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 = create_table(url, species, version);
int ret_code = 0;
size_t max_batches = 20;
size_t 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, *batch_item = NULL;
gff_batch_t *batch;
gff_record_t *record;
while ( (item = list_remove_item(read_list)) != NULL ) {
batch = item->data_p;
// For each record in the batch, generate a new region
for (batch_item = batch->first_p; batch_item != NULL; batch_item = batch_item->next_p) {
record = batch_item->data_p;
region_t *region = (region_t*) malloc (sizeof(region_t));
region->chromosome = (char*) calloc ((strlen(record->sequence)+1), sizeof(char));
strncat(region->chromosome, record->sequence, strlen(record->sequence));
region->start_position = record->start;
region->end_position = record->end;
LOG_DEBUG_F("region '%s:%u-%u'\n", region->chromosome, region->start_position, region->end_position);
insert_region(region, regions_table);
}
gff_batch_free(item->data_p);
list_item_free(item);
}
}
}
gff_close(file, 0);
return regions_table;
}
vcf_batch_t *fetch_vcf_batch_non_blocking(vcf_file_t *file) {
assert(file);
list_item_t *item = list_remove_item_async(file->record_batches);
if (item) {
vcf_batch_t *batch = item->data_p;
list_item_free(item);
return batch;
}
return NULL;
}
void write_output_body(enum ASSOC_task task, list_t* output_list, FILE *fd) {
assert(fd);
list_item_t* item = NULL;
if (task == CHI_SQUARE) {
while (item = list_remove_item(output_list)) {
assoc_basic_result_t *result = item->data_p;
double freq_a1 = (result->affected1 + result->affected2 > 0) ? (double) result->affected1 / (result->affected1 + result->affected2) : 0.0f;
double freq_u1 = (result->unaffected1 + result->unaffected2 > 0) ? (double) result->unaffected1 / (result->unaffected1 + result->unaffected2) : 0.0f;
double freq_a2 = (result->affected1 + result->affected2 > 0) ? (double) result->affected2 / (result->affected1 + result->affected2) : 0.0f;
double freq_u2 = (result->unaffected1 + result->unaffected2 > 0) ? (double) result->unaffected2 / (result->unaffected1 + result->unaffected2) : 0.0f;
fprintf(fd, "%s\t%8ld\t%s\t%s\t%3d\t%3d\t%6f\t%6f\t%s\t%3d\t%3d\t%6f\t%6f\t%6f\t%6f\t%6f\n",
result->chromosome, result->position, result->id,
result->reference, result->affected1, result->unaffected1, freq_a1, freq_u1,
result->alternate, result->affected2, result->unaffected2, freq_a2, freq_u2,
result->odds_ratio, result->chi_square, result->p_value);
assoc_basic_result_free(result);
list_item_free(item);
}
} else if (task == FISHER) {
while (item = list_remove_item(output_list)) {
assoc_fisher_result_t *result = item->data_p;
double freq_a1 = (result->affected1 + result->affected2 > 0) ? (double) result->affected1 / (result->affected1 + result->affected2) : 0.0f;
double freq_u1 = (result->unaffected1 + result->unaffected2 > 0) ? (double) result->unaffected1 / (result->unaffected1 + result->unaffected2) : 0.0f;
double freq_a2 = (result->affected1 + result->affected2 > 0) ? (double) result->affected2 / (result->affected1 + result->affected2) : 0.0f;
double freq_u2 = (result->unaffected1 + result->unaffected2 > 0) ? (double) result->unaffected2 / (result->unaffected1 + result->unaffected2) : 0.0f;
fprintf(fd, "%s\t%8ld\t%s\t%s\t%3d\t%3d\t%6f\t%6f\t%s\t%3d\t%3d\t%6f\t%6f\t%6f\t%6f\n",
result->chromosome, result->position, result->id,
result->reference, result->affected1, result->unaffected1, freq_a1, freq_u1,
result->alternate, result->affected2, result->unaffected2, freq_a2, freq_u2,
result->odds_ratio, result->p_value);
assoc_fisher_result_free(result);
list_item_free(item);
}
}
}
void precalculate_aux_values_for_annotation(int calculate_stats, int calculate_dp, int calculate_mq, vcf_record_t *record,
variant_stats_t **variant_stats, file_stats_t *file_stats, list_t *stats_list,
int *dp, int *mq0, double *mq) {
// Variant statistics
if (calculate_stats) {
get_variants_stats(&record, 1, NULL, NULL,0, stats_list, file_stats);
list_item_t *item = list_remove_item(stats_list);
*variant_stats = item->data_p;
list_item_free(item);
}
// Read depth
if (calculate_dp) {
int dp_pos = -1;
*dp = 0;
for (int j = 0; j < record->samples->size; j++) {
char *aux = strndup(record->format, record->format_len);
dp_pos = get_field_position_in_format("DP", aux);
free(aux);
if (dp_pos >= 0) {
aux = strdup((char*) array_list_get(j, record->samples));
*dp += atoi(get_field_value_in_sample(aux, dp_pos));
free(aux);
}
}
}
// Mapping quality
if (calculate_mq) {
for (int j = 0; j < record->samples->size; j++) {
char *aux = strndup(record->format, record->format_len);
int mq_pos = get_field_position_in_format("GQ", aux);
free(aux);
if (mq_pos < 0) {
continue;
}
aux = strdup((char*) array_list_get(j, record->samples));
int cur_gq = atoi(get_field_value_in_sample(aux, mq_pos));
free(aux);
// printf("sample = %s\tmq_pos = %d\tvalue = %d\n", array_list_get(j, record->samples), mq_pos,
// atoi(get_field_value_in_sample(strdup((char*) array_list_get(j, record->samples)), mq_pos)));
if (cur_gq == 0) {
(*mq0)++;
} else {
*mq += cur_gq * cur_gq;
}
}
*mq = sqrt(*mq / record->samples->size);
}
}
XdgListItem *_xdg_list_remove(XdgListItem *item, XdgListItemFree list_item_free)
{
XdgListItem *res;
if (item->prev)
if (item->prev->next = res = item->next)
res->prev = item->prev;
else
item->list->tail = item->prev;
else
if (item->list->head = res = item->next)
res->prev = NULL;
else
item->list->tail = NULL;
list_item_free(item);
return res;
}
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;
}
int run_effect(char **urls, shared_options_data_t *shared_options_data, effect_options_data_t *options_data) {
int ret_code = 0;
double start, stop, total;
vcf_file_t *vcf_file = vcf_open(shared_options_data->vcf_filename, shared_options_data->max_batches);
if (!vcf_file) {
LOG_FATAL("VCF file does not exist!\n");
}
ped_file_t *ped_file = NULL;
if (shared_options_data->ped_filename) {
ped_file = ped_open(shared_options_data->ped_filename);
if (!ped_file) {
LOG_FATAL("PED file does not exist!\n");
}
LOG_INFO("About to read PED file...\n");
// Read PED file before doing any processing
ret_code = ped_read(ped_file);
if (ret_code != 0) {
LOG_FATAL_F("Can't read PED file: %s\n", ped_file->filename);
}
}
char *output_directory = shared_options_data->output_directory;
size_t output_directory_len = strlen(output_directory);
ret_code = create_directory(output_directory);
if (ret_code != 0 && errno != EEXIST) {
LOG_FATAL_F("Can't create output directory: %s\n", output_directory);
}
// Remove all .txt files in folder
ret_code = delete_files_by_extension(output_directory, "txt");
if (ret_code != 0) {
return ret_code;
}
// Initialize environment for connecting to the web service
ret_code = init_http_environment(0);
if (ret_code != 0) {
return ret_code;
}
// Output file descriptors
static cp_hashtable *output_files = NULL;
// Lines of the output data in the main .txt files
static list_t *output_list = NULL;
// Consequence type counters (for summary, must be kept between web service calls)
static cp_hashtable *summary_count = NULL;
// Gene list (for genes-with-variants, must be kept between web service calls)
static cp_hashtable *gene_list = NULL;
// Initialize collections of file descriptors and summary counters
ret_code = initialize_output_files(output_directory, output_directory_len, &output_files);
if (ret_code != 0) {
return ret_code;
}
initialize_output_data_structures(shared_options_data, &output_list, &summary_count, &gene_list);
initialize_ws_buffers(shared_options_data->num_threads);
// Create job.status file
char job_status_filename[output_directory_len + 10];
sprintf(job_status_filename, "%s/job.status", output_directory);
FILE *job_status = new_job_status_file(job_status_filename);
if (!job_status) {
LOG_FATAL("Can't create job status file\n");
} else {
update_job_status_file(0, job_status);
}
#pragma omp parallel sections private(start, stop, total)
{
