> >(dict_f[i]->half_size,dict_f[i]->gap_size);
for(s=0,a=0;a<=dict_f[i]->last_word;a++) {
dict_bp[i]->revcomp_gt(a, number_of_gt_basepairs, aux_array, &aux_array_length);
for(;aux_array_length>0;aux_array_length--) {
b = aux_array[aux_array_length-1];
if(rel) {
for(p=dict_f[i]->index[a];p<dict_f[i]->index[a+1];p++) {
for(q=dict_r[i]->index[b];q<dict_r[i]->index[b+1];q++) {
if(rel->check(dict_f[i]->table[p].getid(), dict_r[i]->table[q].getid())) s++;
}
}
}
else {
s+=(dict_f[i]->index[a+1]-dict_f[i]->index[a])*(dict_r[i]->index[b+1]-dict_r[i]->index[b]);
}
}
}
dict_bp[i]->table = (PAIR<ATOMIC>*)malloc((size_t)sizeof(PAIR<ATOMIC>)*(s + ARRAY_MARGIN));
r=0;
for(a=0;a<=dict_f[i]->last_word;a++) {
dict_bp[i]->index[a]=r;
dict_bp[i]->revcomp_gt(a, number_of_gt_basepairs, aux_array, &aux_array_length);
for(;aux_array_length>0;aux_array_length--) {
b = aux_array[aux_array_length-1];
for(p=dict_f[i]->index[a];p<dict_f[i]->index[a+1];p++) {
for(q=dict_r[i]->index[b];q<dict_r[i]->index[b+1];q++) {
if(rel) if(!rel->check(dict_f[i]->table[p].getid(), dict_r[i]->table[q].getid())) continue;
if(redundant_pairs==2 || redundant_pairs==1 && (dict_f[i]->table[p].getid()<dict_r[i]->table[q].getid() || dict_f[i]->table[p].getid()==dict_r[i]->table[q].getid() && dict_f[i]->table[p].getpos() + dict_f[i]->full_size<dict_r[i]->table[q].getpos()) || redundant_pairs==0 && dict_f[i]->table[p].getid()<dict_r[i]->table[q].getid())
dict_bp[i]->table[r++].set(dict_f[i]->table[p], dict_r[i]->table[q]);
}
}
}
PAIR<ATOMIC>::quicksort_less(dict_bp[i]->table, dict_bp[i]->index[a], r-1);
}
dict_bp[i]->index[a]=r;
if(verbose) fprintf(logfile,"%li/%li/%li ",(long)dict_bp[i]->last_word,(long)r,(long)s);
free(dict_bp[i]->count);
dict_bp[i]->phase = PHASE_COMPLETED;
/** end of times procedure **/
dict_bp[i]->info();
dict_bp[i]->check();
dict_f[i]->drop();
dict_r[i]->drop();
if(verbose) fprintf(logfile,"]\n");
}
dictionary<PAIR<ATOMIC> >::intersect_many(dict_bp, n_species, weight, threshold*tot_weight, (char*)"Intersection of products \t");
if(joint_fold) {
dictionary<PAIR<ATOMIC> >::foldall(outfile, dict_bp, specie_name, n_species, weight, threshold*tot_weight, cons_f, cons_r, min_cons, min_length);
}
else {
if(verbose) fprintf(logfile,"[Folding and saving to %s...]\n",outfilename);
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile,"[%s ",specie_name[i]);
dict_bp[i]->info();
n = dict_bp[i]->fold_and_save_standalone(outfile, i, cons_f[i], cons_r[i], min_length);
if(verbose) fprintf(logfile,", %i structures]\n",n);
}
}
fclose(outfile);
timestamp_report();
return(0);
}
static void* working_thread(void* ctx)
{
struct task_dispatcher_t* td = (struct task_dispatcher_t*)ctx;
LOGI("Task dispatcher working thread started");
pthread_mutex_lock(&td->event_lock);
while (1)
{
if (pool_is_empty(td->tasks))
{
LOGD("Waiting for event");
pthread_cond_wait(&td->event, &td->event_lock);
}
else
{
struct task_t* task = pool_get_next(td->tasks, NULL);
struct timespec activate_time = {0};
timestamp_to_timespec(&task->activate_time, &activate_time);
timestamp_t current = {0};
timestamp_set(¤t);
LOGD("Waiting for task [%ld:%d -> %ld:%d]", current.value.tv_sec, current.value.tv_usec, task->activate_time.value.tv_sec, task->activate_time.value.tv_usec);
pthread_cond_timedwait(&td->event, &td->event_lock, &activate_time);
}
if (!td->running)
{
LOGI("Stopping working thread");
break;
}
if (!pool_is_empty(td->tasks))
{
struct task_t* task = pool_get_next(td->tasks, NULL);
timestamp_t current = {0};
timestamp_set(¤t);
if (timestamp_diff(¤t, &task->activate_time) >= 0)
{
pool_remove(td->tasks, task);
LOGD("Removed task %p [queue empty %d]", task, pool_is_empty(td->tasks));
if (task->interval > 0)
{
task_dispatcher_enqueue_task(td, task->callback, task->ctx, task->interval, task->interval);
}
pthread_mutex_unlock(&td->event_lock);
LOGD("Running task");
task->callback(td, task, &task->enqueue_time, ¤t, task->ctx);
pthread_mutex_lock(&td->event_lock);
}
}
}
pthread_mutex_unlock(&td->event_lock);
LOGI("Task dispatcher working thread stopped");
return NULL;
}
int main(int argc, char* argv[]) {
char aln_file_name[MAXBUFFLENGTH];
char out_file_name[MAXBUFFLENGTH]="";
char buff[MAXBUFFLENGTH];
char chr1[MAXBUFFLENGTH];
char chr2[MAXBUFFLENGTH];
double dthreshold = 1.50;
int dlimit = 100000;
int max_depth = 4;
int** chr_t;
int** str_t;
int** pos_t;
int* chr_q;
int* str_q;
int* pos_q;
int **score;
int **jbest;
int **lbest;
int a,b,d,dmin,lmin,s;
char c,c1,c2;
int *count;
int *ptr;
int max_rec=0;
int pos1, pos2, str1, str2;
int i, j, k, l, n;
int s_max, k_max;
if(argc==1) {
fprintf(stderr,"This utility takes a non-unique mapping in cps3+cps3 format and does ad-hoc filtering of the projected coordinates by maximum synteny\n");
fprintf(stderr,"Last update by Dmitri Pervouchine ([email protected]) on Mar 26, 2013\n");
fprintf(stderr,"Usage: %s -in <aln_file> -out <output_file> [-maxdepth <int>] [-threshold <double>] [-lendiff <diff>] [-quiet]\n",argv[0]);
fprintf(stderr," -in cps3+cps3 file, remember to sort by position in ascending order\n");
fprintf(stderr," -out <output_file> [default=stdout]\n");
fprintf(stderr," -maxdepth <integer> how many preceding positions can be skipped [default=%i]\n", max_depth);
fprintf(stderr," -threshold <double> max change of segment length, in percent [default=%2.2lf]\n", dthreshold);
fprintf(stderr," -lendiff <integer>, [default=%i]\n",dlimit);
fprintf(stderr," -quiet suppress verbose output [default=NO]\n");
fprintf(stderr,"Note: the mapping [x,x+dx] -> [y,y+dy] is OK if |dy-dx|/dx<threshold OR |dy-dx|<dlimit\n");
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
if(strcmp(argv[i],"-in")==0) {
sscanf(argv[++i], "%s", &aln_file_name[0]);
}
if(strcmp(argv[i],"-out")==0) {
sscanf(argv[++i], "%s", &out_file_name[0]);
}
if(strcmp(argv[i],"-lendiff")==0) {
sscanf(argv[++i], "%i", &dlimit);
}
if(strcmp(argv[i],"-threshold")==0) {
sscanf(argv[++i], "%lf", &dthreshold);
}
if(strcmp(argv[i],"-maxdepth")==0) {
sscanf(argv[++i], "%i", &max_depth);
}
if(strcmp(argv[i],"-quiet")==0) {
verbose=0;
}
}
if(out_file_name[0]==0) {
fprintf(stderr,"[WARNING: output file not specified, redirect to stdout]\n");
