bsp_node_t *clone_bsp_tree(bsp_node_t *tree) {
bsp_node_t *copy = alloc_bsp_node();
check_mem(copy);
kliter_t(poly) *iter = kl_begin(tree->polygons);
for(; iter != kl_end(tree->polygons); iter = kl_next(iter)) {
poly_t *poly_copy = clone_poly(kl_val(iter));
check_mem(poly_copy);
*kl_pushp(poly, copy->polygons) = poly_copy;
}
free_poly(copy->divider, 1);
if(tree->divider) {
copy->divider = clone_poly(tree->divider);
check_mem(copy->divider);
}
else {
copy->divider = NULL;
}
if(tree->front != NULL) {
copy->front = clone_bsp_tree(tree->front);
check_mem(copy->front);
}
if(tree->back != NULL) {
copy->back = clone_bsp_tree(tree->back);
check_mem(copy->back);
}
return copy;
error:
if(copy != NULL) free_bsp_tree(copy);
return NULL;
}
void test_bsp__cube_can_invert(void) {
float3 point = {0.0, 0.0, 0.5};
kliter_t(poly) *iter = NULL;
// Make sure that all polygons consider the point in the center
// behind them.
klist_t(poly) *polys = bsp_to_polygons(cube_bsp, 0, NULL);
for(iter = kl_begin(polys); iter < kl_end(polys); iter = kl_next(iter)) {
cl_assert_equal_i(poly_classify_vertex(kl_val(iter), point), BACK);
}
kl_destroy(poly, polys);
// INVERT
cl_assert(bsp_invert(cube_bsp) == cube_bsp);
// Repeat the test and expect the center to now be FRONT
polys = bsp_to_polygons(cube_bsp, 0, NULL);
for(iter = kl_begin(polys); iter < kl_end(polys); iter = kl_next(iter)) {
cl_assert_equal_i(poly_classify_vertex(kl_val(iter), point), FRONT);
}
kl_destroy(poly, polys);
}
// Called when the manager sends a complete message
void messageArrivedFromManager() {
printf ("Message arrived: >%s< for >%s<\r\n", commandMessage, commandClientId);
// See if the client is connected, if so immediately forward
khiter_t k = kh_get(clientStatuses, clientStatuses, (char*)commandClientId); // Find it in the hash
if (k != kh_end(clientStatuses)) { // Was it in the hash?
clientStatus* status = kh_value(clientStatuses, k); // Grab the clientStatus from the hash
snprintf(httpResponse, HTTP_RESPONSE_SIZE, HTTP_TEMPLATE, commandMessageLen, commandMessage); // Compose the response message
write(status->io.fd, httpResponse, strlen(httpResponse)); // Send it
closeConnection((ev_io*)status); // Close the conn
return;
}
// If not, add to a queue
khiter_t q = kh_get(queue, queue, (char*)commandClientId); // See if this client is already in the queue
if (q == kh_end(queue)) {
printf("Creating queue for %s\r\n", commandClientId);
// This client needs to be added to the queue
// First make a new list
klist_t(messages) *newMessageList = kl_init(messages);
*kl_pushp(messages, newMessageList) = strdup((char*)commandMessage); // Add the message to the list
// Now make a new hash entry pointing to this new list
int ret;
q = kh_put(queue, queue, strdup((char*)commandClientId), &ret);
kh_value(queue, q) = newMessageList;
} else {
printf("Adding to the queue for %s\r\n", commandClientId);
// This client is in the queue already eg it has a hash entry
// Pushp puts this message at the end of the queue, so that shift will grab the oldest first (like a FIFO)
*kl_pushp(messages, kh_value(queue, q)) = strdup((char*)commandMessage);
}
// Now do a printout of the hash list
for (khiter_t qi = kh_begin(queue); qi < kh_end(queue); qi++) {
if (kh_exist(queue, qi)) {
printf("Queue for %s\n", kh_key(queue,qi));
klist_t(messages) *list = kh_value(queue, qi);
kliter_t(messages) *li;
for (li = kl_begin(list); li != kl_end(list); li = kl_next(li))
printf("%s\n", kl_val(li));
printf("----\n");
}
}
}
static void trans_tbl_init(bam_hdr_t* out, bam_hdr_t* translate, trans_tbl_t* tbl, bool merge_rg, bool merge_pg)
{
tbl->n_targets = translate->n_targets;
tbl->tid_trans = (int*)calloc(translate->n_targets, sizeof(int));
tbl->rg_trans = kh_init(c2c);
tbl->pg_trans = kh_init(c2c);
if (!tbl->tid_trans || !tbl->rg_trans || !tbl->pg_trans) { perror("out of memory"); exit(-1); }
int32_t out_len = out->l_text;
while (out_len > 0 && out->text[out_len-1] == '\n') {--out_len; } // strip trailing \n's
kstring_t out_text = { 0, 0, NULL };
kputsn(out->text, out_len, &out_text);