#pragma omp section
{
LOG_DEBUG_F("Thread %d reads the VCF file\n", omp_get_thread_num());
start = omp_get_wtime();
ret_code = vcf_read(vcf_file, 1,
(shared_options_data->batch_bytes > 0) ? shared_options_data->batch_bytes : shared_options_data->batch_lines,
shared_options_data->batch_bytes <= 0);
stop = omp_get_wtime();
total = stop - start;
if (ret_code) {
LOG_ERROR_F("Error %d while reading the file %s\n", ret_code, vcf_file->filename);
}
LOG_INFO_F("[%dR] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%dR] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
notify_end_parsing(vcf_file);
}
#pragma omp section
{
// Enable nested parallelism and set the number of threads the user has chosen
omp_set_nested(1);
LOG_DEBUG_F("Thread %d processes data\n", omp_get_thread_num());
// Filters and files for filtering output
filter_t **filters = NULL;
int num_filters = 0;
if (shared_options_data->chain != NULL) {
filters = sort_filter_chain(shared_options_data->chain, &num_filters);
}
FILE *passed_file = NULL, *failed_file = NULL, *non_processed_file = NULL;
get_filtering_output_files(shared_options_data, &passed_file, &failed_file);
// Pedigree information (used in some filters)
individual_t **individuals = NULL;
khash_t(ids) *sample_ids = NULL;
// Filename structure outdir/vcfname.errors
char *prefix_filename = calloc(strlen(shared_options_data->vcf_filename), sizeof(char));
get_filename_from_path(shared_options_data->vcf_filename, prefix_filename);
char *non_processed_filename = malloc((strlen(shared_options_data->output_directory) + strlen(prefix_filename) + 9) * sizeof(char));
sprintf(non_processed_filename, "%s/%s.errors", shared_options_data->output_directory, prefix_filename);
non_processed_file = fopen(non_processed_filename, "w");
free(non_processed_filename);
// Maximum size processed by each thread (never allow more than 1000 variants per query)
if (shared_options_data->batch_lines > 0) {
shared_options_data->entries_per_thread = MIN(MAX_VARIANTS_PER_QUERY,
ceil((float) shared_options_data->batch_lines / shared_options_data->num_threads));
} else {
shared_options_data->entries_per_thread = MAX_VARIANTS_PER_QUERY;
}
LOG_DEBUG_F("entries-per-thread = %d\n", shared_options_data->entries_per_thread);
int i = 0;
vcf_batch_t *batch = NULL;
int ret_ws_0 = 0, ret_ws_1 = 0, ret_ws_2 = 0;
start = omp_get_wtime();
while (batch = fetch_vcf_batch(vcf_file)) {
if (i == 0) {
// Add headers associated to the defined filters
vcf_header_entry_t **filter_headers = get_filters_as_vcf_headers(filters, num_filters);
for (int j = 0; j < num_filters; j++) {
add_vcf_header_entry(filter_headers[j], vcf_file);
}
// Write file format, header entries and delimiter
if (passed_file != NULL) { write_vcf_header(vcf_file, passed_file); }
if (failed_file != NULL) { write_vcf_header(vcf_file, failed_file); }
if (non_processed_file != NULL) { write_vcf_header(vcf_file, non_processed_file); }
LOG_DEBUG("VCF header written\n");
if (ped_file) {
// Create map to associate the position of individuals in the list of samples defined in the VCF file
sample_ids = associate_samples_and_positions(vcf_file);
// Sort individuals in PED as defined in the VCF file
individuals = sort_individuals(vcf_file, ped_file);
}
}
// printf("batch loaded = '%.*s'\n", 50, batch->text);
// printf("batch text len = %zu\n", strlen(batch->text));
// if (i % 10 == 0) {
LOG_INFO_F("Batch %d reached by thread %d - %zu/%zu records \n",
i, omp_get_thread_num(),
batch->records->size, batch->records->capacity);
// }
int reconnections = 0;
int max_reconnections = 3; // TODO allow to configure?
// Write records that passed to a separate file, and query the WS with them as args
array_list_t *failed_records = NULL;
int num_variables = ped_file? get_num_variables(ped_file): 0;
array_list_t *passed_records = filter_records(filters, num_filters, individuals, sample_ids, num_variables, batch->records, &failed_records);
if (passed_records->size > 0) {
// Divide the list of passed records in ranges of size defined in config file
int num_chunks;
int *chunk_sizes;
int *chunk_starts = create_chunks(passed_records->size, shared_options_data->entries_per_thread, &num_chunks, &chunk_sizes);
do {
// OpenMP: Launch a thread for each range
#pragma omp parallel for num_threads(shared_options_data->num_threads)
for (int j = 0; j < num_chunks; j++) {
int tid = omp_get_thread_num();
LOG_DEBUG_F("[%d] WS invocation\n", tid);
LOG_DEBUG_F("[%d] -- effect WS\n", tid);
if (!reconnections || ret_ws_0) {
ret_ws_0 = invoke_effect_ws(urls[0], (vcf_record_t**) (passed_records->items + chunk_starts[j]),
chunk_sizes[j], options_data->excludes);
parse_effect_response(tid, output_directory, output_directory_len, output_files, output_list, summary_count, gene_list);
free(effect_line[tid]);
effect_line[tid] = (char*) calloc (max_line_size[tid], sizeof(char));
}
if (!options_data->no_phenotypes) {
if (!reconnections || ret_ws_1) {
LOG_DEBUG_F("[%d] -- snp WS\n", omp_get_thread_num());
ret_ws_1 = invoke_snp_phenotype_ws(urls[1], (vcf_record_t**) (passed_records->items + chunk_starts[j]), chunk_sizes[j]);
parse_snp_phenotype_response(tid, output_list);
free(snp_line[tid]);
snp_line[tid] = (char*) calloc (snp_max_line_size[tid], sizeof(char));
}
if (!reconnections || ret_ws_2) {
LOG_DEBUG_F("[%d] -- mutation WS\n", omp_get_thread_num());
ret_ws_2 = invoke_mutation_phenotype_ws(urls[2], (vcf_record_t**) (passed_records->items + chunk_starts[j]), chunk_sizes[j]);
parse_mutation_phenotype_response(tid, output_list);
free(mutation_line[tid]);
mutation_line[tid] = (char*) calloc (mutation_max_line_size[tid], sizeof(char));
}
}
}
LOG_DEBUG_F("*** %dth web services invocation finished\n", i);
if (ret_ws_0 || ret_ws_1 || ret_ws_2) {
if (ret_ws_0) {
LOG_ERROR_F("Effect web service error: %s\n", get_last_http_error(ret_ws_0));
}
if (ret_ws_1) {
LOG_ERROR_F("SNP phenotype web service error: %s\n", get_last_http_error(ret_ws_1));
}
if (ret_ws_2) {
LOG_ERROR_F("Mutations phenotype web service error: %s\n", get_last_http_error(ret_ws_2));
}
// In presence of errors, wait 4 seconds before retrying
reconnections++;
LOG_ERROR_F("Some errors ocurred, reconnection #%d\n", reconnections);
sleep(4);
} else {
free(chunk_starts);
free(chunk_sizes);
}
} while (reconnections < max_reconnections && (ret_ws_0 || ret_ws_1 || ret_ws_2));
}
// If the maximum number of reconnections was reached still with errors,
// write the non-processed batch to the corresponding file
if (reconnections == max_reconnections && (ret_ws_0 || ret_ws_1 || ret_ws_2)) {
#pragma omp critical
{
write_vcf_batch(batch, non_processed_file);
}
}
// Write records that passed and failed filters to separate files, and free them
write_filtering_output_files(passed_records, failed_records, passed_file, failed_file);
free_filtered_records(passed_records, failed_records, batch->records);
// Free batch and its contents
vcf_batch_free(batch);
i++;
}
stop = omp_get_wtime();
total = stop - start;
LOG_INFO_F("[%d] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%d] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
// Free resources
if (passed_file) { fclose(passed_file); }
if (failed_file) { fclose(failed_file); }
if (non_processed_file) { fclose(non_processed_file); }
// Free filters
for (i = 0; i < num_filters; i++) {
filter_t *filter = filters[i];
filter->free_func(filter);
}
free(filters);
// Decrease list writers count
for (i = 0; i < shared_options_data->num_threads; i++) {
list_decr_writers(output_list);
}
}
#pragma omp section
{
// Thread which writes the results to all_variants, summary and one file per consequence type
int ret = 0;
char *line;
list_item_t* item = NULL;
FILE *fd = NULL;
FILE *all_variants_file = cp_hashtable_get(output_files, "all_variants");
FILE *snp_phenotype_file = cp_hashtable_get(output_files, "snp_phenotypes");
FILE *mutation_phenotype_file = cp_hashtable_get(output_files, "mutation_phenotypes");