out_file = stdout;
}
else {
out_file = fopen(out_file_name,"w");
if(out_file == NULL) {
fprintf(stderr,"[ERROR: output file (%s) cannot be opened, exiting]\n", out_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[>%s]\n",out_file_name);
}
/*******************************************************************************************************/
aln_file= fopen(aln_file_name,"r");
if(aln_file==NULL) {
fprintf(stderr,"[ERROR: cannot access %s, exiting]\n", aln_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[<%s, pass 1", aln_file_name);
while(fgets(buff, MAXBUFFLENGTH, aln_file)) {
if(strlen(buff)<2) break;
max_rec++;
}
if(verbose) fprintf(stderr,"]\n");
chr_q = (int*)malloc(sizeof(int)*(max_rec + ARRAY_MARGIN));
str_q = (int*)malloc(sizeof(int)*(max_rec + ARRAY_MARGIN));
pos_q = (int*)malloc(sizeof(int)*(max_rec + ARRAY_MARGIN));
chr_t = (int**)malloc(sizeof(int*)*(max_rec + ARRAY_MARGIN));
str_t = (int**)malloc(sizeof(int*)*(max_rec + ARRAY_MARGIN));
pos_t = (int**)malloc(sizeof(int*)*(max_rec + ARRAY_MARGIN));
score = (int**)malloc(sizeof(int*)*(max_rec + ARRAY_MARGIN));
lbest = (int**)malloc(sizeof(int*)*(max_rec + ARRAY_MARGIN));
jbest = (int**)malloc(sizeof(int*)*(max_rec + ARRAY_MARGIN));
count = (int*)malloc(sizeof(int)*(max_rec + ARRAY_MARGIN));
ptr = (int*)malloc(sizeof(int)*(max_rec + ARRAY_MARGIN));
if(chr_q == NULL || str_q == NULL || pos_q == NULL || count == NULL || ptr == NULL || chr_t == NULL || str_t == NULL || pos_t == NULL) {
fprintf(stderr,"[ERROR: not enough memory, exiting]\n");
exit(1);
}
for(i=0;i<max_rec;i++) count[i] = ptr[i] = 0;
if(verbose) fprintf(stderr,"[<%s, pass 2", aln_file_name);
fseek (aln_file, 0, SEEK_SET);
n=0;
while(fgets(buff, MAXBUFFLENGTH, aln_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s %i %c" , &chr1[0], &pos1, &c);
str1 = strand_c2i(c);
if(assign_code(chr1) != chr_q[n] || str1 != str_q[n] || pos1 != pos_q[n]) {
n++;
chr_q[n] = assign_code(chr1);
str_q[n] = str1;
pos_q[n] = pos1;
}
count[n]++;
}
if(verbose) fprintf(stderr,"]\n");
for(i=1; i<=n; i++) {
chr_t[i] = (int*)malloc(sizeof(int)*(count[i] + ARRAY_MARGIN));
pos_t[i] = (int*)malloc(sizeof(int)*(count[i] + ARRAY_MARGIN));
str_t[i] = (int*)malloc(sizeof(int)*(count[i] + ARRAY_MARGIN));
score[i] = (int*)malloc(sizeof(int)*(count[i] + ARRAY_MARGIN));
lbest[i] = (int*)malloc(sizeof(int)*(count[i] + ARRAY_MARGIN));
jbest[i] = (int*)malloc(sizeof(int)*(count[i] + ARRAY_MARGIN));
if(chr_t[i] == NULL || str_t[i] == NULL || pos_t[i] == NULL) {
fprintf(stderr,"[ERROR: not enough memory, exiting]\n");
exit(1);
}
}
if(verbose) fprintf(stderr,"[<%s, pass 3", aln_file_name);
fseek (aln_file, 0, SEEK_SET);
n=0;
while(fgets(buff, MAXBUFFLENGTH, aln_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s %i %c %s %i %c" , &chr1[0], &pos1, &c1, &chr2[0], &pos2, &c2);
str1 = strand_c2i(c1);
str2 = strand_c2i(c2);
if(assign_code(chr1) != chr_q[n] || str1 != str_q[n] || pos1 != pos_q[n]) n++;
chr_t[n][ptr[n]] = assign_code(chr2);
pos_t[n][ptr[n]] = pos2;
str_t[n][ptr[n]] = str2;
ptr[n]++;
}
if(verbose) fprintf(stderr,"]\n");
for(i=1; i<=n; i++) {
progressbar(i, n, (char*)"Filtering ", verbose);
for(k=0; k<count[i]; k++) {
score[i][k] = 0;
lbest[i][k] = -1;
jbest[i][k] = -1;
for(j=i-1; j>0 && i-j<=max_depth; j--) {
a = abs(pos_q[i] - pos_q[j]);
dmin = INFTY;
lmin = -1;
for(l=0; l<count[j]; l++) {
if(chr_t[i][k] == chr_t[j][l] && str_t[i][k]*str_t[j][l] == str_q[i]*str_q[j]) {
b = abs(pos_t[i][k] - pos_t[j][l]);
d = abs(b-a);
if(d<dmin) {
dmin = d;
lmin = l;
}
}
}
s = (lmin>=0 && (((double)dmin/a) < dthreshold || dmin < dlimit)) ? score[j][lmin] + a : 0;
if(s > score[i][k]) {
score[i][k] = s;
jbest[i][k] = j;
lbest[i][k] = lmin;
}
}
}
}
for(i=n;i>0;i--) {
s_max = 0;
k_max = -1;
for(k=0; k<count[i]; k++) {
if(score[i][k]>s_max) {
s_max = score[i][k];
k_max = k;
}
}
if(k_max>=0) {
k = k_max;
while(jbest[i][k]>=0 && lbest[i][k]>=0) {
fprintf(out_file,"%s\t%i\t%c\t", get_chr_name(chr_q[i]), pos_q[i], strand_i2c(str_q[i]));
fprintf(out_file,"%s\t%i\t%c\n", get_chr_name(chr_t[i][k]), pos_t[i][k], strand_i2c(str_t[i][k]));
j = jbest[i][k];
l = lbest[i][k];
i = j;
k = l;
}
}
}
timestamp_report();
exit(0);
}
long timestamp_update(timestamp_t* timestamp)
{
timestamp_t prev = *timestamp;
timestamp_set(timestamp);
return timestamp_diff(timestamp, &prev);
}
long timestamp_elapsed(const timestamp_t* timestamp)
{
timestamp_t current;
timestamp_set(¤t);
return timestamp_diff(¤t, timestamp);
}
void
shadowauth(const char *myname, int persist)
{
const char *hash;
char *encrypted;
struct passwd *pw;
char *challenge, *response, rbuf[1024], cbuf[128];
#ifdef USE_TIMESTAMP
int fd = -1;
int valid = 0;
if (persist)
fd = timestamp_open(&valid, 5 * 60);
if (fd != -1 && valid == 1)
goto good;
#else
(void) persist;
#endif
if ((pw = getpwnam(myname)) == NULL)
err(1, "getpwnam");
hash = pw->pw_passwd;
if (hash[0] == 'x' && hash[1] == '\0') {
struct spwd *sp;
if ((sp = getspnam(myname)) == NULL)
errx(1, "Authorization failed");
hash = sp->sp_pwdp;
} else if (hash[0] != '*') {
errx(1, "Authorization failed");
}
char host[HOST_NAME_MAX + 1];
if (gethostname(host, sizeof(host)))
snprintf(host, sizeof(host), "?");
snprintf(cbuf, sizeof(cbuf),
"\rdoas (%.32s@%.32s) password: "******"tty required for %s", myname);
errx(1, "a tty is required");
}
if (response == NULL)
err(1, "readpassphrase");
if ((encrypted = crypt(response, hash)) == NULL) {
explicit_bzero(rbuf, sizeof(rbuf));
errx(1, "Authorization failed");
}
explicit_bzero(rbuf, sizeof(rbuf));
if (strcmp(encrypted, hash) != 0) {
syslog(LOG_AUTHPRIV | LOG_NOTICE, "failed auth for %s", myname);
errx(1, "Authorization failed");
}
#ifdef USE_TIMESTAMP
good:
if (fd != -1) {
timestamp_set(fd, 5 * 60);
close(fd);
}
#endif
}
int init(const platform_env_t* env)
{
paused = 0;
LOGI("Environment:\n Platform: %d\n Assets: %s\n Shared: %s\n Config: %s\n Tmp: %s\n",
env->platform,
env->assets_dir,
env->shared_dir,
env->config_dir,
env->tmp_dir);
io_driver_t* assets = NULL;
io_driver_t* config = NULL;
io_driver_t* tmp = NULL;
io_driver_t* shared = NULL;
if (io_init(&io) != 0 ||
#ifdef ANDROID
