vcf_batch_t* vcf_batch_new(size_t size) {
vcf_batch_t *vcf_batch = calloc (1, sizeof(vcf_batch_t));
vcf_batch->text = NULL;
if (size > 0) {
vcf_batch->records = array_list_new(size, 1.2, COLLECTION_MODE_ASYNCHRONIZED);
} else {
vcf_batch->records = array_list_new(100, 1.2, COLLECTION_MODE_ASYNCHRONIZED);
}
return vcf_batch;
}
/*
old key path: key1_path, new key path: key2_path
if key1_path == key2_path, if either type or cb is different , add a new item. or do noting
if key1_path is the parent of key2_path, if either type or cb is different , add a new item. or do nothing.
if key1_path is the child of key2 path, a. either type or cb is different, add a new item or replace the item with key1_path using item with key2_path
==>
1. either type or cb is different, add a new item
2. if both type anc cb are the same one, check key1_path and key2_path, if key1_path is the child of key2_path, replace key1_path using key2_path
*/
INT32 tg_shared_preferences_register(const CHAR* path,const CHAR* keys,SharedPreferences_Notification_Callback cb,SharedPreferences_WRITE_TYPE type)
{
INT32* idx_list = NULL;
INT32 idx=0;
CHAR* normalize_key = NULL;
Shared_Preferences_Register_Item* item = NULL;
INT32 ret = SharedPreferences_SUCC;//SharedPreferences_ERROR;
//sem_wait (&s_shared_preferences_sem);
tg_os_WaitSemaphore(s_shared_preferences_sem);
if (s_shared_preferences_register_list.list == NULL)
{
s_shared_preferences_register_list.list = array_list_new(tg_shared_preferences_register_free);
}
//sem_post (&s_shared_preferences_sem);
tg_os_SignalSemaphore(s_shared_preferences_sem);
return_val_if_fail(path,SharedPreferences_PATH_ERROR);
normalize_key = tg_shared_preferences_normalize_keys(keys);
return_val_if_fail(normalize_key,SharedPreferences_ERROR);
item = tg_shared_preferences_find_register_item(path,normalize_key,cb,type,&idx);
if (!item) //found at least one item
{
tg_shared_preferences_add_new_register_item(path,normalize_key,cb,type);
}
TG_FREE(normalize_key);
#ifdef SharedPreferences_DEBUG
tg_shared_preferences_travel_register_list();
#endif
return ret;
}
vcf_header_entry_t* vcf_header_entry_new() {
vcf_header_entry_t *entry = (vcf_header_entry_t*) malloc (sizeof(vcf_header_entry_t));
entry->name = NULL;
entry->name_len = 0;
entry->values = array_list_new(4, 1.5, COLLECTION_MODE_ASYNCHRONIZED);
return entry;
}
struct jstruct_result
_jstruct_import(struct json_object *obj, const void *data,
const struct jstruct_object_property *properties, struct json_object *errors) {
_init_importers();
if (errors != NULL && json_object_get_type(errors) != json_type_array) {
return jstruct_error_new(jstruct_error_errors_not_array_or_null, NULL, json_object_get_type(errors));
}
const struct jstruct_object_property *property;
struct json_object *prop;
struct jstruct_result result = JSTRUCT_OK;
result.allocated = array_list_new(jstruct_allocated_free);
for (property = properties; property->name; ++property) {
void *ptr = jstruct_prop_ptr(data, property, JSTRUCT_PROP_PTR_GET_NO_DEREF);
struct jstruct_result err;
if (json_object_object_get_ex(obj, property->name, &prop)) {
if (json_object_get_type(prop) != property->type.json) {
err = jstruct_error_new(jstruct_error_incorrect_type, property->name, json_object_get_type(prop));
} else {
jstruct_import_importer import = importers[json_type_index(property->type.json)];
err = import(prop, data, ptr, property);
}
} else {
if (!set_null(ptr, property)) {
err = jstruct_error_array_add(errors, jstruct_error_not_nullable, property->name, 0);
}
}
jstruct_error_consume(&result, &err, errors, property->name, -1);
}
if (result.allocated->length == 0) {
array_list_free(result.allocated);
result.allocated = NULL;
}
return result;
}
json_object * tg_shared_preferences_find_parent_of_leaf(SharedPreferences* thiz,const CHAR* key_path,CHAR** leaf_key)
{
struct json_object *jso=NULL;
struct array_list* key_list = NULL;
INT32 key_list_len = 0;
INT32 idx = 0;
return_val_if_fail((thiz&&key_path),NULL);
key_list = array_list_new(tg_shared_preferences_key_free);
return_val_if_fail((key_list),NULL);
return_val_if_fail(tg_shared_preferences_parse_keypath(key_path,key_list,&key_list_len),NULL);
for (jso=thiz->obj; idx<key_list_len-1; idx++)
{
jso = json_object_object_get(jso,(CHAR*)array_list_get_idx(key_list,idx));
if (jso==NULL)
break;
}
if (jso!=NULL)
{
CHAR* key = (CHAR*)array_list_get_idx(key_list,key_list_len-1);
//ASSERT(key);
*leaf_key = TG_CALLOC((strlen(key)+1),1);
strcpy(*leaf_key,key);
}
array_list_free(key_list);
return jso;
}
void workflow_set_stages(int num_stages, workflow_stage_function_t *functions,
char **labels, workflow_t *wf) {
