region_table_t *parse_regions(char *input_regions, int as_positions, const char *url, const char *species, const char *version) {
region_table_t *regions_table = new_region_table_from_ws(url, species, version);
char *saveptr, *token;
size_t token_len;
int num_regions;
char **regions_data = split(input_regions, ",", &num_regions);
region_t *regions[num_regions];
for (int i = 0; i < num_regions; i++) {
// Set chromosome
token = strtok_r(regions_data[i], ":", &saveptr);
token_len = strlen(token);
char *chromosome = strndup(token, token_len);
// Set start position
token = strtok_r(NULL, "-", &saveptr);
size_t start_position, end_position;
start_position = (token != NULL) ? atol(token) : 1;
// Set end position
token = strtok_r(NULL, "-", &saveptr);
if (token != NULL) {
end_position = atol(token);
} else {
if (as_positions) {
end_position = start_position;
} else {
end_position = UINT_MAX;
}
}
regions[i] = region_new(chromosome, start_position, end_position, NULL, NULL);
LOG_DEBUG_F("region '%s:%u-%u'\n", regions[i]->chromosome, regions[i]->start_position, regions[i]->end_position);
}
insert_regions(regions, num_regions, regions_table);
finish_region_table_loading(regions_table);
for (int i = 0; i < num_regions; i++) {
free(regions_data[i]);
free(regions[i]);
}
free(regions_data);
return regions_table;
}
int insert_region(region_t *region, region_table_t *table) {
return insert_regions(®ion, 1, table);
}
region_table_t *parse_regions_from_gff_file(char *filename, const char *url, const char *species, const char *version) {
gff_file_t *file = gff_open(filename);
if (file == NULL) {
return NULL;
}
region_table_t *regions_table = new_region_table_from_ws(url, species, version);
int ret_code = 0;
size_t max_batches = 20, batch_size = 2000;
list_t *read_list = (list_t*) malloc (sizeof(list_t));
list_init("batches", 1, max_batches, read_list);
#pragma omp parallel sections
{
// The producer reads the GFF file
#pragma omp section
{
LOG_DEBUG_F("Thread %d reads the GFF file\n", omp_get_thread_num());
ret_code = gff_read_batches(read_list, batch_size, file);
list_decr_writers(read_list);
if (ret_code) {
LOG_FATAL_F("Error while reading GFF file %s (%d)\n", filename, ret_code);
}
}
// The consumer inserts regions in the structure
#pragma omp section
{
list_item_t *item = NULL;
gff_batch_t *batch;
gff_record_t *record;
region_t *regions_batch[REGIONS_CHUNKSIZE];
int avail_regions = 0;
while ( item = list_remove_item(read_list) ) {
batch = item->data_p;
// For each record in the batch, generate a new region
for (int i = 0; i < batch->records->size; i++) {
record = batch->records->items[i];
region_t *region = region_new(strndup(record->sequence, record->sequence_len),
record->start, record->end,
record->strand ? strndup(&record->strand, 1) : NULL,
record->feature ? strndup(record->feature, record->feature_len) : NULL);
LOG_DEBUG_F("region '%s:%u-%u'\n", region->chromosome, region->start_position, region->end_position);
regions_batch[avail_regions++] = region;
// Save when the recommended size is reached
if (avail_regions == REGIONS_CHUNKSIZE) {
insert_regions(regions_batch, avail_regions, regions_table);
for (int i = 0; i < avail_regions; i++) {
free(regions_batch[i]);
}
avail_regions = 0;
}
}
gff_batch_free(batch);
list_item_free(item);
}
// Save the remaining regions that did not fill a batch
if (avail_regions > 0) {
insert_regions(regions_batch, avail_regions, regions_table);
for (int i = 0; i < avail_regions; i++) {
free(regions_batch[i]);
}
avail_regions = 0;
}
}
}
finish_region_table_loading(regions_table);
list_free_deep(read_list, NULL);
gff_close(file, 1);
return regions_table;
}
void physical_allocator_init(struct multiboot_info *multiboot_tables) {
insert_regions(multiboot_tables);
}