int i, min_tid = -1;
tbl->lost_coord_sort = false;
khash_t(c2i) *out_tid = kh_init(c2i);
for (i = 0; i < out->n_targets; ++i) {
int ret;
khiter_t iter = kh_put(c2i, out_tid, out->target_name[i], &ret);
if (ret <= 0) abort();
kh_value(out_tid, iter) = i;
}
for (i = 0; i < translate->n_targets; ++i) {
khiter_t iter = kh_get(c2i, out_tid, translate->target_name[i]);
if (iter == kh_end(out_tid)) { // Append missing entries to out
tbl->tid_trans[i] = out->n_targets++;
out->target_name = (char**)realloc(out->target_name, sizeof(char*)*out->n_targets);
out->target_name[out->n_targets-1] = strdup(translate->target_name[i]);
out->target_len = (uint32_t*)realloc(out->target_len, sizeof(uint32_t)*out->n_targets);
out->target_len[out->n_targets-1] = translate->target_len[i];
// grep line with regex '^@SQ.*\tSN:%s(\t.*$|$)', translate->target_name[i]
// from translate->text
regex_t sq_id;
regmatch_t* matches = (regmatch_t*)calloc(2, sizeof(regmatch_t));
if (matches == NULL) { perror("out of memory"); exit(-1); }
kstring_t seq_regex = { 0, 0, NULL };
ksprintf(&seq_regex, "^@SQ.*\tSN:%s(\t.*$|$)", translate->target_name[i]);
regcomp(&sq_id, seq_regex.s, REG_EXTENDED|REG_NEWLINE);
free(seq_regex.s);
if (regexec(&sq_id, translate->text, 1, matches, 0) != 0)
{
fprintf(pysamerr, "[trans_tbl_init] @SQ SN (%s) found in binary header but not text header.\n",translate->target_name[i]);
exit(1);
}
regfree(&sq_id);
// Produce our output line and append it to out_text
kputc('\n', &out_text);
kputsn(translate->text+matches[0].rm_so, matches[0].rm_eo-matches[0].rm_so, &out_text);
free(matches);
} else {
tbl->tid_trans[i] = kh_value(out_tid, iter);
}
if (tbl->tid_trans[i] > min_tid) {
min_tid = tbl->tid_trans[i];
} else {
tbl->lost_coord_sort = true;
}
}
kh_destroy(c2i, out_tid);
// grep @RG id's
regex_t rg_id;
regmatch_t* matches = (regmatch_t*)calloc(2, sizeof(regmatch_t));
if (matches == NULL) { perror("out of memory"); exit(-1); }
regcomp(&rg_id, "^@RG.*\tID:([!-)+-<>-~][ !-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
char* text = translate->text;
klist_t(hdrln) *rg_list = kl_init(hdrln);
while(1) { // foreach rg id in translate's header
if (regexec(&rg_id, text, 2, matches, 0) != 0) break;
// matches[0] is the whole @RG line; matches[1] is the ID field value
kstring_t match_id = { 0, 0, NULL };
kputsn(text+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &match_id);
// is our matched ID in our output list already
regex_t rg_id_search;
kstring_t rg_regex = { 0, 0, NULL };
ksprintf(&rg_regex, "^@RG.*\tID:%s(\t.*$|$)", match_id.s);
regcomp(&rg_id_search, rg_regex.s, REG_EXTENDED|REG_NEWLINE|REG_NOSUB);
free(rg_regex.s);
kstring_t transformed_id = { 0, 0, NULL };
bool transformed_equals_match;
if (regexec(&rg_id_search, out->text, 0, NULL, 0) != 0 || merge_rg) {
// Not in there so can add it as 1-1 mapping
kputs(match_id.s, &transformed_id);
transformed_equals_match = true;
} else {
// It's in there so we need to transform it by appending random number to id
ksprintf(&transformed_id, "%s-%0lX", match_id.s, lrand48());
transformed_equals_match = false;
}
regfree(&rg_id_search);
// Insert it into our translation map
int in_there = 0;
khiter_t iter = kh_put(c2c, tbl->rg_trans, ks_release(&match_id), &in_there);
char *transformed_id_s = ks_release(&transformed_id);
kh_value(tbl->rg_trans,iter) = transformed_id_s;
// take matched line and replace ID with transformed_id
kstring_t transformed_line = { 0, 0, NULL };
if (transformed_equals_match) {
kputsn(text+matches[0].rm_so, matches[0].rm_eo-matches[0].rm_so, &transformed_line);
} else {
kputsn(text+matches[0].rm_so, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id_s, &transformed_line);
kputsn(text+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
}
if (!(transformed_equals_match && merge_rg)) {
// append line to linked list for PG processing
char** ln = kl_pushp(hdrln, rg_list);
*ln = ks_release(&transformed_line); // Give away to linked list
}
else free(transformed_line.s);
text += matches[0].rm_eo; // next!