if (functions && wf) {
pthread_mutex_lock(&wf->main_mutex);
wf->num_stages = num_stages;
wf->stage_functions = functions;
wf->stage_times = (double *) calloc(num_stages, sizeof(double));
wf->stage_times_mutex = (pthread_mutex_t *) calloc(num_stages, sizeof(pthread_mutex_t));
for (int i = 0; i < num_stages; i++) {
pthread_mutex_init(&wf->stage_times_mutex[i], NULL);
}
wf->pending_items = (array_list_t **) calloc(num_stages, sizeof(array_list_t *));
if (labels) wf->stage_labels = (char **) calloc(num_stages, sizeof(char *));
for (int i = 0; i < num_stages; i++) {
wf->pending_items[i] = array_list_new(100, 1.25f, COLLECTION_MODE_ASYNCHRONIZED);
if (labels && labels[i]) wf->stage_labels[i] = strdup(labels[i]);
}
pthread_mutex_unlock(&wf->main_mutex);
}
}
array_list_t *snp_filter(array_list_t *input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void *f_args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
int include_snps = ((snp_filter_args*)f_args)->include_snps;
LOG_DEBUG_F("snp_filter (preserve SNPs = %d) over %zu records\n", include_snps, input_records->size);
vcf_record_t *record;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
if (record->id_len == 1 && strncmp(".", record->id, 1) == 0) {
if (include_snps) {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
} else {
array_list_insert(record, passed);
}
} else {
if (include_snps) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
}
return passed;
}
array_list_t *indel_filter(array_list_t *input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void *f_args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
int include_indels = ((indel_filter_args*)f_args)->include_indels;
LOG_DEBUG_F("indel_filter (preserve indels = %d) over %zu records\n", include_indels, input_records->size);
vcf_record_t *record;
variant_stats_t *variant_stats;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
variant_stats = input_stats[i];
if (variant_stats->is_indel) {
if (include_indels) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
} else {
if (include_indels) {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
} else {
array_list_insert(record, passed);
}
}
}
return passed;
}
array_list_t* mendelian_errors_filter(array_list_t* input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void* args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
int max_errors = ((mendelian_errors_filter_args*) args)->max_mendelian_errors;
float allele_count;
variant_stats_t *variant_stats;
// The stats returned by get_variants_stats are related to a record in the same
// position of the input_records list, so when a variant_stats_t fulfills the condition,
// it means the related vcf_record_t passes the filter
vcf_record_t *record;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
variant_stats = input_stats[i];
allele_count = 0;
if (variant_stats->mendelian_errors <= max_errors) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
return passed;
}
array_list_t* maf_filter(array_list_t* input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void* args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
float min_maf = ((maf_filter_args*) args)->min_maf;
float record_maf = 1.0;
variant_stats_t *variant_stats;
// The stats returned by get_variants_stats are related to a record in the same
// position of the input_records list, so when a variant_stats_t fulfills the condition,
// it means the related vcf_record_t passes the filter
vcf_record_t *record;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
variant_stats = input_stats[i];
record_maf = 1.0;
for (int j = 0; j < variant_stats->num_alleles; j++) {
record_maf = fmin(record_maf, variant_stats->alleles_freq[j]);
}
if (record_maf >= min_maf) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
return passed;
}
gff_batch_t* gff_batch_new(size_t size) {
gff_batch_t *gff_batch = malloc(sizeof(gff_batch_t));
gff_batch->text = NULL;
if (size < 1) {
size = 100;
}
gff_batch->records = array_list_new(size, 1.4, COLLECTION_MODE_ASYNCHRONIZED);
return gff_batch;
}
void *fastq_reader(void *input) {
struct timeval start, end;
double time;
extern size_t fd_read_bytes;
size_t read_bytes;
//if (time_on) { start_timer(start); }
wf_input_t *wf_input = (wf_input_t *) input;
batch_t *new_batch = NULL;
batch_t *batch = wf_input->batch;
fastq_batch_reader_input_t *fq_reader_input = wf_input->fq_reader_input;
array_list_t *reads = array_list_new(10000, 1.25f, COLLECTION_MODE_ASYNCHRONIZED);
if (fq_reader_input->gzip) {
//Gzip fastq file
if (fq_reader_input->flags == SINGLE_END_MODE) {
fastq_gzread_bytes_se(reads, fq_reader_input->batch_size, fq_reader_input->fq_gzip_file1);