io_driver_apk_init(&assets, env->platform_specific) != 0 ||
#else
io_driver_fs_init(&assets, env->assets_dir) != 0 ||
#endif
io_driver_fs_init(&config, env->config_dir) != 0 ||
io_driver_fs_init(&shared, env->shared_dir) != 0 ||
io_driver_fs_init(&tmp, env->tmp_dir) != 0 ||
io_bind(io, "/config", config) ||
io_bind(io, "/tmp", tmp) ||
io_bind(io, "/shared", shared) ||
io_bind(io, "/assets", assets)
)
{
LOGE("Error initializing I/O system");
return -1;
}
io_set_working_dir(io, "/assets");
io_set_default(io);
if (gfx_init(&gfx) != 0)
{
LOGE("Error initializing GFX system");
return -1;
}
font_info_t info =
{
.name = "fonts/default.ttf",
.face_index = 0,
.width = 0,
.height = 14 * 64,
.dpi_x = 0,
.dpi_y = 72,
};
if (font_init(&font, &info, NULL) != 0)
{
LOGE("Error loading font");
return -1;
}
info.height = 22 * 64;
if (font_init(&big_font, &info, NULL) != 0)
{
LOGE("Error loading font");
return -1;
}
if (atlases_load(&atlases, "atlases.dat") != 0)
{
LOGE("Error loading atlases metadata");
return -1;
}
if (sprites_load(&sprites, "sprites.dat") != 0)
{
LOGE("Error loading sprites metadata");
return -1;
}
stats_load(&global_stats, "/config/player.dat");
if (am_init(&am, achievements_get_all(), achievements_get_count(), achievement_progress, achievement_unlocked))
{
LOGE("Unable to initialize achievements manager");
return -1;
}
achievements_context.am = am;
am_load(am, "/config/achievements.dat");
timestamp_set(&timer);
timestamp_set(&fps_timer);
push_screen(SCREEN_MAIN_MENU);
return 0;
}
void shutdown()
{
LOGI("shutdown");
atlases_free(atlases);
sprites_free(sprites);
font_free(font);
font_free(big_font);
gfx_free(gfx);
stats_dump(&global_stats);
stats_save(&global_stats, "/config/player.dat");
stats_free(&global_stats);
if (am != NULL)
{
am_save(am, "/config/achievements.dat");
am_dump(am);
am_free(am);
am = NULL;
}
io_free(io);
io = NULL;
atlases = NULL;
sprites = NULL;
font = NULL;
big_font = NULL;
gfx = NULL;
}
int update()
{
if (get_active_screen() == NULL)
{
return 1;
}
timestamp_t current = {0};
timestamp_set(¤t);
long dt = timestamp_diff(¤t, &timer);
if (dt > 0)
{
timer = current;
screen_update(dt);
}
long fps_dt = timestamp_diff(¤t, &fps_timer);
LOGD("DT: %ld", fps_dt);
if (fps_dt > 500)
{
fps = frames * 1000.0f / (float)fps_dt;
fps_timer = current;
frames = 0;
LOGI("FPS: %.2f", fps);
}
else
{
++frames;
}
char fps_str[32] = {0};
sprintf(fps_str, "FPS: %.2f", fps);
const rect_t fps_rect = { 8.0f, 8.0f, 256.0f, 32.0f };
const rgba_t fps_color = { 1.0f, 0.0f, 0.0f, 0.8f };
mat4f_t transform = {0};
mat4_mult(&transform, &camera.proj, &camera.view);
rect_t screen = { 0, 0, screen_size.x, screen_size.y };
rgba_t color = {0.7f, 0.7f, 0.0f, 1.0f };
gfx_set_target(gfx, "test_target", &screen);
gfx_enable_depth_buffer(gfx, 1);
gfx_clear(gfx);
screen_render(gfx, &camera);
gfx_set_shader(gfx, "text");
gfx_set_uniform_mat4f(gfx, "uMVP", 1, &transform);
draw_text(fps_str, &fps_rect, 0.0f, 4.9f, &fps_color);
gfx_flush(gfx);
static int take_screenshot = 0;
if (take_screenshot && frames == 0)
{
take_screenshot = 0;
image_t* img = NULL;
if (gfx_take_screenshot(gfx, &img) == 0)
{
image_save_to_png(img, "screenshot.png");
image_free(img);
}
}
gfx_set_target(gfx, NULL, &screen);
gfx_enable_depth_buffer(gfx, 0);
gfx_clear(gfx);
int32_t sampler = 0;
rect_t uv = { 0, screen.height/buffer_size.y, screen.width/buffer_size.x, -screen.height/buffer_size.y };
gfx_set_shader(gfx, "postprocess");
gfx_set_uniform_mat4f(gfx, "uMVP", 1, &transform);
gfx_set_uniform_1i(gfx, "uTex", 1, &sampler);
gfx_set_texture(gfx, "test_texture", sampler);
gfx_render_textured_rect(gfx, &screen, 1.0f, &uv);
gfx_set_texture(gfx, NULL, sampler);
gfx_flush(gfx);
return 0;
}
int main(int argc, char* argv[]) {
char cpsfilename[MAXBUFFLENGTH];
char chainfilename[MAXBUFFLENGTH];
char outfilename[MAXBUFFLENGTH]="";
int marginlength = 0;
int MAXREC;
char c;
char *pc;
int x;
char buff[MAXBUFFLENGTH+1];
char aux[MAXBUFFLENGTH+1];
long score;
int start1,end1,len1,start2,end2,len2;
char strand1, strand2, chr1[MAXBUFFLENGTH], chr2[MAXBUFFLENGTH];
int *size, *dq, *dt;
int a,b,k,i,j,s,m;
int *position;
char *strand;
int *ids;
int *idg;
char *type;
int chridx[MAXCHR+1];
int chroff[MAXCHR+1];
char resstr;
int rescrd;
if(argc==1) {
fprintf(stderr,"Finds matches of the given set of sites (CPS file) in the BLASTZ chain alignment (CHAIN file)\n");
fprintf(stderr,"Last update by (dp) on Sep 21, 2011\n");
fprintf(stderr,"Keys:\n -i CPS file (remember to sort by position in ascending order)\n -d CHAIN alignment file\n -o output file\n");
fprintf(stderr," -m margin length [0]\n -v suppress verbose output [NO]\n");
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
pc = argv[i];
if(*pc != '-') continue;
if(*(pc+1) == 'i') {
sscanf(argv[++i], "%s", &cpsfilename[0]);
}
if(*(pc+1) == 'd') {
sscanf(argv[++i], "%s", &chainfilename[0]);
}
if(*(pc+1) == 'o') {
sscanf(argv[++i], "%s", &outfilename[0]);
}
if(*(pc+1) == 'm') {
sscanf(argv[++i], "%i", &marginlength);
}
if(*(pc+1) == 'v') {
verbose=0;
}
}
if(outfilename[0]==0) {
fprintf(stderr,"No output file privided, exiting\n");
exit(1);
}
outfile = fopen(outfilename,"w");
if(outfile == NULL) {
fprintf(stderr,"Can't open output file, exiting\n");
exit(1);
}
for(i=0;i<MAXCHR;i++) {
chridx[i]=chroff[i]=0;
}
MAXREC = 0;
cpsfile= fopen(cpsfilename,"r");
if(cpsfile==NULL) {
fprintf(stderr,"Can't access CPS file. Exiting\n");
exit(1);
}
if(verbose) fprintf(stderr,"Reading CPS input pass 1");
while(!feof(cpsfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,cpsfile);
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
chridx[assign_code(aux)]++;
MAXREC++;
}
fclose(cpsfile);
for(s=i=0;i<MAXCHR;i++) {
x = chridx[i];
chridx[i] =s;
s+=x;
}
chridx[i] = s;
position = (int*) malloc(sizeof(int)*(s+4));
strand = (char*) malloc(sizeof(char)*(s+4));
type = (char*) malloc(sizeof(char)*(s+4));
ids = (int*) malloc(sizeof(int)*(s+4));
idg = (int*) malloc(sizeof(int)*(s+4));
if(position==NULL || strand==NULL || type==NULL || ids==NULL || idg==NULL) {
fprintf(stderr,"Not enough memory. Terminated\n");
exit(1);
}
cpsfile= fopen(cpsfilename,"r");