while ((item = list_remove_item(output_list)) != NULL) {
line = item->data_p;
// Type greater than 0: consequence type identified by its SO code
// Type equals to -1: SNP phenotype
// Type equals to -2: mutation phenotype
if (item->type > 0) {
// Write entry in the consequence type file
fd = cp_hashtable_get(output_files, &(item->type));
int ret = fprintf(fd, "%s\n", line);
if (ret < 0) {
LOG_ERROR_F("Error writing to file: '%s'\n", line);
}
// Write in all_variants
ret = fprintf(all_variants_file, "%s\n", line);
if (ret < 0) {
LOG_ERROR_F("Error writing to all_variants: '%s'\n", line);
}
} else if (item->type == SNP_PHENOTYPE) {
ret = fprintf(snp_phenotype_file, "%s\n", line);
if (ret < 0) {
LOG_ERROR_F("Error writing to snp_phenotypes: '%s'\n", line);
}
} else if (item->type == MUTATION_PHENOTYPE) {
ret = fprintf(mutation_phenotype_file, "%s\n", line);
if (ret < 0) {
LOG_ERROR_F("Error writing to mutation_phenotypes: '%s'\n", line);
}
}
free(line);
list_item_free(item);
}
}
}
write_summary_file(summary_count, cp_hashtable_get(output_files, "summary"));
write_genes_with_variants_file(gene_list, output_directory);
write_result_file(shared_options_data, options_data, summary_count, output_directory);
free_output_data_structures(output_files, summary_count, gene_list);
free_ws_buffers(shared_options_data->num_threads);
free(output_list);
vcf_close(vcf_file);
update_job_status_file(100, job_status);
close_job_status_file(job_status);
return ret_code;
}
static struct mode_list_elem *read_mode_file(const gchar *filename)
{
GKeyFile *settingsfile;
gboolean test = FALSE;
struct mode_list_elem *list_item = NULL;
settingsfile = g_key_file_new();
test = g_key_file_load_from_file(settingsfile, filename, G_KEY_FILE_NONE, NULL);
if(!test)
{
return(NULL);
}
list_item = malloc(sizeof(struct mode_list_elem));
list_item->mode_name = g_key_file_get_string(settingsfile, MODE_ENTRY, MODE_NAME_KEY, NULL);
log_debug("Dynamic mode name = %s\n", list_item->mode_name);
list_item->mode_module = g_key_file_get_string(settingsfile, MODE_ENTRY, MODE_MODULE_KEY, NULL);
log_debug("Dynamic mode module = %s\n", list_item->mode_module);
list_item->appsync = g_key_file_get_integer(settingsfile, MODE_ENTRY, MODE_NEEDS_APPSYNC_KEY, NULL);
list_item->mass_storage = g_key_file_get_integer(settingsfile, MODE_ENTRY, MODE_MASS_STORAGE, NULL);
list_item->network = g_key_file_get_integer(settingsfile, MODE_ENTRY, MODE_NETWORK_KEY, NULL);
list_item->network_interface = g_key_file_get_string(settingsfile, MODE_ENTRY, MODE_NETWORK_INTERFACE_KEY, NULL);
list_item->sysfs_path = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_SYSFS_PATH, NULL);
//log_debug("Dynamic mode sysfs path = %s\n", list_item->sysfs_path);
list_item->sysfs_value = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_SYSFS_VALUE, NULL);
//log_debug("Dynamic mode sysfs value = %s\n", list_item->sysfs_value);
list_item->sysfs_reset_value = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_SYSFS_RESET_VALUE, NULL);
list_item->softconnect = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_SOFTCONNECT, NULL);
list_item->softconnect_disconnect = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_SOFTCONNECT_DISCONNECT, NULL);
list_item->softconnect_path = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_SOFTCONNECT_PATH, NULL);
list_item->android_extra_sysfs_path = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_PATH, NULL);
list_item->android_extra_sysfs_path2 = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_PATH2, NULL);
list_item->android_extra_sysfs_path3 = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_PATH3, NULL);
list_item->android_extra_sysfs_path4 = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_PATH4, NULL);
//log_debug("Android extra mode sysfs path2 = %s\n", list_item->android_extra_sysfs_path2);
list_item->android_extra_sysfs_value = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_VALUE, NULL);
list_item->android_extra_sysfs_value2 = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_VALUE2, NULL);
list_item->android_extra_sysfs_value3 = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_VALUE3, NULL);
list_item->android_extra_sysfs_value4 = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_ANDROID_EXTRA_SYSFS_VALUE4, NULL);
//log_debug("Android extra value2 = %s\n", list_item->android_extra_sysfs_value2);
list_item->idProduct = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_IDPRODUCT, NULL);
list_item->idVendorOverride = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_IDVENDOROVERRIDE, NULL);
list_item->nat = g_key_file_get_integer(settingsfile, MODE_OPTIONS_ENTRY, MODE_HAS_NAT, NULL);
list_item->dhcp_server = g_key_file_get_integer(settingsfile, MODE_OPTIONS_ENTRY, MODE_HAS_DHCP_SERVER, NULL);
#ifdef CONNMAN
list_item->connman_tethering = g_key_file_get_string(settingsfile, MODE_OPTIONS_ENTRY, MODE_CONNMAN_TETHERING, NULL);
#endif
g_key_file_free(settingsfile);
if(list_item->mode_name == NULL || list_item->mode_module == NULL)
{
/* free list_item as it will not be used */
list_item_free(list_item);
return NULL;
}
if(list_item->network && list_item->network_interface == NULL)
{
/* free list_item as it will not be used */
list_item_free(list_item);
return NULL;
}
if(list_item->sysfs_path && list_item->sysfs_value == NULL)
{
/* free list_item as it will not be used */
list_item_free(list_item);
return NULL;
}
if(list_item->softconnect && list_item->softconnect_path == NULL)
{
/* free list_item as it will not be used */
list_item_free(list_item);
return NULL;
}
else
return(list_item);
}
void batch_aligner(batch_aligner_input_t *input) {
// printf("START: batch_aligner\n", omp_get_thread_num());
size_t total_batches = 0;
list_t *read_list = input->read_list;
list_t *write_list = input->write_list;
write_batch_t* write_batch = NULL;
aligner_batch_t *aligner_batch = NULL;
list_item_t *read_item = NULL, *write_item = NULL;
unsigned int tid = omp_get_thread_num();
struct timeval t1, t2;
array_list_t *list1, *list2;
// main loop
while ( (read_item = list_remove_item(read_list)) != NULL ) {
aligner_batch = aligner_batch_new((fastq_batch_t *) read_item->data_p);
thr_batches[tid]++;
//printf("********************** BATCH %d (batch aligner %d)\n", total_batches, omp_get_thread_num());
// Burros-Wheeler transform
gettimeofday(&t1, NULL);
apply_bwt(input->bwt_input, aligner_batch);
gettimeofday(&t2, NULL);
bwt_time[tid] += ((t2.tv_sec - t1.tv_sec) * 1e6 + (t2.tv_usec - t1.tv_usec));
//printf("---> %d, bwt, num targets = %d\n", tid, aligner_batch->num_targets);
if (aligner_batch->num_targets > 0) {
// seeding
gettimeofday(&t1, NULL);
apply_seeding(input->region_input, aligner_batch);
gettimeofday(&t2, NULL);
seeding_time[tid] += ((t2.tv_sec - t1.tv_sec) * 1e6 + (t2.tv_usec - t1.tv_usec));
thr_seeding_items[tid] += aligner_batch->num_targets;
//printf("---> %d, seeding, num targets = %d\n", tid, aligner_batch->num_targets);
// seeking CALs
gettimeofday(&t1, NULL);
apply_caling(input->cal_input, aligner_batch);
gettimeofday(&t2, NULL);
cal_time[tid] += ((t2.tv_sec - t1.tv_sec) * 1e6 + (t2.tv_usec - t1.tv_usec));
thr_cal_items[tid] += aligner_batch->num_targets;
//printf("---> %d, cal, num targets = %d\n", tid, aligner_batch->num_targets);
}
// pair-mode managing
if (input->pair_input != NULL) {
apply_pair(input->pair_input, aligner_batch);
// printf("---> %d, pair, num targets = %d\n", tid, aligner_batch->num_targets);
}
if (aligner_batch->num_targets > 0) {
// Smith-Waterman
gettimeofday(&t1, NULL);
apply_sw(input->sw_input, aligner_batch);
gettimeofday(&t2, NULL);
sw_time[tid] += ((t2.tv_sec - t1.tv_sec) * 1e6 + (t2.tv_usec - t1.tv_usec));
//thr_sw_items[tid] += aligner_batch->num_targets;
//printf("---> %d, sw, num targets = %d\n", tid, aligner_batch->num_targets);
}
if (aligner_batch->num_targets > 0) {
// prepare alignments (converts sw-output to alignment, searches pairs...)