} else {
//printf("Gzip Reader for pair-end not implemented\n");;
fastq_gzread_bytes_pe(reads, fq_reader_input->batch_size, fq_reader_input->fq_gzip_file1, fq_reader_input->fq_gzip_file2);
//fastq_fread_bytes_aligner_pe(reads, fq_reader_input->batch_size,
// fq_reader_input->fq_gzip_file1, fq_reader_input->fq_gzip_file2);
}
} else {
//Fastq file
if (fq_reader_input->flags == SINGLE_END_MODE) {
read_bytes = fastq_fread_bytes_se(reads, fq_reader_input->batch_size, fq_reader_input->fq_file1);
} else {
read_bytes = fastq_fread_bytes_aligner_pe(reads, fq_reader_input->batch_size,
fq_reader_input->fq_file1, fq_reader_input->fq_file2);
}
fd_read_bytes += read_bytes;
}
size_t num_reads = array_list_size(reads);
if (num_reads == 0) {
array_list_free(reads, (void *)fastq_read_free);
} else {
mapping_batch_t *mapping_batch = mapping_batch_new(reads,
batch->pair_input->pair_mng);
new_batch = batch_new(batch->bwt_input, batch->region_input, batch->cal_input,
batch->pair_input, batch->preprocess_rna, batch->sw_input, batch->writer_input,
batch->mapping_mode, mapping_batch);
}
//if (time_on) { stop_timer(start, end, time); timing_add(time, FASTQ_READER, timing); }
//printf("Read batch %i\n", num_reads);
return new_batch;
}
BOOL tg_shared_preferences_lock(const CHAR* path,BOOL lock)
{
INT32 i = 0;
INT32 len = 0;
struct array_list* list = NULL;
INT32 idx = -1;
//sem_wait (&s_shared_preferences_sem);
tg_os_WaitSemaphore(s_shared_preferences_sem);
if (s_shared_preferences_lock_list.lock_list == NULL)
{
s_shared_preferences_lock_list.lock_list = array_list_new(tg_shared_preferences_lock_free);
}
//sem_post (&s_shared_preferences_sem);
tg_os_SignalSemaphore(s_shared_preferences_sem);
list = s_shared_preferences_lock_list.lock_list;
return_val_if_fail(path,FALSE);
return_val_if_fail(list,FALSE);
idx = tg_shared_preferences_find_lock_path(path);
if (idx>=0)
{
if (!lock)
{
//sem_wait (&s_shared_preferences_sem);
tg_os_WaitSemaphore(s_shared_preferences_sem);
array_list_put_idx(list, idx, NULL);
//sem_post (&s_shared_preferences_sem);
tg_os_SignalSemaphore(s_shared_preferences_sem);
}
return TRUE;
}
else
{
if (lock)
{
CHAR* lock_path = TG_CALLOC((strlen(path)+1),1);
strcpy(lock_path,path);
//sem_wait (&s_shared_preferences_sem);
tg_os_WaitSemaphore(s_shared_preferences_sem);
array_list_put_idx(list, tg_shared_preferences_get_first_free_slot(s_shared_preferences_lock_list.lock_list), (void*)lock_path);
//sem_post (&s_shared_preferences_sem);
tg_os_SignalSemaphore(s_shared_preferences_sem);
}
return TRUE;
}
}
array_list_t *region_filter(array_list_t *input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void *f_args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
region_filter_args *args = (region_filter_args*) f_args;
region_table_t *regions = args->regions;
LOG_DEBUG_F("region_filter over %zu records\n", input_records->size);
vcf_record_t *record;
region_t *region = (region_t*) malloc (sizeof(region_t));
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
// LOG_DEBUG_F("record = %s, %ld\n", record->chromosome, record->position);
region->chromosome = strndup(record->chromosome, record->chromosome_len);
region->start_position = record->position;
region->end_position = record->position;
int found = 0;
if (args->type) {
region->type = args->type;
found = find_region_by_type(region, regions);
} else {
found = find_region(region, regions);
}
if (found) {
// Add to the list of records that pass all checks for at least one region
array_list_insert(record, passed);
// LOG_DEBUG_F("%.*s, %ld passed\n", record->chromosome_len, record->chromosome, record->position);
} else {
// Add to the list of records that fail all checks for all regions
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
free(region->chromosome);
}
free(region);
return passed;
}
array_list_t *inheritance_pattern_filter(array_list_t *input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void *f_args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
enum inheritance_pattern pattern = ((inheritance_pattern_filter_args*)f_args)->pattern;
float min_following_pattern = ((inheritance_pattern_filter_args*)f_args)->min_following_pattern;
if (pattern == DOMINANT) {
LOG_DEBUG_F("inheritance_pattern_filter (dominant in %.2f% of samples) over %zu records\n",
min_following_pattern * 100, input_records->size);
} else {
LOG_DEBUG_F("inheritance_pattern_filter (recessive in %.2f% of samples) over %zu records\n",
min_following_pattern * 100, input_records->size);
}
vcf_record_t *record;
variant_stats_t *stats;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
stats = input_stats[i];
if (pattern == DOMINANT) {