if(verbose) fprintf(stderr,", records = %i\nReading CPS input pass 2",MAXREC);
while(!feof(cpsfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,cpsfile);
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
i = assign_code(aux);
m = chridx[i]+chroff[i];
sscanf(buff,"%*s %i %c %i %i %c" , position+m, strand+m, idg+m, ids+m, type+m);
chroff[i]++;
}
fclose(cpsfile);
if(verbose) fprintf(stderr,"\nSorting segments");
/*
for(i=0;i<MAXCHR;i++) {
quickSort_ic(position,strand,chridx[i],chridx[i+1]-1);
}
*/
for(i=0;i<MAXCHR;i++) {
k=1;
while(k) {
k=0;
for(j=chridx[i];j<chridx[i+1]-1;j++) {
if(position[j]>position[j+1]) {
k=1;
swapi(position+j,position+j+1);
swapc(strand+j,strand+j+1);
swapc(type+j,type+j+1);
swapi(ids+j,ids+j+1);
swapi(idg+j,idg+j+1);
}
}
}
}
if(verbose) fprintf(stderr," done\nProcessing chains");
/**********************************************************************************************/
size = (int*) malloc(sizeof(int)*MAXALN);
dq = (int*) malloc(sizeof(int)*MAXALN);
dt = (int*) malloc(sizeof(int)*MAXALN);
if(size ==0 || dq ==0 || dt==0) {
fprintf(stderr,"Not enough memory for such long chains. Terminated\n");
exit(1);
}
/**********************************************************************************************/
chainfile = fopen(chainfilename,"r");
while(!feof(chainfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,chainfile);
if(strlen(buff)<2) break;
buff[5]=0;
if(strcmp(buff,"chain")==0) {
sscanf(buff+6,"%li %s %i %c %i %i %s %i %c %i %i",&score, &chr1[0], &len1, &strand1, &start1, &end1, &chr2[0], &len2, &strand2, &start2, &end2);
k=0;
while(!feof(chainfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,chainfile);
if(strlen(buff)<2) break;
sscanf(buff,"%i %i %i",&size[k],&dt[k],&dq[k]);
k++;
if(k>MAXALN) {
fprintf(stderr,"Chain length exceeded. Terminating");
exit(1);
}
}
x = get_chr_code(chr1);
if(x<0) continue;
a=start1;b=start2;
j=0;
for(i=chridx[x];i<chridx[x+1] && position[i]<start1;i++);
for(;i<chridx[x+1]&& position[i]<end1;i++) {
while(position[i]>a+size[j]+dt[j] && j<k){
a+=size[j]+dt[j];
b+=size[j]+dq[j];
j++;
}
if(j>=k) break;
if(position[i]-a > marginlength && a+size[j]-position[i] >= marginlength) {
if(strand1==strand2) {
resstr = strand[i];
rescrd = position[i] - a + b;
}
else {
resstr = (strand[i]=='+') ? '-' : '+';
rescrd = len2 - (position[i] - a + b - 1) ;
}
fprintf(outfile,"%s\t%i\t%c\t%s\t%i\t%c\t%i\t%i\t%c\t%li\n",chr1, position[i], strand[i],chr2,rescrd, resstr, idg[i], ids[i],type[i],score);
}
}
}
}
if(verbose) fprintf(stderr," done\n");
fclose(chainfile);
fclose(outfile);
timestamp_report();
exit(0);
}
int main(int argc, char* argv[]) {
char cps_file_name[MAXBUFFLENGTH];
char chain_file_name[MAXBUFFLENGTH];
char out_file_name[MAXBUFFLENGTH]="";
int marginlength = 0;
char buff[MAXBUFFLENGTH+1];
char aux[MAXBUFFLENGTH+1];
long score;
int start1,end1,len1,start2,end2,len2;
char strand1, strand2, chr1[MAXBUFFLENGTH], chr2[MAXBUFFLENGTH];
int *size, *dq, *dt;
int a,b,k,i,j,s,m,x;
int *position;
int *strand;
int *idg;
int *ids;
char *type;
char c;
int chridx[MAXCHR+1];
int chroff[MAXCHR+1];
char resstr;
int rescrd;
long chain_id;
if(argc==1) {
fprintf(stderr,"This utility does liftOver of coordinates (cps) by using chain alignment\n");
fprintf(stderr,"Gene information is included in the output\n");
fprintf(stderr,"Last update by Dmitri Pervouchine ([email protected]) on Mar 22, 2013\n");
fprintf(stderr,"Usage: %s -in <cps_file> -chain <chain_alignment_file> [-margin <length>] [-quiet]\n", argv[0]);
fprintf(stderr," -in cps6, i.e. chr1/position1/strand1/gene/site/type tab-delimited file, strand is +/-\n");
fprintf(stderr," -chain UCSC chain alignment file, species1=>2\n");
fprintf(stderr," -out <output_file> [default=stdout]\n");
fprintf(stderr," -margin margin length [default=0]\n -quiet suppress verbose output [default=NO]\n");
fprintf(stderr,"NOTE: Input has to be sorted by position!\n");
fprintf(stderr,"Output format cps3+cps6: chr1/position1/strand1/chr2/position2/strand2/gene/site/type/score\n");
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
if(strcmp(argv[i],"-in")==0) {
sscanf(argv[++i], "%s", &cps_file_name[0]);
}
if(strcmp(argv[i],"-chain")==0) {
sscanf(argv[++i], "%s", &chain_file_name[0]);
}
if(strcmp(argv[i],"-out")==0) {
sscanf(argv[++i], "%s", &out_file_name[0]);
}
if(strcmp(argv[i],"-margin")==0) {
sscanf(argv[++i], "%i", &marginlength);
}
if(strcmp(argv[i],"-quiet")==0) {
verbose=0;
}
}
if(out_file_name[0]==0) {
fprintf(stderr,"[WARNING: output file not specified, redirect to stdout]\n");
out_file = stdout;
}
else {
out_file = fopen(out_file_name,"w");
if(out_file == NULL) {
fprintf(stderr,"[ERROR: output file %s cannot be opened for writing, exiting]\n", out_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[>%s]\n",out_file_name);
}
cps_file= fopen(cps_file_name,"r");
if(cps_file==NULL) {
fprintf(stderr,"[ERROR: cannot access %s, exiting]\n", cps_file_name);
exit(1);
}
for(i=0;i<MAXCHR;i++) chridx[i] = chroff[i] = 0;
if(verbose) fprintf(stderr,"[<%s, pass 1",cps_file_name);
while(fgets(buff,MAXBUFFLENGTH,cps_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
chridx[assign_code(aux)]++;
}
if(verbose) fprintf(stderr,"]\n");
for(s=i=0;i<MAXCHR;i++) {
x = chridx[i];
chridx[i] =s;
s+=x;
}
chridx[i] = s;
position = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
strand = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
ids = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
idg = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
type = (char*) malloc(sizeof(char)*(s + ARRAY_MARGIN));
if(position==NULL || strand==NULL || type==NULL || ids==NULL || idg==NULL) {
fprintf(stderr,"[ERROR: failed to create index tables, exiting]\n");
exit(1);
}
fseek (cps_file, 0, SEEK_SET);
if(verbose) fprintf(stderr,"[<%s, pass 2", cps_file_name);
while(fgets(buff,MAXBUFFLENGTH,cps_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
i = assign_code(aux);
m = chridx[i]+chroff[i];
sscanf(buff,"%*s %i %c %i %i %c" , &position[m], &c,&idg[m],&ids[m],&type[m]);
strand[m] = strand_c2i(c);
chroff[i]++;
}
fclose(cps_file);
if(verbose) fprintf(stderr,"]\n");