prepare_alignments(input->pair_input, aligner_batch);
}
write_item = list_item_new(total_batches, 0, aligner_batch);
list_insert_item(write_item, write_list);
list_item_free(read_item);
total_batches++;
} // main loop
/*
printf("Thread %d: BWT time = %0.4f s\n", tid, bwt_time / 1e6);
printf("Thread %d: Seeding time = %0.4f s\n", tid, seeding_time / 1e6);
printf("Thread %d: CAL time = %0.4f s\n", tid, cal_time / 1e6);
printf("Thread %d: SW time = %0.4f s\n", tid, sw_time / 1e6);
*/
// decreasing writers
if (write_list != NULL) list_decr_writers(write_list);
// printf("END: batch_aligner (%d), (total batches %d): END\n", omp_get_thread_num(), total_batches);
}
void region_seeker_server(region_seeker_input_t *input_p){
printf("region_seeker_server(%d): START\n", omp_get_thread_num());
list_item_t *item_p = NULL;
list_item_t *cal_item_p = NULL;
fastq_batch_t *unmapped_batch_p;
size_t num_reads;
array_list_t **allocate_mapping_p;
cal_batch_t *cal_batch_p;
size_t num_mappings, total_mappings = 0, num_batches = 0;
size_t num_threads = input_p->region_threads;
size_t chunk;
size_t total_reads = 0;
omp_set_num_threads(num_threads);
while ( (item_p = list_remove_item(input_p->unmapped_read_list_p)) != NULL ) {
//printf("Region Seeker Processing batch...\n");
num_batches++;
if (time_on) { timing_start(REGION_SEEKER, 0, timing_p); }
unmapped_batch_p = (fastq_batch_t *)item_p->data_p;
num_reads = unmapped_batch_p->num_reads;
total_reads += num_reads;
allocate_mapping_p = (array_list_t **)malloc(sizeof(array_list_t *)*num_reads);
if (input_p->gpu_enable) {
//******************************* GPU PROCESS *********************************//
for (size_t i = 0; i < num_reads; i++) {
allocate_mapping_p[i] = array_list_new(1000,
1.25f,
COLLECTION_MODE_ASYNCHRONIZED);
}
#ifdef HPG_GPU
num_mappings = bwt_map_exact_seed_batch_gpu(unmapped_batch_p,
input_p->bwt_optarg_p,
input_p->cal_optarg_p,
input_p->bwt_index_p,
input_p->gpu_context,
allocate_mapping_p);
#endif
//****************************************************************************//
} else {
//******************************* CPU PROCESS *********************************//
//printf("Region Seeker :: Process Batch with %d reads\n", num_reads);
chunk = MAX(1, num_reads/(num_threads*10));
//printf("Region Seeker :: Process Batch with %d reads\n", num_reads);
#pragma omp parallel for private(num_mappings) reduction(+:total_mappings) schedule(dynamic, chunk)
//#pragma omp parallel for private(num_mappings) reduction(+:total_mappings) schedule(static)
for (size_t i = 0; i < num_reads; i++) {
//printf("Threads region zone: %d\n", omp_get_num_threads());
allocate_mapping_p[i] = array_list_new(1000,
1.25f,
COLLECTION_MODE_ASYNCHRONIZED);
num_mappings = bwt_map_exact_seeds_seq(&(unmapped_batch_p->seq[unmapped_batch_p->data_indices[i]]),
input_p->cal_optarg_p->seed_size,
input_p->cal_optarg_p->min_seed_size,
input_p->bwt_optarg_p, input_p->bwt_index_p, allocate_mapping_p[i]);
total_mappings += num_mappings;
//printf("----------------->>>>>>>>>>>Regions found %d\n", num_mappings);
}
//****************************************************************************//
}
cal_batch_p = cal_batch_new(allocate_mapping_p, unmapped_batch_p);
list_item_free(item_p);
cal_item_p = list_item_new(0, 0, cal_batch_p);
//region_batch_free(region_batch_p);
if (time_on) { timing_stop(REGION_SEEKER, 0, timing_p); }
list_insert_item(cal_item_p, input_p->region_list_p);
//printf("Region Seeker Processing batch finish!\n");
} //End of while
list_decr_writers(input_p->region_list_p);
if (statistics_on) {
statistics_set(REGION_SEEKER_ST, 0, num_batches, statistics_p);
statistics_set(REGION_SEEKER_ST, 1, total_reads, statistics_p);
}
printf("region_seeker_server: END\n");
}
int main (int argc, char *argv[])
{
size_t max_batches = 20;
size_t batch_size = 2000;
list_t *read_list = (list_t*) malloc (sizeof(list_t));
list_init("batches", 1, max_batches, read_list);
int ret_code;
double start, stop, total;
char *filename = (char*) malloc ((strlen(argv[1])+1) * sizeof(char));
strncat(filename, argv[1], strlen(argv[1]));
gff_file_t* file;
init_log_custom(LOG_LEVEL_DEBUG, 1, NULL, "w");
#pragma omp parallel sections private(start, stop, total) lastprivate(file)
{
#pragma omp section
{
LOG_DEBUG_F("Thread %d reads the GFF file\n", omp_get_thread_num());
// Reading
start = omp_get_wtime();
file = gff_open(filename);
ret_code = gff_read_batches(read_list, batch_size, file);
stop = omp_get_wtime();
total = (stop - start);
if (ret_code) {
LOG_FATAL_F("[%dR] Error code = %d\n", omp_get_thread_num(), ret_code);
}
LOG_INFO_F("[%dR] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%dR] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
// Writing to a new file
if (argc == 3)
{
start = omp_get_wtime();
ret_code = gff_write(file, argv[2]);
stop = omp_get_wtime();
total = (stop - start);
if (ret_code) {
LOG_ERROR_F("[%dW] Error code = %d\n", omp_get_thread_num(), ret_code);
}
LOG_INFO_F("[%dW] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%dW] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
}
list_decr_writers(read_list);
gff_close(file, 0);
}
#pragma omp section
{
printf("1st log debug\n");
LOG_DEBUG_F("OMP num threads = %d\n", omp_get_num_threads());
LOG_DEBUG_F("Thread %d prints info\n", omp_get_thread_num());
printf("after 1st log debug\n");
start = omp_get_wtime();
int i = 0;
list_item_t* item = NULL;
FILE *out = fopen("result.gff", "w");
while ( (item = list_remove_item(read_list)) != NULL ) {
if (i % 200 == 0)
{
int debug = 1;
LOG_DEBUG_F("Batch %d reached by thread %d - %zu/%zu records \n", i, omp_get_thread_num(),
((gff_batch_t*) item->data_p)->length, ((gff_batch_t*) item->data_p)->max_length);
}
// gff_write_to_file(file, out);
// gff_batch_print(stdout, item->data_p);
write_gff_batch(item->data_p, out);
gff_batch_free(item->data_p);
list_item_free(item);
i++;
}
fclose(out);
stop = omp_get_wtime();
total = (stop - start);
LOG_INFO_F("[%d] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%d] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
}
}
free(read_list);
return 0;
}
void batch_writer(batch_writer_input_t* input_p) {
struct timespec ts;
ts.tv_sec = 1;
ts.tv_nsec = 0;
alignment_t **buffer_p;
bam1_t* bam1_p;
bam_header_t* bam_header_p;
bam_file_t* bam_file_p;
char* match_filename = input_p->match_filename;
//char* mismatch_filename = input_p->mismatch_filename;
char* splice_exact_filename = input_p->splice_exact_filename;
char* splice_extend_filename = input_p->splice_extend_filename;
list_t* list_p = input_p->list_p;
printf("batch_writer (%i): START\n", omp_get_thread_num());
list_item_t *item_p = NULL;
write_batch_t* batch_p;
FILE* fd;