if (stats->cases_percent_dominant >= min_following_pattern &&
stats->controls_percent_dominant >= min_following_pattern) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
} else if (pattern == RECESSIVE) {
if (stats->cases_percent_recessive >= min_following_pattern &&
stats->controls_percent_recessive >= min_following_pattern) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
}
return passed;
}
int insert_position_read(char key[64], vcf_record_file_link* link, kh_pos_t* positions_read) {
int ret;
array_list_t *records_in_position;
khiter_t iter = kh_get(pos, positions_read, key);
if (iter != kh_end(positions_read)) {
records_in_position = kh_value(positions_read, iter);
ret = array_list_insert(link, records_in_position);
} else {
records_in_position = array_list_new(8, 1.5, COLLECTION_MODE_SYNCHRONIZED);
ret = array_list_insert(link, records_in_position);
iter = kh_put(pos, positions_read, strdup(key), &ret);
if (ret) {
kh_value(positions_read, iter) = records_in_position;
}
}
return ret;
}
void *sa_fq_reader(void *input) {
sa_wf_input_t *wf_input = (sa_wf_input_t *) input;
sa_wf_batch_t *new_wf_batch = NULL;
sa_wf_batch_t *curr_wf_batch = wf_input->wf_batch;
fastq_batch_reader_input_t *fq_reader_input = wf_input->fq_reader_input;
array_list_t *reads = array_list_new(fq_reader_input->batch_size, 1.25f, COLLECTION_MODE_ASYNCHRONIZED);
if (fq_reader_input->gzip) {
// Gzip fastq file
if (fq_reader_input->flags == SINGLE_END_MODE) {
fastq_gzread_bytes_se(reads, fq_reader_input->batch_size, fq_reader_input->fq_gzip_file1);
} else {
fastq_gzread_bytes_pe(reads, fq_reader_input->batch_size, fq_reader_input->fq_gzip_file1, fq_reader_input->fq_gzip_file2);
}
} else {
// Fastq file
if (fq_reader_input->flags == SINGLE_END_MODE) {
fastq_fread_bytes_se(reads, fq_reader_input->batch_size, fq_reader_input->fq_file1);
} else {
fastq_fread_bytes_aligner_pe(reads, fq_reader_input->batch_size,
fq_reader_input->fq_file1, fq_reader_input->fq_file2);
}
}
size_t num_reads = array_list_size(reads);
if (num_reads == 0) {
array_list_free(reads, (void *)fastq_read_free);
} else {
sa_mapping_batch_t *sa_mapping_batch = sa_mapping_batch_new(reads);
sa_mapping_batch->bam_format = wf_input->bam_format;
new_wf_batch = sa_wf_batch_new(curr_wf_batch->options,
curr_wf_batch->sa_index,
curr_wf_batch->writer_input,
sa_mapping_batch,
NULL);
}
return new_wf_batch;
}
static void report_vcf_variant_stats_sqlite3(sqlite3 *db, int num_variants, variant_stats_t **stats_batch) {
array_list_t *fields = array_list_new(num_variants + 1, 1.1, COLLECTION_MODE_ASYNCHRONIZED);
variant_stats_t *var_stats;
for (int i = 0; i < num_variants; i++) {
var_stats = stats_batch[i];
variant_stats_db_fields_t *f = variant_stats_db_fields_new(var_stats->chromosome, var_stats->position, var_stats->ref_allele, var_stats->alt_alleles,
var_stats->maf_allele, var_stats->maf, var_stats->mgf_genotype, var_stats->mgf,
var_stats->missing_alleles, var_stats->missing_genotypes,
var_stats->mendelian_errors, var_stats->is_indel,
var_stats->cases_percent_dominant, var_stats->controls_percent_dominant,
var_stats->cases_percent_recessive, var_stats->controls_percent_recessive);
array_list_insert(f, fields);
}
insert_variant_stats_db_fields_list(fields, db);
array_list_free(fields, (void *)variant_stats_db_fields_free);
}
workflow_t *workflow_new() {
workflow_t *wf = calloc(1, sizeof(workflow_t));
wf->num_threads = 0;
wf->max_num_work_items = 0;
wf->num_stages = 0;
wf->completed_producer = 0;
wf->num_pending_items = 0;
wf->running_producer = 0;
wf->running_consumer = 0;
pthread_mutex_init(&wf->producer_mutex, NULL);
pthread_mutex_init(&wf->consumer_mutex, NULL);
pthread_mutex_init(&wf->main_mutex, NULL);
wf->workflow_time = 0;
wf->producer_time = 0;
wf->consumer_time = 0;
wf->stage_times = NULL;
wf->pending_items = NULL;
wf->completed_items = array_list_new(100, 1.25f, COLLECTION_MODE_ASYNCHRONIZED);
wf->stage_functions = NULL;
wf->stage_labels = NULL;
wf->producer_function = NULL;
wf->producer_label = NULL;
wf->consumer_function = NULL;
wf->consumer_label = NULL;
wf->complete_extra_stage = 1;
//wf->status_function = workflow_get_status_;
return wf;
}
array_list_t* coverage_filter(array_list_t* input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void* f_args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
int min_coverage = ((coverage_filter_args*)f_args)->min_coverage;
LOG_DEBUG_F("coverage_filter (min coverage = %d) over %zu records\n", min_coverage, input_records->size);
char *aux_buffer = (char*) calloc (128, sizeof(char));
vcf_record_t *record;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