if(verbose) fprintf(stderr,"[Sort by position (if not done before)");
for(i=0;i<MAXCHR;i++) {
k=1;
while(k) {
k=0;
for(j=chridx[i];j<chridx[i+1]-1;j++) {
if(position[j]>position[j+1]) {
k=1;
swapi(position+j,position+j+1);
swapi(strand+j,strand+j+1);
swapi(idg+j,idg+j+1);
swapi(ids+j,ids+j+1);
swapc(type+j,type+j+1);
}
}
}
}
if(verbose) fprintf(stderr,"]\n");
/**********************************************************************************************/
size = (int*) malloc(sizeof(int)*(MAXALN + ARRAY_MARGIN));
dq = (int*) malloc(sizeof(int)*(MAXALN + ARRAY_MARGIN));
dt = (int*) malloc(sizeof(int)*(MAXALN + ARRAY_MARGIN));
if(size ==0 || dq ==0 || dt==0) {
fprintf(stderr,"[ERROR: not enough memory for chains, exiting]\n");
exit(1);
}
/**********************************************************************************************/
chain_file = fopen(chain_file_name,"r");
if(chain_file==NULL) {
fprintf(stderr,"[ERROR: cannot access %s, exiting]\n", chain_file_name);
exit(1);
}
fseek(chain_file, 0, SEEK_END);
unsigned int last_pos = ftell(chain_file);
fseek(chain_file, 0, SEEK_SET);
while(fgets(buff,MAXBUFFLENGTH,chain_file)) {
if(strlen(buff)<2) break;
buff[5]=0;
if(strcmp(buff,"chain")==0) {
sscanf(buff+6,"%li %s %i %c %i %i %s %i %c %i %i %li",&score, &chr1[0], &len1, &strand1, &start1, &end1, &chr2[0], &len2, &strand2, &start2, &end2, &chain_id);
k=0;
while(fgets(buff,MAXBUFFLENGTH,chain_file)) {
if(strlen(buff)<2) break;
progressbar(ftell(chain_file), last_pos-1, (char*)"Processing ", verbose);
sscanf(buff,"%i %i %i",size + k, dt + k, dq + k);
k++;
if(k>=MAXALN) {
fprintf(stderr,"[ERROR: chain too long, exiting]\n");
exit(1);
}
}
x = get_chr_code(chr1);
if(x<0) continue;
a=start1;b=start2;
j=0;
for(i=chridx[x];i<chridx[x+1] && position[i]<start1;i++);
for(;i<chridx[x+1]&& position[i]<end1;i++) {
while(position[i]>a+size[j]+dt[j] && j<k){
a+=size[j]+dt[j];
b+=size[j]+dq[j];
j++;
}
if(j>=k) break;
if(position[i]-a > marginlength && a+size[j]-position[i] >= marginlength) {
if(strand1==strand2) {
resstr = strand[i];
rescrd = position[i] - a + b;
}
else {
resstr = -strand[i];
rescrd = len2 - (position[i] - a + b - 1) ;
}
fprintf(out_file,"%s\t%i\t%c\t%s\t%i\t%c\t%i\t%i\t%c\t%li\n",chr1, position[i], strand_i2c(strand[i]), chr2, rescrd, strand_i2c(resstr), idg[i], ids[i],type[i],score);
}
}
}
}
fclose(chain_file);
fclose(out_file);
timestamp_report();
free(size);
free(dq);
free(dt);
free(position);
free(strand);
exit(0);
}
int main(int argc, char** argv) {
char outputfilename[MAXBUFFLENGTH]="";
char chr[MAXBUFFLENGTH];
char* filename[MAXSPECIES];
char buff[MAXLONGBUFFLENGTH];
char seq[MAXLONGBUFFLENGTH];
int key[MAXKEYS];
FILE *inpfile;
FILE *outputfile;
char *pc;
int x, max_key;
int i, j, nk, n_species;
long pos, len, total;
char strand;
int *ind;
char **muf;
if(argc==1) {
fprintf(stderr, "MUF builder\n");
fprintf(stderr, "Usage: %s -i [input_file_1] [input_file_2] ... [input_file_n] -o [output file]\n STDIN: cps file for subsetting\n",argv[0]);
exit(1);
}
timestamp_set();
n_species=0;
for(i=1; i<argc; i++) {
pc = argv[i];
if(*pc != '-') continue;
if(*(pc+1) == 'o') {
sscanf(argv[++i], "%s", &outputfilename[0]);
}
if(*(pc+1) == 'i') {
for(;i+1<argc;i++) {
pc = argv[i+1];
if(*pc == '-') break;
filename[n_species] = (char*)malloc(sizeof(char)*MAXBUFFLENGTH);
strcpy(filename[n_species++],pc);
}
}
if(*(pc+1) == 'v') {
verbose=0;
}
}
outputfile = fopen(outputfilename,"w");
if(outputfile == NULL) {
fprintf(stderr,"Can't open output file, exiting\n");
exit(1);
}
max_key=0;
nk=0;
while(fgets(buff,MAXBUFFLENGTH,stdin)) {
sscanf(buff,"%*s %*i %*c %*i %i",&x);
if(x>max_key) max_key=x;
key[nk++]=x;
if(nk>=MAXKEYS-1) {fprintf(stderr,"[WARNING: too many keys to hold, ignoring the rest]\n");break;}
}
ind = (int*)malloc(sizeof(int)*(max_key + 16));
muf = (char**)malloc(sizeof(char*)*(max_key + 16));
if(ind==NULL) {
fprintf(stderr,"Can't create index (%i), exiting\n",max_key);
exit(1);
}
for(i=0;i<=max_key;i++) ind[i]=0;
for(j=0;j<nk;j++) {
ind[key[j]]=1;
muf[key[j]]=(char*)malloc(sizeof(char)*MAXLONGBUFFLENGTH*MAXSPECIES);
if(muf[key[j]]==NULL) {
fprintf(stderr,"Can't allocate enough memory, exiting\n");
exit(1);
}
muf[key[j]][0]=0;
if(verbose) fprintf(stderr,"[%i]",key[j]);
}
if(verbose) fprintf(stderr,"\n");
for(i=0;i<n_species;i++) {
inpfile = fopen(filename[i], "r");
if(verbose) fprintf(stderr,"[%s, ", filename[i]);
if(inpfile==NULL) {
fprintf(stderr,"Cannot open %s, exiting",filename[i]);
exit(1);
}
for(j=strlen(filename[i])-1;filename[i][j]!='.' && j>=0;j--);
filename[i][j]=0;
for(j--;filename[i][j]!='/' && j>=0;j--);
if(verbose) fprintf(stderr,"tag=%s", filename[i] + j + 1);
while(fgets(buff, MAXLONGBUFFLENGTH, inpfile)) {
x=0;
sscanf(buff,"%i %s %li %li %c %li %s", &x, &chr[0], &pos, &len, &strand, &total, &seq[0]);
if(x==0) {fprintf(stderr,"!");continue; }
if(x<=max_key) {
if(ind[x]) {
sprintf(buff,"s %s.%s %li %li %c %li %s\n", filename[i] + j + 1, chr, pos, len, strand, total, seq);
strcat(muf[x],buff);
}
}
}
if(verbose) fprintf(stderr,"]\n");
}
for(i=0;i<=max_key;i++) {
if(ind[i]) if(strlen(muf[i])>1) fprintf(outputfile,"a id=%i\n%s\n", i, muf[i]);
}
fclose(outputfile);
timestamp_report();
exit(0);
}
int main(int argc, char* argv[]) {
char out_file_name[MAXBUFFLENGTH]="";
char input_file_name[MAXBUFFLENGTH]="";
char idx_file_name[MAXBUFFLENGTH];
char dbx_file_name[MAXBUFFLENGTH];
long offset;
long seqlen;
long intronic_window = 150;
long exonic_window = 0;
char filename[MAXBUFFLENGTH];
char name[MAXBUFFLENGTH];
char chr_name[MAXBUFFLENGTH];
char buff[MAXBUFFLENGTH];
char longbuff[MAXLONGBUFFLENGTH];
char longbuffm[MAXLONGBUFFLENGTH];
FILE *idx_file;
FILE *dbx_file;
FILE *input_file;
FILE *outfile;
int b,i,j,q,k,n,a,m,s;
char c;
long position,y;
int strand;
long** pos;
int** str;
char** typ;
char*** ids;
long p,l;
int record_count[MAXCHR];
int record_idx[MAXCHR];
int cis = 0;
int coord = 0;
int all=0;
int warnings = 0;
char format[][64] = {"%*s %*i %*i %s %li %i %*s %s %c", "%s %li %i %*s %s %c"};
if(argc==1) {
fprintf(stderr,"This routine get sequence segments from a custom compressed FASTA repository (see transf)\n");