FILE* splice_exact_fd = fopen(splice_exact_filename, "w");
FILE* splice_extend_fd = fopen(splice_extend_filename, "w");
//printf("HEADER FROM WRITE: %s\n", input_p->header_filename);
bam_header_p = bam_header_new(HUMAN, NCBI37, input_p->header_filename);
//bam_file_p = bam_fopen(match_filename);
bam_file_p = bam_fopen_mode(match_filename, bam_header_p, "w");
bam_fwrite_header(bam_header_p, bam_file_p);
// main loop
while ( (item_p = list_remove_item(list_p)) != NULL ) {
if (time_on) {
timing_start(BATCH_WRITER, 0, timing_p);
}
batch_p = (write_batch_t*) item_p->data_p;
//printf("*********************************Extract one item*********************************\n");
if (batch_p->flag == MATCH_FLAG || batch_p->flag == MISMATCH_FLAG) { //fd = match_fd;
//printf("start write alignment. Total %d\n", batch_p->size);
buffer_p = (alignment_t **)batch_p->buffer_p;
for(int i = 0; i < batch_p->size; i++) {
//alignment_print(buffer_p[i]);
bam1_p = convert_to_bam(buffer_p[i], 33);
bam_fwrite(bam1_p, bam_file_p);
bam_destroy1(bam1_p);
alignment_free(buffer_p[i]);
}
} else {
if (batch_p->flag == SPLICE_EXACT_FLAG) {
fd = splice_exact_fd;
}
else if (batch_p->flag == SPLICE_EXTEND_FLAG) {
fd = splice_extend_fd;
}
else {
fd = NULL;
}
if (fd != NULL) {
//printf("start write batch, %i bytes...\n", batch_p->size);
fwrite((char *)batch_p->buffer_p, batch_p->size, 1, fd);
//printf("write done !!\n");
//if (time_on) { stop_timer(t1_write, t2_write, write_time); }
}
}
//printf("Free batch\n");
write_batch_free(batch_p);
list_item_free(item_p);
if (time_on) {
timing_stop(BATCH_WRITER, 0, timing_p);
}
} // end of batch loop
//fclose(match_fd);
//fclose(mismatch_fd);
fclose(splice_exact_fd);
fclose(splice_extend_fd);
bam_fclose(bam_file_p);
//bam_header_free(bam_header_p);
printf("batch_writer: END\n");
}
void batch_writer2(batch_writer_input_t* input) {
printf("START: batch_writer (%i): START, for file %s\n",
omp_get_thread_num(), input->match_filename);
bam1_t *bam1;
bam_header_t *bam_header;
bam_file_t *bam_file;
alignment_t *alig;
char* match_filename = input->match_filename;
// char* splice_filename = input->splice_filename;
list_t *write_list = input->list_p;
array_list_t *array_list;
list_item_t *item = NULL;
aligner_batch_t *batch = NULL;
fastq_batch_t *fq_batch = NULL;
FILE* fd;
static char aux[10];
size_t read_len;
bam_header = bam_header_new(HUMAN, NCBI37, input->header_filename);
bam_file = bam_fopen_mode(match_filename, bam_header, "w");
bam_fwrite_header(bam_header, bam_file);
size_t num_reads = 0, num_items = 0, total_mappings = 0;
// main loop
while ( (item = list_remove_item(write_list)) != NULL ) {
// if (array_list == NULL) printf("batch_writer.c...\n");
batch = (aligner_batch_t *) item->data_p;
fq_batch = batch->fq_batch;
num_reads = batch->num_mapping_lists;
for (size_t i = 0; i < num_reads; i++) {
array_list = batch->mapping_lists[i];
// if (array_list == NULL) printf("READ %d, writer, list is NULL\n", i);
// printf("----> list == NULL ? %d\n", (array_list == NULL));
num_items = (array_list == NULL ? 0 : array_list_size(array_list));
// printf("----> number of items = %d, num_items <= 0 ? %d\n", num_items, num_items <= 0);
read_len = fq_batch->data_indices[i + 1] - fq_batch->data_indices[i] - 1;
// mapped or not mapped ?
if (num_items == 0) {
//printf("\tWRITE : read %i (%d items): unmapped...\n", i, num_items);
// calculating cigar
sprintf(aux, "%luX", read_len);
alig = alignment_new();
alignment_init_single_end(&(fq_batch->header[fq_batch->header_indices[i]])+1,
&(fq_batch->seq[fq_batch->data_indices[i]]),
&(fq_batch->quality[fq_batch->data_indices[i]]),
0,
0,
0,
aux, 1, 255, 0, 0, alig);
bam1 = convert_to_bam(alig, 33);
bam_fwrite(bam1, bam_file);
bam_destroy1(bam1);
// some cosmetic stuff before freeing the alignment,
// (in order to not free twice some fields)
alig->query_name = NULL;
alig->sequence = NULL;
alig->quality = NULL;
alig->cigar = NULL;
alignment_free(alig);
// printf("\tWRITE : read %i (%d items): unmapped...done !!\n", i, num_items);
} else {
// printf("\tWRITE : read %d (%d items): mapped...\n", i, num_items);
for (size_t j = 0; j < num_items; j++) {
alig = (alignment_t *) array_list_get(j, array_list);
if (alig != NULL) {
bam1 = convert_to_bam(alig, 33);
bam_fwrite(bam1, bam_file);
bam_destroy1(bam1);
alignment_free(alig);
}
}
// printf("\tWRITE : read %d (%d items): mapped...done !!\n", i, num_items);
}
if (array_list != NULL) array_list_free(array_list, NULL);
}
if (batch != NULL) aligner_batch_free(batch);
if (item != NULL) list_item_free(item);
if (time_on) {
timing_stop(BATCH_WRITER, 0, timing_p);
}
} // end of batch loop
bam_fclose(bam_file);
printf("END: batch_writer (total mappings %lu)\n", total_mappings);
}
int run_stats(shared_options_data_t *shared_options_data, stats_options_data_t *options_data) {
file_stats_t *file_stats = file_stats_new();
sample_stats_t **sample_stats;
// List that stores the batches of records filtered by each thread
list_t *output_list[shared_options_data->num_threads];
// List that stores which thread filtered the next batch to save
list_t *next_token_list = malloc(sizeof(list_t));
int ret_code;
double start, stop, total;
vcf_file_t *vcf_file = vcf_open(shared_options_data->vcf_filename, shared_options_data->max_batches);
if (!vcf_file) {
LOG_FATAL("VCF file does not exist!\n");
}
ped_file_t *ped_file = NULL;
if (shared_options_data->ped_filename) {
ped_file = ped_open(shared_options_data->ped_filename);
if (!ped_file) {
LOG_FATAL("PED file does not exist!\n");
}
if(options_data->variable) {
set_variable_field(options_data->variable, 0, ped_file);
} else {
set_variable_field("PHENO", 6, ped_file);
}
if(options_data->variable_groups) {
int n, m;
char *variable_groups = strdup(options_data->variable_groups);
char **groups;
char **phenos_in_group;
groups = split(variable_groups, ":", &n);
for(int i = 0; i < n; i++){
phenos_in_group = split(groups[i], ",", &m);
if(set_phenotype_group(phenos_in_group, m, ped_file) < 0) {
LOG_ERROR("Variable can't appear in two groups\n");
return DUPLICATED_VARIABLE;
}
free(phenos_in_group);
}
ped_file->accept_new_values = 0;
free(variable_groups);
free(groups);
} else {
ped_file->accept_new_values = 1;
}
if(options_data->phenotype) {
int n;
char* phenotypes = strdup(options_data->phenotype);
char** pheno_values = split(phenotypes, ",", &n);
if(n != 2) {
LOG_ERROR("To handle case-control test, only two phenotypes are supported\n");
return MORE_THAN_TWO_PHENOTYPES;
} else {
set_unaffected_phenotype(pheno_values[0],ped_file);
set_affected_phenotype(pheno_values[1],ped_file);
}
} else {
set_unaffected_phenotype("1", ped_file);
set_affected_phenotype("2", ped_file);
}
LOG_INFO("About to read PED file...\n");