if (record->info_len > strlen(aux_buffer)) {
aux_buffer = realloc (aux_buffer, record->info_len+1);
memset(aux_buffer, 0, (record->info_len+1) * sizeof(char));
}
strncpy(aux_buffer, record->info, record->info_len);
char *record_coverage = get_field_value_in_info("DP", aux_buffer);
if (record_coverage != NULL && is_numeric(record_coverage)) {
if (atoi(record_coverage) >= min_coverage) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
free(aux_buffer);
return passed;
}
/*
require interface
*/
json_object * tg_shared_preferences_find_leaf_obj(SharedPreferences* thiz,const CHAR* key_path)
{
struct json_object *jso=NULL;
struct array_list* key_list = NULL;
INT32 key_list_len = 0;
INT32 idx = 0;
return_val_if_fail((thiz&&key_path),NULL);
if (strcmp(key_path,"/")==0)
return thiz->obj;
key_list = array_list_new(tg_shared_preferences_key_free);
return_val_if_fail((key_list),NULL);
return_val_if_fail(tg_shared_preferences_parse_keypath(key_path,key_list,&key_list_len),NULL);
for (jso=thiz->obj; idx<key_list_len &&jso; idx++)
{
jso = json_object_object_get(jso,(CHAR*)array_list_get_idx(key_list,idx));
}
array_list_free(key_list);
return jso;
}
array_list_t* quality_filter(array_list_t* input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void* f_args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
int min_quality = ((quality_filter_args*)f_args)->min_quality;
LOG_DEBUG_F("quality_filter (min quality = %d) over %zu records\n", min_quality, input_records->size);
vcf_record_t *record;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
if (record->quality >= min_quality) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
return passed;
}
vcf_record_t *vcf_record_copy(vcf_record_t *orig) {
vcf_record_t *record = (vcf_record_t*) calloc (1, sizeof(vcf_record_t));
record->chromosome = strndup(orig->chromosome, orig->chromosome_len);
record->chromosome_len = orig->chromosome_len;
record->position = orig->position;
record->id = strndup(orig->id, orig->id_len);
record->id_len = orig->id_len;
record->reference = strndup(orig->reference, orig->reference_len);
record->reference_len = orig->reference_len;
record->alternate = strndup(orig->alternate, orig->alternate_len);
record->alternate_len = orig->alternate_len;
record->filter = strndup(orig->filter, orig->filter_len);
record->filter_len = orig->filter_len;
record->info = strndup(orig->info, orig->info_len);
record->info_len = orig->info_len;
record->format = strndup(orig->format, orig->format_len);
record->format_len = orig->format_len;
record->samples = array_list_new(orig->samples->size + 1, 1.5, COLLECTION_MODE_ASYNCHRONIZED);
for (int i = 0; i < orig->samples->size; i++) {
array_list_insert(strdup(array_list_get(i, orig->samples)), record->samples);
}
return record;
}
array_list_t* missing_values_filter(array_list_t* input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void* args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
float max_missing = ((missing_values_filter_args*) args)->max_missing;
float record_missing;
float allele_count;
list_item_t *stats_item = NULL;
variant_stats_t *variant_stats;
// The stats returned by get_variants_stats are related to a record in the same
// position of the input_records list, so when a variant_stats_t fulfills the condition,
// it means the related vcf_record_t passes the filter
vcf_record_t *record;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
variant_stats = input_stats[i];
allele_count = 0;
for (int j = 0; j < variant_stats->num_alleles; j++) {
allele_count += variant_stats->alleles_count[j];
}
record_missing = variant_stats->missing_alleles / (allele_count + variant_stats->missing_alleles);
if (record_missing <= max_missing) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
return passed;
}
array_list_t *variant_type_filter(array_list_t *input_records, array_list_t *failed, variant_stats_t **input_stats, char *filter_name, void *f_args) {
assert(input_records);
assert(failed);
array_list_t *passed = array_list_new(input_records->size + 1, 1, COLLECTION_MODE_ASYNCHRONIZED);
size_t filter_name_len = strlen(filter_name);
enum variant_type type = ((variant_type_filter_args*)f_args)->type;
LOG_DEBUG_F("variant_type_filter (variant_type %d) over %zu records\n", type, input_records->size);
vcf_record_t *record;
for (int i = 0; i < input_records->size; i++) {
record = input_records->items[i];
if (record->type == type) {
array_list_insert(record, passed);
} else {
annotate_failed_record(filter_name, filter_name_len, record);
array_list_insert(record, failed);
}
}
return passed;
}
size_t bwt_search_pair_anchors(array_list_t *list, unsigned int read_length) {