fprintf(stderr,"Last update by Dmitri Pervouchine ([email protected]) on Mar 22, 2013\n");
fprintf(stderr," -in <aln_file>\n -dbx <database_file>\n -idx <index_file>\n -out <output_file>\n");
fprintf(stderr," -we <exonic_window> [default=%i]\n -wi <intronic_window> [default=%i]\n -cis [use colunms 1-3] [default=%i]\n", exonic_window, intronic_window, cis);
fprintf(stderr," -quiet <suppress verbose output> [default=no]\n -all <include all sites>\n -coord <offset for 3'-sites> [default=%i]\n",coord);
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
if(strcmp(argv[i],"-in")==0) {
sscanf(argv[++i], "%s", &input_file_name[0]);
}
if(strcmp(argv[i],"-dbx")==0) {
sscanf(argv[++i], "%s", &dbx_file_name[0]);
}
if(strcmp(argv[i],"-idx")==0) {
sscanf(argv[++i], "%s", &idx_file_name[0]);
}
if(strcmp(argv[i],"-out")==0) {
sscanf(argv[++i], "%s", &out_file_name[0]);
}
if(strcmp(argv[i],"-we")==0) {
sscanf(argv[++i], "%li", &exonic_window);
}
if(strcmp(argv[i],"-wi")==0) {
sscanf(argv[++i], "%li", &intronic_window);
}
if(strcmp(argv[i],"-coord")==0) {
sscanf(argv[++i], "%i", &coord);
}
if(strcmp(argv[i],"-quiet")==0) {
verbose = 0;
}
if(strcmp(argv[i],"-cis")==0) {
cis = 1;
}
if(strcmp(argv[i],"-all")==0) {
all = 1;
}
}
if(out_file_name[0]==0) {
fprintf(stderr,"[WARNING: output file not specified, redirect to stdout]\n");
outfile = stdout;
}
else {
outfile = fopen(out_file_name,"w");
if(outfile == NULL) {
fprintf(stderr,"[ERROR: output file %s cannot be opened for writing, exiting]\n", out_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[>%s]\n",out_file_name);
}
input_file = fopen(input_file_name,"r");
if(input_file == NULL) {
fprintf(stderr,"[ERROR: cannot access %s, exiting]\n", input_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[<%s, pass 1",input_file_name);
while(fgets(buff,MAXBUFFLENGTH,input_file)) {
if(strlen(buff)<2) break;
sscanf(buff, format[cis], &chr_name[0], &position, &strand, &name[0], &c);
n = assign_code(chr_name);
record_count[n]++;
}
if(verbose) fprintf(stderr,"]\n");
pos = (long**) malloc(sizeof(long*)*(N_CHR_NAMES+1));
str = (int**) malloc(sizeof(int*)*(N_CHR_NAMES+1));
typ = (char**) malloc(sizeof(char*)*(N_CHR_NAMES+1));
ids = (char***)malloc(sizeof(char**)*(N_CHR_NAMES+1));
if(pos==NULL || str==NULL || typ==NULL || ids==NULL) {
fprintf(stderr,"[ERROR: failed to create index tables, exiting]\n");
exit(1);
}
for(i=0;i<N_CHR_NAMES;i++) {
if(record_count[i]>0) {
pos[i] = (long*) malloc(sizeof(long)*(record_count[i]+1));
str[i] = (int*) malloc(sizeof(int)*(record_count[i]+1));
typ[i] = (char*) malloc(sizeof(char)*(record_count[i]+1));
ids[i] = (char**) malloc(sizeof(char*)*(record_count[i]+1));
if(pos[i]==NULL || str[i]==NULL || typ[i]==NULL || ids[i]==NULL) {
fprintf(stderr,"[ERROR: failed to create index tables, exiting]\n");
exit(1);
}
record_idx[i]=0;
}
}
if(verbose) fprintf(stderr,"[<%s, pass 2",input_file_name);
fseek(input_file, 0, SEEK_SET);
while(fgets(buff,MAXBUFFLENGTH,input_file)) {
if(strlen(buff)<2) break;
sscanf(buff, format[cis], &chr_name[0], &position, &strand, &name[0], &c);
i = get_chr_code(chr_name);
j = record_idx[i];
pos[i][j] = position + (c=='D' ? coord*strand : 0);
str[i][j] = strand;
typ[i][j] = c;
ids[i][j] = (char*) malloc(sizeof(char)*(strlen(name)+1));
strcpy(ids[i][j],name);
record_idx[i]++;
}
if(verbose) fprintf(stderr,"]\n");
if(verbose) fprintf(stderr,"[<%s,%s",idx_file_name,dbx_file_name);
idx_file = fopen(idx_file_name,"r");
dbx_file = fopen(dbx_file_name,"r");
if(idx_file == NULL || dbx_file == NULL) {
fprintf(stderr,"[ERROR: cannot access %s or %s, exiting]\n", idx_file_name, dbx_file_name);
exit(1);
}
offset = 0;
while(fgets(buff,MAXBUFFLENGTH,idx_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s" , &name[0]);
while(fgets(buff,MAXBUFFLENGTH,idx_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s %li" , &chr_name[0], &seqlen);
i = get_chr_code(chr_name);
for(k=0;k<record_count[i];k++) {
if(pos[i][k]>seqlen) {
warnings++;
continue;
}
l = exonic_window + intronic_window;
if(typ[i][k]=='D' || typ[i][k]=='A' || all) {
if(str[i][k]>0) {
p = pos[i][k] - 1 - (typ[i][k]=='D' ? exonic_window : intronic_window);
}
else {
p = pos[i][k] - (typ[i][k]=='D' ? intronic_window : exonic_window);
}
fget_segment(longbuff, dbx_file, offset, p, l);
if(str[i][k]<0) {
rev1(longbuff);
}
if(is_all_n(longbuff)) continue;
fprintf(outfile,"%s\t%s\t%li\t%li\t%i\t%li\t%s\t%c\n",ids[i][k], chr_name, (str[i][k]>0 ? p + 1 : seqlen - (p + l)), l, str[i][k], seqlen, longbuff,typ[i][k]);
}
}
offset+= (seqlen % 8 == 0) ? seqlen/8 : (seqlen/8 + 1);
}
}
fclose(outfile);
fclose(idx_file);
fclose(dbx_file);
if(verbose) fprintf(stderr,"]\n");
if(verbose && warnings>0) fprintf(stderr,"[WARNING: %i windows were out of range, they were ignored]\n", warnings);
timestamp_report();
exit(0);
}
int main(int argc, char** argv) {
dictionary<ATOMIC>* dict[MAXSPECIES];
dictionary<ATOMIC>* filter;
conservation_table* cons[MAXSPECIES];
int i,j;
FILE *configfile, *metacalc;
wordexp_t exp_result;
char buff[MAXBUFFLENGTH];
char tag[MAXBUFFLENGTH];
char aux[MAXBUFFLENGTH];
char path[MAXBUFFLENGTH]="";
char suffix[MAXBUFFLENGTH]="";
char configfilename[MAXBUFFLENGTH];
char restrictionfilename[MAXBUFFLENGTH];
char metacalcfilename[MAXBUFFLENGTH]="";
char maffilename[MAXBUFFLENGTH]="";
int n_species=0;
char* file_name[MAXSPECIES];
double weight[MAXSPECIES];
double threshold=0;
double tot_weight=0;
int halfsize=4;
int gap=2;
int min_gc=1;
int repeat_length=2;
int length_limit=0;
subset *restriction=NULL;
index_t p,q,r,s;
word_t a;
char *pc;
char *p_file_name;
int reverse_complement=0;
/***************************************************************************************************************************************/
if(argc==1) {
fprintf(stderr, "TRIM - this program takes sequences, creates corresponding hash tables, and intersects them by trimmming\n");
fprintf(stderr, "Usage: %s -i config_file [-maf maf_file_name] -r restriction_file -o output_metafile\n",argv[0]);
fprintf(stderr, "Other parameters are:\n -verbose [suppress verbose output]\n -rc [reverse complement sequences before adding]\n");
exit(1);
}
timestamp_set();