// Read PED file before doing any processing
ret_code = ped_read(ped_file);
if (ret_code != 0) {
LOG_FATAL_F("Can't read PED file: %s\n", ped_file->filename);
}
if(!ped_file->num_field) {
LOG_ERROR_F("Can't find the specified field \"%s\" in file: %s \n", options_data->variable, ped_file->filename);
return VARIABLE_FIELD_NOT_FOUND;
}
}
ret_code = create_directory(shared_options_data->output_directory);
if (ret_code != 0 && errno != EEXIST) {
LOG_FATAL_F("Can't create output directory: %s\n", shared_options_data->output_directory);
}
// Initialize variables related to the different threads
for (int i = 0; i < shared_options_data->num_threads; i++) {
output_list[i] = (list_t*) malloc(sizeof(list_t));
list_init("input", 1, shared_options_data->num_threads * shared_options_data->batch_lines, output_list[i]);
}
list_init("next_token", shared_options_data->num_threads, INT_MAX, next_token_list);
LOG_INFO("About to retrieve statistics from VCF file...\n");
#pragma omp parallel sections private(start, stop, total)
{
#pragma omp section
{
LOG_DEBUG_F("Thread %d reads the VCF file\n", omp_get_thread_num());
// Reading
start = omp_get_wtime();
if (shared_options_data->batch_bytes > 0) {
ret_code = vcf_parse_batches_in_bytes(shared_options_data->batch_bytes, vcf_file);
} else if (shared_options_data->batch_lines > 0) {
ret_code = vcf_parse_batches(shared_options_data->batch_lines, vcf_file);
}
stop = omp_get_wtime();
total = stop - start;
if (ret_code) { LOG_FATAL_F("[%dR] Error code = %d\n", omp_get_thread_num(), ret_code); }
LOG_INFO_F("[%dR] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%dR] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
notify_end_parsing(vcf_file);
}
#pragma omp section
{
// Enable nested parallelism and set the number of threads the user has chosen
omp_set_nested(1);
LOG_DEBUG_F("Thread %d processes data\n", omp_get_thread_num());
individual_t **individuals = NULL;
khash_t(ids) *sample_ids = NULL;
khash_t(str) *phenotype_ids = NULL;
int num_phenotypes;
start = omp_get_wtime();
int i = 0;
vcf_batch_t *batch = NULL;
while ((batch = fetch_vcf_batch(vcf_file)) != NULL) {
if (i == 0) {
sample_stats = malloc (get_num_vcf_samples(vcf_file) * sizeof(sample_stats_t*));
for (int j = 0; j < get_num_vcf_samples(vcf_file); j++) {
sample_stats[j] = sample_stats_new(array_list_get(j, vcf_file->samples_names));
}
if (ped_file) {
// Create map to associate the position of individuals in the list of samples defined in the VCF file
sample_ids = associate_samples_and_positions(vcf_file);
// Sort individuals in PED as defined in the VCF file
individuals = sort_individuals(vcf_file, ped_file);
// Get the khash of the phenotypes in PED file
phenotype_ids = get_phenotypes(ped_file);
num_phenotypes = get_num_variables(ped_file);
}
}
if (i % 50 == 0) {
LOG_INFO_F("Batch %d reached by thread %d - %zu/%zu records \n",
i, omp_get_thread_num(),
batch->records->size, batch->records->capacity);
}
// Divide the list of passed records in ranges of size defined in config file
int num_chunks;
int *chunk_sizes = NULL;
array_list_t *input_records = batch->records;
int *chunk_starts = create_chunks(input_records->size,
ceil((float) shared_options_data->batch_lines / shared_options_data->num_threads),
&num_chunks, &chunk_sizes);
// OpenMP: Launch a thread for each range
#pragma omp parallel for num_threads(shared_options_data->num_threads)
for (int j = 0; j < num_chunks; j++) {
LOG_DEBUG_F("[%d] Stats invocation\n", omp_get_thread_num());
// Invoke variant stats and/or sample stats when applies
if (options_data->variant_stats) {
int index = omp_get_thread_num() % shared_options_data->num_threads;
ret_code = get_variants_stats((vcf_record_t**) (input_records->items + chunk_starts[j]),
chunk_sizes[j], individuals, sample_ids,num_phenotypes, output_list[index], file_stats);
}
if (options_data->sample_stats) {
ret_code |= get_sample_stats((vcf_record_t**) (input_records->items + chunk_starts[j]),
chunk_sizes[j], individuals, sample_ids, sample_stats, file_stats);
}
}
if (options_data->variant_stats) {
// Insert as many tokens as elements correspond to each thread
for (int t = 0; t < num_chunks; t++) {
for (int s = 0; s < chunk_sizes[t]; s++) {
list_item_t *token_item = list_item_new(t, 0, NULL);
list_insert_item(token_item, next_token_list);
}
}
}
free(chunk_starts);
free(chunk_sizes);
vcf_batch_free(batch);
i++;
}
stop = omp_get_wtime();
total = stop - start;
LOG_INFO_F("[%d] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%d] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
// Decrease list writers count
for (i = 0; i < shared_options_data->num_threads; i++) {
list_decr_writers(next_token_list);
list_decr_writers(output_list[i]);
}
if (sample_ids) { kh_destroy(ids, sample_ids); }
if (individuals) { free(individuals); }
}
#pragma omp section
{
LOG_DEBUG_F("Thread %d writes the output\n", omp_get_thread_num());
char *stats_prefix = get_vcf_stats_filename_prefix(shared_options_data->vcf_filename,
shared_options_data->output_filename,
shared_options_data->output_directory);
// File names and descriptors for output to plain text files
char *stats_filename, *summary_filename, *phenotype_filename;
FILE *stats_fd, *summary_fd, **phenotype_fd;
char *stats_db_name;
sqlite3 *db = NULL;
khash_t(stats_chunks) *hash;
khash_t(str) *phenotype_ids;
int num_phenotypes;
if(ped_file){
phenotype_ids = get_phenotypes(ped_file);
num_phenotypes = get_num_variables(ped_file);
}
if (options_data->save_db) {
delete_files_by_extension(shared_options_data->output_directory, "db");
stats_db_name = calloc(strlen(stats_prefix) + strlen(".db") + 2, sizeof(char));
sprintf(stats_db_name, "%s.db", stats_prefix);
create_stats_db(stats_db_name, VCF_CHUNKSIZE, create_vcf_query_fields, &db);
hash = kh_init(stats_chunks);
}
// Write variant (and global) statistics
if (options_data->variant_stats) {
stats_filename = get_variant_stats_output_filename(stats_prefix);
if (!(stats_fd = fopen(stats_filename, "w"))) {
LOG_FATAL_F("Can't open file for writing statistics of variants: %s\n", stats_filename);
}
//Open one file for each phenotype
if(ped_file){
phenotype_fd = malloc(sizeof(FILE*)*num_phenotypes);
if(options_data->variable_groups){
int n;
char *variable_groups = strdup(options_data->variable_groups);
char ** names = split(variable_groups, ":", &n);
for(int i = 0; i < n; i++) {
phenotype_filename = get_variant_phenotype_stats_output_filename(stats_prefix, names[i]);
if(!(phenotype_fd[i] = fopen(phenotype_filename, "w"))) {
LOG_FATAL_F("Can't open file for writing statistics of variants per phenotype: %s\n", stats_filename);
}
free(phenotype_filename);
}
free(names);
free(variable_groups);