bwt_anchor_t *bwt_anchor;
int max_anchor_length = 0;
bwt_anchor_t *bwt_anchor_back, *bwt_anchor_forw;
int anchor_length_tmp, anchor_back, anchor_forw;
int strand = 0, type = 0;
int found_anchor = 0, found_double_anchor = 0;
const int MIN_ANCHOR = 25;
const int MIN_SINGLE_ANCHOR = 40;
//const int MIN_DOUBLE_ANCHOR = MIN_ANCHOR*2;
const int MAX_BWT_REGIONS = 50;
const int MAX_BWT_ANCHOR_DISTANCE = 500000;
array_list_t *anchor_list_tmp, *forward_anchor_list, *backward_anchor_list;
cal_t *cal;
int seed_size, gap_read, gap_genome;
array_list_t *backward_anchor_list_0 = array_list_new(MAX_BWT_REGIONS, 1.25f, COLLECTION_MODE_ASYNCHRONIZED);
array_list_t *forward_anchor_list_0 = array_list_new(MAX_BWT_REGIONS, 1.25f , COLLECTION_MODE_ASYNCHRONIZED);
array_list_t *backward_anchor_list_1 = array_list_new(MAX_BWT_REGIONS, 1.25f, COLLECTION_MODE_ASYNCHRONIZED);
array_list_t *forward_anchor_list_1 = array_list_new(MAX_BWT_REGIONS, 1.25f , COLLECTION_MODE_ASYNCHRONIZED);
array_list_t *big_anchor_list = array_list_new(MAX_BWT_REGIONS, 1.25f , COLLECTION_MODE_ASYNCHRONIZED);
//printf("Tot Anchors %i\n", array_list_size(list));
for (int i = 0; i < array_list_size(list); i++) {
bwt_anchor = array_list_get(i, list);
if (bwt_anchor->strand == 1) {
//printf("(-)bwt anchor %i:%lu-%lu (%i): \n", bwt_anchor->chromosome + 1, bwt_anchor->start, bwt_anchor->end, bwt_anchor->end - bwt_anchor->start + 1);
if (bwt_anchor->type == FORWARD_ANCHOR) {
array_list_insert(bwt_anchor, forward_anchor_list_1);
//printf("FORW\n");
} else {
array_list_insert(bwt_anchor, backward_anchor_list_1);
//printf("BACK\n");
}
} else {
//printf("(+)bwt anchor %i:%lu-%lu (%i): \n", bwt_anchor->chromosome + 1, bwt_anchor->start, bwt_anchor->end, bwt_anchor->end - bwt_anchor->start + 1);
if (bwt_anchor->type == FORWARD_ANCHOR) {
array_list_insert(bwt_anchor, forward_anchor_list_0);
//printf("FORW\n");
} else {
array_list_insert(bwt_anchor, backward_anchor_list_0);
//printf("BACK\n");
}
}
anchor_length_tmp = bwt_anchor->end - bwt_anchor->start + 1;
if (anchor_length_tmp > MIN_SINGLE_ANCHOR && anchor_length_tmp > max_anchor_length) {
max_anchor_length = anchor_length_tmp;
found_anchor = 1;
strand = bwt_anchor->strand;
type = bwt_anchor->type;
}
if (read_length - anchor_length_tmp < 16) {
array_list_insert(bwt_anchor, big_anchor_list);
}
}
array_list_clear(list, NULL);
if (array_list_size(big_anchor_list) > 0) {
for (int i = array_list_size(big_anchor_list) - 1; i >= 0; i--) {
//printf("Insert cal %i\n", i);
bwt_anchor = array_list_remove_at(i, big_anchor_list);
size_t seed_size = bwt_anchor->end - bwt_anchor->start;
if (bwt_anchor->type == FORWARD_ANCHOR) {
cal = convert_bwt_anchor_to_CAL(bwt_anchor, 0, seed_size);
} else {
cal = convert_bwt_anchor_to_CAL(bwt_anchor, read_length - seed_size - 1, read_length - 1);
}
array_list_insert(cal, list);
}
array_list_set_flag(SINGLE_ANCHORS, list);
goto exit;
}
for (int type = 1; type >= 0; type--) {
if (!type) {
forward_anchor_list = forward_anchor_list_1;
backward_anchor_list = backward_anchor_list_1;
//printf("Strand (+): %i-%i\n", array_list_size(forward_anchor_list), array_list_size(backward_anchor_list));
} else {
forward_anchor_list = forward_anchor_list_0;
backward_anchor_list = backward_anchor_list_0;
//printf("Strand (-): %i-%i\n", array_list_size(forward_anchor_list), array_list_size(backward_anchor_list));
}
int *set_forward = (int *)calloc(array_list_size(forward_anchor_list), sizeof(int));
int *set_backward = (int *)calloc(array_list_size(backward_anchor_list), sizeof(int));
//Associate Anchors (+)/(-)
for (int i = 0; i < array_list_size(forward_anchor_list); i++) {
if (set_forward[i]) { continue; }
bwt_anchor_forw = array_list_get(i, forward_anchor_list);
for (int j = 0; j < array_list_size(backward_anchor_list); j++) {
if (set_backward[j]) { continue; }
bwt_anchor_back = array_list_get(j, backward_anchor_list);
anchor_forw = (bwt_anchor_forw->end - bwt_anchor_forw->start + 1);
anchor_back = (bwt_anchor_back->end - bwt_anchor_back->start + 1);
anchor_length_tmp = anchor_forw + anchor_back;
//printf("\tCommpare %i:%lu-%lu with %i:%lu-%lu\n", bwt_anchor_forw->chromosome + 1,
// bwt_anchor_forw->start, bwt_anchor_forw->end, bwt_anchor_back->chromosome + 1,
// bwt_anchor_back->start, bwt_anchor_back->end);
if (bwt_anchor_forw->chromosome == bwt_anchor_back->chromosome &&
abs(bwt_anchor_back->start - bwt_anchor_forw->end) <= MAX_BWT_ANCHOR_DISTANCE &&
anchor_forw >= MIN_ANCHOR && anchor_back >= MIN_ANCHOR) {
if (bwt_anchor_back->start < bwt_anchor_forw->end) { continue; }
gap_read = read_length - (anchor_forw + anchor_back);