maffilename[0]=0;
for(i=1;i<argc;i++) {
pc = argv[i];
if(*pc == '-') {
if(strcmp(pc+1,"i") == 0) {
configfile = fopen(argv[++i],"r");
if(configfile==NULL) {
fprintf(logfile,"Input file (%s) cannot be opened, exiting", argv[i]);
exit(1);
}
n_species = 0;
tot_weight= 0;
while(fgets(buff,MAXBUFFLENGTH,configfile)) {
tag[0]=0;
sscanf(buff,"%s %*s",tag);
if(strcmp(tag,"path")==0) sscanf(buff,"%*s %s", &path[0]);
if(strcmp(tag,"extention")==0) sscanf(buff,"%*s %s", &suffix[0]);
if(strcmp(tag,"halfsize")==0) sscanf(buff,"%*s %i", &halfsize);
if(strcmp(tag,"gap")==0) sscanf(buff,"%*s %i", &gap);
if(strcmp(tag,"repeatmask")==0) sscanf(buff,"%*s %i", &repeat_length);
if(strcmp(tag,"gccontent")==0) sscanf(buff,"%*s %i", &min_gc);
if(strcmp(tag,"lowercase")==0) sscanf(buff,"%*s %i", &lowercase_allowed);
if(strcmp(tag,"threshold")==0) sscanf(buff,"%*s %lf",&threshold);
if(strcmp(tag,"samewindow")==0) sscanf(buff,"%*s %i", &SAMEWINDOW);
if(strcmp(tag,"limit")==0) sscanf(buff,"%*s %i", &length_limit);
if(strcmp(tag,"species")==0) {
file_name[n_species] = (char*)malloc(sizeof(char)*MAXBUFFLENGTH);
sscanf(buff,"%*s %s %lf", &file_name[n_species][0], &weight[n_species]);
tot_weight+=weight[n_species];
n_species++;
}
}
fclose(configfile);
}
if(strcmp(pc+1,"maf") == 0) sscanf(argv[++i],"%s",&maffilename[0]);
if(strcmp(pc+1,"r") == 0) restriction = new subset(argv[++i]);
if(strcmp(pc+1,"o") == 0) sscanf(argv[++i], "%s", &metacalcfilename[0]);
if(strcmp(pc+1,"verbose") == 0) verbose = 0;
if(strcmp(pc+1,"rc") == 0) reverse_complement = 1;
if(strcmp(pc+1,"log")==0) {
logfile = fopen(argv[++i], "w");
if(logfile==NULL) logfile = stderr;
}
}
}
if(halfsize<2 || gap>3) {
if(verbose) fprintf(logfile,"Word size or gap are incorrect, exiting\n");
exit(1);
}
metacalc = fopen(metacalcfilename,"wb");
if(metacalc==NULL) {
if(verbose) fprintf(logfile,"Output metacalc file cannot be opened, exiting\n");
exit(1);
}
/***************************************************************************************************************************************/
if(threshold==0) threshold = 0.5;
if(verbose) fprintf(logfile, "[Numeric parameters are: pattern=%i-%i-%i, minGC=%i, repeat=%i, threshold=%2.1lf%%]\n", halfsize, gap, halfsize, min_gc, repeat_length, threshold*100);
if(verbose) fprintf(logfile, "[Boolean parameters are: lowercase=%s, reverse_complement=%s]\n",yesno(lowercase_allowed), yesno(reverse_complement));
if(verbose) fprintf(logfile, "[Extra parameters are: SAMEWINDOW=%i, sequence length limit=%i]\n",SAMEWINDOW,length_limit);
wordexp(path, &exp_result, 0);
sprintf(&path[0],"%s",exp_result.we_wordv[0]);
/***************************************************************************************************************************************/
filter = new dictionary<ATOMIC>(halfsize,gap);
filter->mask_low_complexity(repeat_length);
if(min_gc>0) filter->mask_low_GCcontent(min_gc);
for(i=0;i<n_species;i++) {
dict[i] = new dictionary<ATOMIC>(halfsize,gap);
dict[i]->filter = filter;
}
if(maffilename[0]==0) {
for(i=0;i<n_species;i++) {
p_file_name = getfullname(path,file_name[i],suffix);
if(verbose) fprintf(logfile,"[Reading %s: ",p_file_name);
dict[i]->read_from_suf(p_file_name, restriction, reverse_complement,length_limit);
dict[i]->check();
cons[i] = new conservation_table(dict[i]->max_key);
cons[i]->before = dict[i]->fill_cons();
if(verbose) fprintf(logfile,", weight=%2.1lf]\n",weight[i]);
}
}
else {
if(verbose) fprintf(logfile,"[Reading %s: ", maffilename);
dictionary<ATOMIC>::read_from_muf(maffilename, dict, restriction, file_name, n_species, reverse_complement,length_limit);
if(verbose) fprintf(logfile,"]\n");
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile,"[%s",file_name[i]);
dict[i]->info();
dict[i]->check();
cons[i] = new conservation_table(dict[i]->max_key);
cons[i]->before = dict[i]->fill_cons();
if(verbose) fprintf(logfile,", weight=%2.1lf]\n",weight[i]);
}
}
dictionary<ATOMIC>::intersect_many(dict, n_species, weight, threshold*tot_weight, (char*)"Intersect ");
if(verbose) fprintf(logfile,"[Compute conservation rates:");
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile," %s",file_name[i]);
cons[i]->after = dict[i]->fill_cons();
}
if(verbose) fprintf(logfile,"]\n");
if(verbose) fprintf(logfile,"[Metacalc: saving data to %s]\n",metacalcfilename);
fprintf(metacalc,"%i %i %i %lf\n", halfsize, gap, n_species, threshold);
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile,"[Saving %s",file_name[i]);
dict[i]->check();
dict[i]->info();
fprintf(metacalc,"%s %lf\n", file_name[i], weight[i]);
dict[i]->save(metacalc);
cons[i]->save(metacalc);
if(verbose) fprintf(logfile,"]\n");
}
fclose(metacalc);
timestamp_report();
return(0);
}
int main(int argc, char* argv[]) {
char alnfilename[MAXBUFFLENGTH];
char cpsfilename[MAXBUFFLENGTH];
char outfilename[MAXBUFFLENGTH]="";
char c;
char buff[MAXBUFFLENGTH];
char aux[MAXBUFFLENGTH];
int start1,end1,len1,start2,end2,len2;
char strand1, strand2;
int a,b,k,l,i,j,s,m,q;
int d,dmin,lmin,score_max;
int x,y;
int qbest, kbest, jbest;
int kprev;
int *gene_idx; //index
int *gene_off; //offset
int *gene_site; //site number
char *gene_styp; //site type
int *gene_pos; //site position
int *gene_chr; //chromosome
char *gene_str; //strand
int max_genes;
int max_sites;
int *site_idx; //index
int *site_off; //offset
int *site_chr; //matching chromosome
int *site_pos; //matching pos
int *site_str; //matching strand
int *site_score; //--- optimal score
int *site_lbest; //--- where it came from
int *site_qbest; //--- where it came from
int specific_site=0;
double dthreshold = 0.50;
int dlimit = 5000;
int max_depth = 4;
int pos, strand;
if(argc==1) {
fprintf(stderr,"Select best unique maping from the ALN file created by map_single\n");
fprintf(stderr,"Last updated by Dmitri Pervouchine ([email protected]) on Jan 28, 2013\n");
fprintf(stderr,"Keys:\n -in <cps file>\n -aln <aln file>\n -out <output file>\n");
//fprintf(stderr," -l length difference limit [%i]\n -t percentage difference threshold [%1.2lf] (ONE OR THE OTHER THRESHOLD IS USED)\n -h max_depth [%i]\n",dlimit, dthreshold,max_depth);