} else {
for (khint_t i = kh_begin(phenotype_ids); i != kh_end(phenotype_ids); ++i) {
if (!kh_exist(phenotype_ids,i)) continue;
phenotype_filename = get_variant_phenotype_stats_output_filename(stats_prefix, kh_key(phenotype_ids,i));
if(!(phenotype_fd[kh_val(phenotype_ids,i)] = fopen(phenotype_filename, "w"))) {
LOG_FATAL_F("Can't open file for writing statistics of variants per phenotype: %s\n", stats_filename);
}
free(phenotype_filename);
}
}
}
// Write header
report_vcf_variant_stats_header(stats_fd);
if(ped_file){
for(int i = 0; i < num_phenotypes; i++)
report_vcf_variant_phenotype_stats_header(phenotype_fd[i]);
}
// For each variant, generate a new line
int avail_stats = 0;
variant_stats_t *var_stats_batch[VCF_CHUNKSIZE];
list_item_t *token_item = NULL, *output_item = NULL;
while ( token_item = list_remove_item(next_token_list) ) {
output_item = list_remove_item(output_list[token_item->id]);
assert(output_item);
var_stats_batch[avail_stats] = output_item->data_p;
avail_stats++;
// Run only when certain amount of stats is available
if (avail_stats >= VCF_CHUNKSIZE) {
report_vcf_variant_stats(stats_fd, db, hash, avail_stats, var_stats_batch);
if(ped_file)
for(int i = 0; i < num_phenotypes; i++)
report_vcf_variant_phenotype_stats(phenotype_fd[i], avail_stats, var_stats_batch, i);
// Free all stats from the "batch"
for (int i = 0; i < avail_stats; i++) {
variant_stats_free(var_stats_batch[i]);
}
avail_stats = 0;
}
// Free resources
list_item_free(output_item);
list_item_free(token_item);
}
if (avail_stats > 0) {
report_vcf_variant_stats(stats_fd, db, hash, avail_stats, var_stats_batch);
if(ped_file)
for(int i = 0; i < num_phenotypes; i++)
report_vcf_variant_phenotype_stats(phenotype_fd[i], avail_stats, var_stats_batch, i);
// Free all stats from the "batch"
for (int i = 0; i < avail_stats; i++) {
variant_stats_free(var_stats_batch[i]);
}
avail_stats = 0;
}
// Write whole file stats (data only got when launching variant stats)
summary_filename = get_vcf_file_stats_output_filename(stats_prefix);
if (!(summary_fd = fopen(summary_filename, "w"))) {
LOG_FATAL_F("Can't open file for writing statistics summary: %s\n", summary_filename);
}
report_vcf_summary_stats(summary_fd, db, file_stats);
free(stats_filename);
free(summary_filename);
// Close variant stats file
if (stats_fd) { fclose(stats_fd); }
if (summary_fd) { fclose(summary_fd); }
if(ped_file){
for(int i = 0; i < num_phenotypes; i++)
if(phenotype_fd[i]) fclose(phenotype_fd[i]);
free(phenotype_fd);
}
}
// Write sample statistics
if (options_data->sample_stats) {
stats_filename = get_sample_stats_output_filename(stats_prefix);
if (!(stats_fd = fopen(stats_filename, "w"))) {
LOG_FATAL_F("Can't open file for writing statistics of samples: %s\n", stats_filename);
}
report_vcf_sample_stats_header(stats_fd);
report_vcf_sample_stats(stats_fd, NULL, vcf_file->samples_names->size, sample_stats);
// Close sample stats file
free(stats_filename);
if (stats_fd) { fclose(stats_fd); }
}
free(stats_prefix);
if (db) {
insert_chunk_hash(VCF_CHUNKSIZE, hash, db);
create_stats_index(create_vcf_index, db);
close_stats_db(db, hash);
}
}
}
for (int i = 0; i < get_num_vcf_samples(vcf_file); i++) {
sample_stats_free(sample_stats[i]);
}
free(sample_stats);
free(file_stats);
free(next_token_list);
for (int i = 0; i < shared_options_data->num_threads; i++) {
free(output_list[i]);
}
vcf_close(vcf_file);
if (ped_file) { ped_close(ped_file, 1,1); }
return 0;
}
int run_merge(shared_options_data_t *shared_options_data, merge_options_data_t *options_data) {
if (options_data->num_files == 1) {
LOG_INFO("Just one VCF file specified, no need to merge");
return 0;
}
list_t *read_list[options_data->num_files];
memset(read_list, 0, options_data->num_files * sizeof(list_t*));
list_t *output_header_list = (list_t*) malloc (sizeof(list_t));
list_init("headers", shared_options_data->num_threads, INT_MAX, output_header_list);
list_t *output_list = (list_t*) malloc (sizeof(list_t));
list_init("output", shared_options_data->num_threads, shared_options_data->max_batches * shared_options_data->batch_lines, output_list);
list_t *merge_tokens = (list_t*) malloc (sizeof(list_t));
list_init("tokens", 1, INT_MAX, merge_tokens);
int ret_code = 0;
double start, stop, total;
vcf_file_t *files[options_data->num_files];
memset(files, 0, options_data->num_files * sizeof(vcf_file_t*));
// Initialize variables related to the different files
for (int i = 0; i < options_data->num_files; i++) {
files[i] = vcf_open(options_data->input_files[i], shared_options_data->max_batches);
if (!files[i]) {
LOG_FATAL_F("VCF file %s does not exist!\n", options_data->input_files[i]);
}
read_list[i] = (list_t*) malloc(sizeof(list_t));
list_init("text", 1, shared_options_data->max_batches, read_list[i]);
}
ret_code = create_directory(shared_options_data->output_directory);
if (ret_code != 0 && errno != EEXIST) {
LOG_FATAL_F("Can't create output directory: %s\n", shared_options_data->output_directory);
}
chromosome_order = get_chromosome_order(shared_options_data->host_url, shared_options_data->species,
shared_options_data->version, &num_chromosomes);
printf("Number of threads = %d\n", shared_options_data->num_threads);
#pragma omp parallel sections private(start, stop, total)
{
#pragma omp section
{
LOG_DEBUG_F("Thread %d reads the VCF file\n", omp_get_thread_num());
// Reading
start = omp_get_wtime();
ret_code = vcf_multiread_batches(read_list, shared_options_data->batch_lines, files, options_data->num_files);
stop = omp_get_wtime();
total = stop - start;
if (ret_code) {
LOG_ERROR_F("Error %d while reading VCF files\n", ret_code);
}
LOG_INFO_F("[%dR] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%dR] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
}
#pragma omp section
{
// Enable nested parallelism
omp_set_nested(1);
LOG_DEBUG_F("Thread %d processes data\n", omp_get_thread_num());
int num_eof_found = 0;
int eof_found[options_data->num_files];
memset(eof_found, 0, options_data->num_files * sizeof(int));
list_item_t *items[options_data->num_files];
memset(items, 0, options_data->num_files * sizeof(list_item_t*));
char *texts[options_data->num_files];
memset(texts, 0, options_data->num_files * sizeof(char*));
khash_t(pos) *positions_read = kh_init(pos);
long max_position_merged = LONG_MAX;
char *max_chromosome_merged = NULL;
int header_merged = 0;
int token = 0;
double start_parsing, start_insertion, total_parsing = 0, total_insertion = 0;
start = omp_get_wtime();
while (num_eof_found < options_data->num_files) {
/* Process:
* - N threads getting batches of VCF records and inserting them in a data structure. The common minimum
* position of each group of batches will also be stored.