}
regfree(&rg_id);
// Do same for PG id's
regex_t pg_id;
regcomp(&pg_id, "^@PG.*\tID:([!-)+-<>-~][ !-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
text = translate->text;
klist_t(hdrln) *pg_list = kl_init(hdrln);
while(1) { // foreach pg id in translate's header
if (regexec(&pg_id, text, 2, matches, 0) != 0) break;
kstring_t match_id = { 0, 0, NULL };
kputsn(text+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &match_id);
// is our matched ID in our output list already
regex_t pg_id_search;
kstring_t pg_regex = { 0, 0, NULL };
ksprintf(&pg_regex, "^@PG.*\tID:%s(\t.*$|$)", match_id.s);
regcomp(&pg_id_search, pg_regex.s, REG_EXTENDED|REG_NEWLINE|REG_NOSUB);
free(pg_regex.s);
kstring_t transformed_id = { 0, 0, NULL };
bool transformed_equals_match;
if (regexec(&pg_id_search, out->text, 0, NULL, 0) != 0 || merge_pg) {
// Not in there so can add it as 1-1 mapping
kputs(match_id.s, &transformed_id);
transformed_equals_match = true;
} else {
// It's in there so we need to transform it by appending random number to id
ksprintf(&transformed_id, "%s-%0lX", match_id.s, lrand48());
transformed_equals_match = false;
}
regfree(&pg_id_search);
// Insert it into our translation map
int in_there = 0;
khiter_t iter = kh_put(c2c, tbl->pg_trans, ks_release(&match_id), &in_there);
char *transformed_id_s = ks_release(&transformed_id);
kh_value(tbl->pg_trans,iter) = transformed_id_s;
// take matched line and replace ID with transformed_id
kstring_t transformed_line = { 0, 0, NULL };
if (transformed_equals_match) {
kputsn(text+matches[0].rm_so, matches[0].rm_eo-matches[0].rm_so, &transformed_line);
} else {
kputsn(text+matches[0].rm_so, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id_s, &transformed_line);
kputsn(text+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
}
if (!(transformed_equals_match && merge_pg)) {
// append line to linked list for PP processing
char** ln = kl_pushp(hdrln, pg_list);
*ln = ks_release(&transformed_line); // Give away to linked list
}
else free(transformed_line.s);
text += matches[0].rm_eo; // next!
}
regfree(&pg_id);
// need to translate PP's on the fly in second pass because they may not be in correct order and need complete tbl->pg_trans to do this
// for each line {
// with ID replaced with tranformed_id and PP's transformed using the translation table
// }
regex_t pg_pp;
regcomp(&pg_pp, "^@PG.*\tPP:([!-)+-<>-~][!-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
kliter_t(hdrln) *iter = kl_begin(pg_list);
while (iter != kl_end(pg_list)) {
char* data = kl_val(iter);
kstring_t transformed_line = { 0, 0, NULL };
// Find PP tag
if (regexec(&pg_pp, data, 2, matches, 0) == 0) {
// Lookup in hash table
kstring_t pp_id = { 0, 0, NULL };
kputsn(data+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &pp_id);
khiter_t k = kh_get(c2c, tbl->pg_trans, pp_id.s);
free(pp_id.s);
char* transformed_id = kh_value(tbl->pg_trans,k);
// Replace
kputsn(data, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id, &transformed_line);
kputsn(data+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
} else { kputs(data, &transformed_line); }
// Produce our output line and append it to out_text
kputc('\n', &out_text);
kputsn(transformed_line.s, transformed_line.l, &out_text);
free(transformed_line.s);
free(data);
iter = kl_next(iter);
}
regfree(&pg_pp);
// Need to also translate @RG PG's on the fly too
regex_t rg_pg;
regcomp(&rg_pg, "^@RG.*\tPG:([!-)+-<>-~][!-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
kliter_t(hdrln) *rg_iter = kl_begin(rg_list);
while (rg_iter != kl_end(rg_list)) {
char* data = kl_val(rg_iter);
kstring_t transformed_line = { 0, 0, NULL };
// Find PG tag
if (regexec(&rg_pg, data, 2, matches, 0) == 0) {
// Lookup in hash table
kstring_t pg_id = { 0, 0, NULL };
kputsn(data+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &pg_id);
khiter_t k = kh_get(c2c, tbl->pg_trans, pg_id.s);
free(pg_id.s);
char* transformed_id = kh_value(tbl->pg_trans,k);
// Replace
kputsn(data, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id, &transformed_line);
kputsn(data+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
} else { kputs(data, &transformed_line); }
// Produce our output line and append it to out_text
kputc('\n', &out_text);
kputsn(transformed_line.s, transformed_line.l, &out_text);
free(transformed_line.s);
free(data);
rg_iter = kl_next(rg_iter);
}
regfree(&rg_pg);
kl_destroy(hdrln,pg_list);
kl_destroy(hdrln,rg_list);
free(matches);
// Add trailing \n and write back to header
free(out->text);
kputc('\n', &out_text);
out->l_text = out_text.l;
out->text = ks_release(&out_text);
}