//fprintf(stderr," -v suppress verbose output [NO]\n");
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
if(strcmp(argv[i],"-in")==0) {
sscanf(argv[++i], "%s", &cpsfilename[0]);
}
if(strcmp(argv[i],"-aln")==0) {
sscanf(argv[++i], "%s", &alnfilename[0]);
}
if(strcmp(argv[i],"-out")==0) {
sscanf(argv[++i], "%s", &outfilename[0]);
}
if(strcmp(argv[i],"-lendiff")==0) {
sscanf(argv[++i], "%i", &dlimit);
}
if(strcmp(argv[i],"-threshold")==0) {
sscanf(argv[++i], "%lf", &dthreshold);
}
if(strcmp(argv[i],"-maxdepth")==0) {
sscanf(argv[++i], "%i", &max_depth);
}
if(strcmp(argv[i],"-quiet")==0) {
verbose=0;
}
if(strcmp(argv[i],"-s")==0) {
sscanf(argv[++i], "%i", &specific_site);
}
}
if(outfilename[0]==0) {
fprintf(stderr,"[WARNING: output file not specified, redirect to stdout]\n");
outfile = stdout;
}
else {
outfile = fopen(outfilename,"w");
if(outfile == NULL) {
fprintf(stderr,"[ERROR: output file (%s) cannot be opened, exiting]\n", outfilename);
exit(1);
}
}
/*******************************************************************************************************/
cpsfile= fopen(cpsfilename,"r");
if(cpsfile==NULL) {
fprintf(stderr,"Can't access CPS file. Exiting\n");
exit(1);
}
if(verbose) fprintf(stderr,"[Reading CPS, pass 0");
max_sites = max_genes = 0;
while(fgets(buff,MAXBUFFLENGTH,cpsfile)) {
if(strlen(buff)<2) break;
sscanf(buff,"%*s %*i %*i %i %i", &i, &j);
if(i>max_genes) max_genes = i;
if(j>max_sites) max_sites = j;
}
max_genes++;
max_sites++;
gene_idx = (int*) malloc(sizeof(int)*(max_genes+1));
gene_off = (int*) malloc(sizeof(int)*(max_genes+1));
gene_chr = (int*) malloc(sizeof(int)*(max_genes+1));
gene_str = (char*) malloc(sizeof(char)*(max_genes+1));
for(i=0;i<max_genes;i++) gene_idx[i]=gene_off[i]=0;
if(verbose) fprintf(stderr,", max_genes = %i, max_sites = %i]\n", max_genes, max_sites);
if(verbose) fprintf(stderr,"[Reading CPS, pass 1");
fseek (cpsfile, 0, SEEK_SET);
while(fgets(buff,MAXBUFFLENGTH,cpsfile)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s %*i %i %i %*i" , aux, &strand, &i);
gene_idx[i]++;
gene_chr[i] = assign_code(aux);
gene_str[i] = strand;
}
for(s=i=0;i<max_genes;i++) {
x = gene_idx[i];
gene_idx[i] =s;
s+=x;
}
gene_idx[i] = s;
gene_site = (int*) malloc(sizeof(int)*(s+1));
gene_styp = (char*) malloc(sizeof(char)*(s+1));
gene_pos = (int*) malloc(sizeof(int)*(s+1));
if(verbose) fprintf(stderr,", records = %i]\n", s);
if(verbose) fprintf(stderr,"[Reading CPS, pass 2");
fseek (cpsfile, 0, SEEK_SET);
while(fgets(buff,MAXBUFFLENGTH,cpsfile)) {
if(strlen(buff)<2) break;
sscanf(buff,"%*s %i %*i %i %i %c" , &x, &i, &j, &c);
gene_site[gene_idx[i]+gene_off[i]]=j;
gene_styp[gene_idx[i]+gene_off[i]]=c;
gene_pos[gene_idx[i]+gene_off[i]]=x;
gene_off[i]++;
}
fclose(cpsfile);
if(verbose) fprintf(stderr,"]\n");
/**********************************************************************************************/
alnfile = fopen(alnfilename,"r");
if(alnfile == NULL) {
fprintf(stderr, "Cant open alignment file, exiting\n");
exit(1);
}
site_idx = (int*) malloc(sizeof(int)*(max_sites+1));
site_off = (int*) malloc(sizeof(int)*(max_sites+1));
for(i=0;i<max_sites;i++) {
site_idx[i]=site_off[i]=0;
}
if(verbose) fprintf(stderr,"[Reading alignment file, pass 1");
while(fgets(buff,MAXBUFFLENGTH,alnfile)) {
if(strlen(buff)<2) break;
sscanf(buff,"%*s %*i %*i %*s %*i %*i %*i %i %*c" , &i);
site_idx[i]++;
}
for(s=i=0;i<max_sites;i++) {
x = site_idx[i];
site_idx[i] =s;
s+=x;
}
site_idx[i] = s;
site_chr = (int*) malloc(sizeof(int)*(s+1));
site_pos = (int*) malloc(sizeof(int)*(s+1));
site_str = (int*) malloc(sizeof(int)*(s+1));
site_score = (int*) malloc(sizeof(int)*(s+1));
site_lbest = (int*) malloc(sizeof(int)*(s+1));
site_qbest = (int*) malloc(sizeof(int)*(s+1));
if(verbose) fprintf(stderr,", records = %i]\n",s);
if(verbose) fprintf(stderr,"[Reading alignment file, pass 2");
fseek (alnfile, 0, SEEK_SET);
while(fgets(buff,MAXBUFFLENGTH,alnfile)) {
if(strlen(buff)<2) break;
sscanf(buff,"%*s %*i %*i %s %i %i %*i %i %*c" , &aux, &pos, &strand, &i);
site_chr[site_idx[i]+site_off[i]] = assign_code(aux);
site_pos[site_idx[i]+site_off[i]] = pos;
site_str[site_idx[i]+site_off[i]] = strand;
site_score[site_idx[i]+site_off[i]] = 0;
site_lbest[site_idx[i]+site_off[i]] = -1;
site_qbest[site_idx[i]+site_off[i]] = -1;
site_off[i]++;
}
fclose(alnfile);
if(verbose) fprintf(stderr,"]\n");
for(i=0;i<max_genes;i++) {
progressbar(i,max_genes-1, (char*)"Processing");
score_max=0;
kbest = -1;
for(j=gene_idx[i];j<gene_idx[i+1];j++) {
x = gene_site[j];
for(k=site_idx[x];k<site_idx[x+1];k++) {
site_score[k] = 0;
site_lbest[k] = site_qbest[k] = -1;
}
for(q=1;q<=max_depth;q++) {
if(j-q>=gene_idx[i]) {
y = gene_site[j-q];
a = abs(gene_pos[j]-gene_pos[j-q]);
for(k=site_idx[x];k<site_idx[x+1];k++) {
dmin = INFTY;
lmin = -1;
for(l=site_idx[y];l<site_idx[y+1];l++) {
if(site_chr[k] == site_chr[l] && site_str[k] == site_str[l]) {
b = abs(site_pos[k]-site_pos[l]);
d = abs(b-a);
if(d<dmin) {
dmin = d;
lmin = l;
}
if(x==specific_site) fprintf(stderr,"[prev=%i curr=%i pos_p=%i pos_c=%i d=%i]\n",y,x,site_pos[l],site_pos[k],d);
}
}
m = (lmin>=0 && (((double)dmin/a)<dthreshold || dmin<dlimit)) ? site_score[lmin] + a : 0;
if(m>site_score[k]) {
site_score[k] = m;
site_lbest[k] = lmin;
site_qbest[k] = q;
}
if(site_score[k]>score_max) {
score_max = site_score[k];
kbest = k; jbest = j;
}
if(x==specific_site) fprintf(stderr,"[curr=%i score=%i]\n",x,site_score[k]);
}
}
}
}
j = jbest;
k = kbest;
if(k>=0 && site_score[k]>0) {
fprintf(outfile,"%s\t%i\t%i\t%s\t%i\t%i\t",get_chr_name(gene_chr[i]),gene_pos[j],gene_str[i],get_chr_name(site_chr[k]),site_pos[k],site_str[k]);
fprintf(outfile,"%i\t%i\t%c\t%i\t%i\n",i,gene_site[j],gene_styp[j],site_pos[site_lbest[k]],0);
while(site_score[k]>0 && site_lbest[k]>=0 && site_qbest[k]>=0) {
kprev = k;
j = j - site_qbest[k];
k = site_lbest[k];
fprintf(outfile,"%s\t%i\t%i\t%s\t%i\t%i\t",get_chr_name(gene_chr[i]),gene_pos[j],gene_str[i],get_chr_name(site_chr[k]),site_pos[k],site_str[k]);
fprintf(outfile,"%i\t%i\t%c\t%i\t%i\n",i,gene_site[j],gene_styp[j],(site_lbest[k]>=0?site_pos[site_lbest[k]]:0),(kprev>=0?site_pos[kprev]:0));
}
}
}
timestamp_report();
exit(0);
}