* - If the data structure reaches certain size or the end of a chromosome, merge positions prior to the
* last minimum registered.
*/
// Getting text elements in a critical region guarantees that each thread gets variants in positions in the same range
for (int i = 0; i < options_data->num_files; i++) {
if (eof_found[i]) {
continue;
}
items[i] = list_remove_item(read_list[i]);
if (items[i] == NULL || !strcmp(items[i]->data_p, "")) {
LOG_INFO_F("[%d] EOF found in file %s\n", omp_get_thread_num(), options_data->input_files[i]);
eof_found[i] = 1;
num_eof_found++;
if(items[i] != NULL && !strcmp(items[i]->data_p, "")) {
free(items[i]->data_p);
list_item_free(items[i]);
LOG_DEBUG_F("[%d] Text batch freed\n", omp_get_thread_num());
} else {
LOG_DEBUG_F("[%d] No need to free text batch\n", omp_get_thread_num());
}
continue;
}
assert(items[i]->data_p != NULL);
texts[i] = items[i]->data_p;
// printf("[%d] text batch from file %d\tcontents = '%s'\n", omp_get_thread_num(), i, texts[i]);
}
for (int i = 0; i < options_data->num_files; i++) {
if (eof_found[i]) {
continue;
}
start_parsing = omp_get_wtime();
char *text_begin = texts[i];
char *text_end = text_begin + strlen(text_begin);
assert(text_end != NULL);
// printf("batch = '%.*s'\n", text_end - text_begin, text_begin);
// Get VCF batches from text batches
vcf_reader_status *status = vcf_reader_status_new(shared_options_data->batch_lines, 0);
ret_code = run_vcf_parser(text_begin, text_end, shared_options_data->batch_lines, files[i], status);
if (ret_code) {
// TODO stop?
LOG_ERROR_F("Error %d while reading the file %s\n", ret_code, files[i]->filename);
continue;
}
// printf("batches = %d\n", files[i]->record_batches->length);
vcf_batch_t *batch = fetch_vcf_batch_non_blocking(files[i]);
if (!batch) {
continue;
}
total_parsing += omp_get_wtime() - start_parsing;
start_insertion = omp_get_wtime();
// Insert records into hashtable
for (int j = 0; j < batch->records->size; j++) {
vcf_record_t *record = vcf_record_copy(array_list_get(j, batch->records));
vcf_record_file_link *link = vcf_record_file_link_new(record, files[i]);
char key[64];
compose_key_value(record->chromosome, record->position, key);
int ret = insert_position_read(key, link, positions_read);
assert(ret);
}
total_insertion += omp_get_wtime() - start_insertion;
// Update minimum position being a maximum of these batches
vcf_record_t *current_record = (vcf_record_t*) array_list_get(batch->records->size - 1, batch->records);
calculate_merge_interval(current_record, &max_chromosome_merged, &max_position_merged, chromosome_order, num_chromosomes);
// Free batch and its contents
vcf_reader_status_free(status);
vcf_batch_free(batch);
list_item_free(items[i]);
}
if (num_eof_found == options_data->num_files) {
max_chromosome_merged = chromosome_order[num_chromosomes-1];
max_position_merged = LONG_MAX;
}
// Merge headers, if not previously done
if (!header_merged) {
merge_vcf_headers(files, options_data->num_files, options_data, output_header_list);
header_merged = 1;
// Decrease list writers count
for (int i = 0; i < shared_options_data->num_threads; i++) {
list_decr_writers(output_header_list);
}
}
// If the data structure reaches certain size or the end of a chromosome,
// merge positions prior to the last minimum registered
if (num_eof_found < options_data->num_files && kh_size(positions_read) > TREE_LIMIT) {
LOG_INFO_F("Merging until position %s:%ld\n", max_chromosome_merged, max_position_merged);
token = merge_interval(positions_read, max_chromosome_merged, max_position_merged, chromosome_order, num_chromosomes,
files, shared_options_data, options_data, output_list);
}
// When reaching EOF for all files, merge the remaining entries
else if (num_eof_found == options_data->num_files && kh_size(positions_read) > 0) {
LOG_INFO_F("Merging remaining positions (last = %s:%ld)\n", chromosome_order[num_chromosomes - 1], LONG_MAX);
token = merge_remaining_interval(positions_read, files, shared_options_data, options_data, output_list);
}
if (token) {
int *token_ptr = malloc (sizeof(int)); *token_ptr = token;
list_item_t *item = list_item_new(1, 0, token_ptr);
list_insert_item(item, merge_tokens);
}
// Set variables ready for next iteration of the algorithm
if (max_chromosome_merged) {
free(max_chromosome_merged);
}
token = 0;
max_chromosome_merged = NULL;
max_position_merged = LONG_MAX;
}
kh_destroy(pos, positions_read);
stop = omp_get_wtime();
total = stop - start;
LOG_INFO_F("[%d] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%d] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
LOG_DEBUG_F("** Time in parsing = %f s\n", total_parsing);
LOG_DEBUG_F("** Time in insertion = %f s\n", total_insertion);
// for (int i = 0; i < shared_options_data->num_threads; i++) {
// printf("[%d] Time in searching = %f s\n", i, total_search[i]);
// printf("[%d] Time in merging = %f s\n", i, total_merge[i]);
// }
// Decrease list writers count
for (int i = 0; i < shared_options_data->num_threads; i++) {
list_decr_writers(output_list);
}
list_decr_writers(merge_tokens);
}
#pragma omp section
{
LOG_DEBUG_F("Thread %d writes the output\n", omp_get_thread_num());
start = omp_get_wtime();
// Create file streams for results
char aux_filename[32]; memset(aux_filename, 0, 32 * sizeof(char));
sprintf(aux_filename, "merge_from_%d_files.vcf", options_data->num_files);
char *merge_filename;
FILE *merge_fd = get_output_file(shared_options_data, aux_filename, &merge_filename);
LOG_INFO_F("Output filename = %s\n", merge_filename);
free(merge_filename);
list_item_t *item1 = NULL, *item2 = NULL;
vcf_header_entry_t *entry;
vcf_record_t *record;
int *num_records;
// Write headers
while ((item1 = list_remove_item(output_header_list)) != NULL) {
entry = item1->data_p;
write_vcf_header_entry(entry, merge_fd);
}
// Write delimiter
array_list_t *sample_names = merge_vcf_sample_names(files, options_data->num_files);
write_vcf_delimiter_from_samples((char**) sample_names->items, sample_names->size, merge_fd);
// Write records
// When a token is present, it means a set of batches has been merged. The token contains the number of records merged.
// In this case, the records must be sorted by chromosome and position, and written afterwards.
while ((item1 = list_remove_item(merge_tokens)) != NULL) {
num_records = item1->data_p;
vcf_record_t *records[*num_records];
for (int i = 0; i < *num_records; i++) {
item2 = list_remove_item(output_list);
if (!item2) {
break;
}
records[i] = item2->data_p;
list_item_free(item2);
}
// Sort records
qsort(records, *num_records, sizeof(vcf_record_t*), record_cmp);
// Write and free sorted records
for (int i = 0; i < *num_records; i++) {
record = records[i];
write_vcf_record(record, merge_fd);
vcf_record_free_deep(record);
}
free(num_records);
list_item_free(item1);
}
// Close file
if (merge_fd != NULL) { fclose(merge_fd); }
stop = omp_get_wtime();
total = stop - start;
LOG_INFO_F("[%dW] Time elapsed = %f s\n", omp_get_thread_num(), total);
LOG_INFO_F("[%dW] Time elapsed = %e ms\n", omp_get_thread_num(), total*1000);
}
}
// Free variables related to the different files
for (int i = 0; i < options_data->num_files; i++) {
if(files[i]) { vcf_close(files[i]); }
if(read_list[i]) { free(read_list[i]); }
}
free(output_list);
return ret_code;
}