gap_genome = bwt_anchor_back->start - bwt_anchor_forw->end;
//printf("anchor_forw = %i, anchor_back = %i, gap_read = %i, gap_genome = %i\n",
// anchor_forw, anchor_back, gap_read, gap_genome);
int apply_flank = 0;
if (gap_read < 2 || gap_genome < 2) {
int gap;
if (gap_read < 0 && gap_genome < 0) {
gap = abs(gap_read) > abs(gap_genome) ? abs(gap_read) : abs(gap_genome);
} else if (gap_read < 0) {
gap = abs(gap_read);
} else if (gap_genome < 0) {
gap = abs(gap_genome);
} else {
gap = 2;
}
int flank = 5;
apply_flank = 1;
if (abs(gap) >= flank*2) {
//Solve read overlap
flank = abs(gap)/2 + flank/2;
}
//printf("\tgap = %i, flank = %i\n", gap, flank);
if (flank >= anchor_forw) {
bwt_anchor_forw->end -= anchor_forw/2;
} else {
bwt_anchor_forw->end -= flank;
}
if (flank >= anchor_back) {
bwt_anchor_back->start += anchor_back/2;
} else {
bwt_anchor_back->start += flank;
}
}
cal = convert_bwt_anchor_to_CAL(bwt_anchor_forw, 0, bwt_anchor_forw->end - bwt_anchor_forw->start);
//printf("INSERT-1 (%i)[%i:%lu-%lu]\n", cal->strand, cal->chromosome_id, cal->start, cal->end);
array_list_insert(cal, list);
seed_size = bwt_anchor_back->end - bwt_anchor_back->start + 1;
//if (bwt_anchor_forw->end + read_length >= bwt_anchor_back->start) {
//seed_region_t *seed_region = seed_region_new(read_length - seed_size, read_length - 1,
//bwt_anchor_back->start, bwt_anchor_back->end, 1);
//cal->end = bwt_anchor_back->end;
//linked_list_insert_last(seed_region, cal->sr_list);
//} else {
cal = convert_bwt_anchor_to_CAL(bwt_anchor_back, read_length - seed_size, read_length - 1);
//printf("INSERT-2 (%i)[%i:%lu-%lu]\n", cal->strand, cal->chromosome_id, cal->start, cal->end);
array_list_insert(cal, list);
if (array_list_size(list) > 5) {
free(set_backward);
free(set_forward);
goto exit;
}
array_list_set_flag(DOUBLE_ANCHORS, list);
found_double_anchor = 1;
set_forward[i] = 1;
set_backward[j] = 1;
break;
}
}
}
free(set_backward);
free(set_forward);
}
if (!found_double_anchor && found_anchor) {
//Not Double anchor found but one Yes!!
if (strand == 1) {
if (type == FORWARD_ANCHOR) {
anchor_list_tmp = forward_anchor_list_1;
} else {
anchor_list_tmp = backward_anchor_list_1;
}
} else {
if (type == FORWARD_ANCHOR) {
anchor_list_tmp = forward_anchor_list_0;
} else {
anchor_list_tmp = backward_anchor_list_0;
}
}
//printf("LIST SIZE %i\n", array_list_size(anchor_list_tmp));
for (int i = 0; i < array_list_size(anchor_list_tmp); i++) {
bwt_anchor = array_list_get(i, anchor_list_tmp);
size_t seed_size = bwt_anchor->end - bwt_anchor->start;
//array_list_insert(bwt_anchor_new(bwt_anchor->strand, bwt_anchor->chromosome,
// bwt_anchor->start, bwt_anchor->end, bwt_anchor->type), anchor_list);
if (bwt_anchor->type == FORWARD_ANCHOR) {
//printf("------------------------> start %i\n", 0);
cal = convert_bwt_anchor_to_CAL(bwt_anchor, 0, seed_size);
} else {
//printf("------------------------> start %i\n", read_length - seed_size);
cal = convert_bwt_anchor_to_CAL(bwt_anchor, read_length - seed_size - 1, read_length - 1);
}
array_list_insert(cal, list);
}
array_list_set_flag(SINGLE_ANCHORS, list);
}
exit:
array_list_free(forward_anchor_list_1, (void *)bwt_anchor_free);
array_list_free(backward_anchor_list_1, (void *)bwt_anchor_free);
array_list_free(forward_anchor_list_0, (void *)bwt_anchor_free);
array_list_free(backward_anchor_list_0, (void *)bwt_anchor_free);
array_list_free(big_anchor_list, (void *)bwt_anchor_free);
return array_list_size(list);
}
vcf_record_t* vcf_record_new() {
vcf_record_t *record = (vcf_record_t*) calloc (1, sizeof(vcf_record_t));
record->samples = array_list_new(16, 1.5, COLLECTION_MODE_ASYNCHRONIZED);
return record;
}
int apply_sw_bs_4nt(sw_server_input_t* input, batch_t *batch) {
mapping_batch_t *mapping_batch = batch->mapping_batch;
genome_t *genome1 = input->genome1_p;
genome_t *genome2 = input->genome2_p;
sw_optarg_t *sw_optarg = &input->sw_optarg;
{
char r[1024];
size_t start = 169312417;
size_t end = start + 99;
genome_read_sequence_by_chr_index(r, 0,
0, &start, &end, genome2);
printf("+++++++++++++ genome2 = %s \n", r);
genome_read_sequence_by_chr_index(r, 0,
0, &start, &end, genome1);
printf("+++++++++++++ genome1 = %s \n", r);
}
// fill gaps between seeds
fill_gaps_bs(mapping_batch, sw_optarg, genome2, genome1, 20, 5, 1);
merge_seed_regions_bs(mapping_batch, 1);
fill_end_gaps_bs(mapping_batch, sw_optarg, genome1, genome2, 20, 400, 1);
fill_gaps_bs(mapping_batch, sw_optarg, genome1, genome2, 20, 5, 0);
merge_seed_regions_bs(mapping_batch, 0);
fill_end_gaps_bs(mapping_batch, sw_optarg, genome2, genome1, 20, 400, 0);
// now we can create the alignments
fastq_read_t *read;
array_list_t *fq_batch = mapping_batch->fq_batch;
char *match_seq, *match_qual;
size_t read_index, read_len, match_len, match_start;
cal_t *cal;
array_list_t *cal_list = NULL;
size_t num_cals;
seed_region_t *s;
cigar_code_t *cigar_code;
cigar_op_t *first_op;
float score, norm_score, min_score = input->min_score;
alignment_t *alignment;
array_list_t *alignment_list;
char *p, *optional_fields;
int optional_fields_length, AS;
array_list_t **mapping_lists;
size_t num_targets;
size_t *targets;
for (int bs_id = 0; bs_id < 2; bs_id++) {
if (bs_id == 0) {
mapping_lists = mapping_batch->mapping_lists;
num_targets = mapping_batch->num_targets;
targets = mapping_batch->targets;
} else {
mapping_lists = mapping_batch->mapping_lists2;
num_targets = mapping_batch->num_targets2;
targets = mapping_batch->targets2;
}
for (size_t i = 0; i < num_targets; i++) {
read_index = targets[i];
read = (fastq_read_t *) array_list_get(read_index, fq_batch);
cal_list = mapping_lists[read_index];
num_cals = array_list_size(cal_list);
if (num_cals <= 0) continue;
read_len = read->length;
alignment_list = array_list_new(num_cals, 1.25f, COLLECTION_MODE_ASYNCHRONIZED);
// processing each CAL from this read
for(size_t j = 0; j < num_cals; j++) {
// get cal and read index
cal = array_list_get(j, cal_list);
if (cal->sr_list->size == 0) continue;
s = (seed_region_t *) linked_list_get_first(cal->sr_list);
cigar_code = (cigar_code_t *) s->info;
norm_score = cigar_code_get_score(read_len, cigar_code);
score = norm_score * 100; //read_len;
LOG_DEBUG_F("score = %0.2f\n", norm_score);
// filter by SW score
if (norm_score > min_score) {
// update cigar and sequence and quality strings
cigar_code_update(cigar_code);
LOG_DEBUG_F("\tcigar code = %s\n", new_cigar_code_string(cigar_code));
match_start = 0;
match_len = cigar_code_nt_length(cigar_code);
first_op = cigar_code_get_first_op(cigar_code);
match_start = (first_op && first_op->name == 'H' ? first_op->number : 0);
match_seq = (char *) malloc((match_len + 1)* sizeof(char));
memcpy(match_seq, &read->sequence[match_start], match_len);
match_seq[match_len] = 0;
match_qual = (char *) malloc((match_len + 1)* sizeof(char));
memcpy(match_qual, &read->quality[match_start], match_len);
match_qual[match_len] = 0;
// set optional fields
optional_fields_length = 100;
optional_fields = (char *) calloc(optional_fields_length, sizeof(char));
p = optional_fields;
AS = (int) norm_score * 100;
sprintf(p, "ASi");
p += 3;
memcpy(p, &AS, sizeof(int));
p += sizeof(int);
sprintf(p, "NHi");
p += 3;
memcpy(p, &num_cals, sizeof(int));
p += sizeof(int);
sprintf(p, "NMi");
p += 3;
memcpy(p, &cigar_code->distance, sizeof(int));
p += sizeof(int);
assert(read->length == cigar_code_nt_length(cigar_code));
// create an alignment and insert it into the list
alignment = alignment_new();
//read_id = malloc(read->length);
size_t header_len = strlen(read->id);
char *head_id = (char *) malloc(header_len + 1);
get_to_first_blank(read->id, header_len, head_id);
alignment_init_single_end(head_id, match_seq, match_qual,
cal->strand, cal->chromosome_id - 1, cal->start - 1,
new_cigar_code_string(cigar_code),
cigar_code_get_num_ops(cigar_code),
norm_score * 254, 1, (num_cals > 1),
optional_fields_length, optional_fields, alignment);
array_list_insert(alignment, alignment_list);
LOG_DEBUG_F("creating alignment (bs_id = %i)...\n", bs_id);
//alignment_print(alignment);
}
}
// free the cal list, and update the mapping list with the alignment list
array_list_free(cal_list, (void *) cal_free);
mapping_lists[read_index] = alignment_list;
}
}
// go to the next stage
return BS_POST_PAIR_STAGE;
}
int main(int argc, char *argv[]) {
if (argc != 4) {
printf("Error.\n");
printf("Usage: %s index-dirname seq num-errors\n", argv[0]);
exit(-1);
}
char *index_dirname = argv[1];
char *seq = argv[2];
int num_errors = atoi(argv[3]);
// initializations
initReplaceTable();
bwt_optarg_t *bwt_optarg = bwt_optarg_new(num_errors, 1, 10000, 1, 0, 0);
bwt_index_t *bwt_index = bwt_index_new(index_dirname);
// seq
{
array_list_t *mapping_list = array_list_new(100000, 1.25f,
COLLECTION_MODE_SYNCHRONIZED);
size_t num_mappings;
num_mappings = bwt_map_seq(seq, bwt_optarg,
bwt_index, mapping_list);
printf("seq: %s\n", seq);
printf("num_mappings = %lu\n", num_mappings);
for (size_t i = 0; i < num_mappings; i++) {
printf("%lu\t---------------------\n", i);
alignment_print(array_list_get(i, mapping_list));
}
}
// seed
{
array_list_t *mapping_list = array_list_new(100000, 1.25f,
COLLECTION_MODE_SYNCHRONIZED);
size_t num_mappings;
size_t len = strlen(seq);
char *code_seq = (char *) calloc(len + 10, sizeof(char));
replaceBases(seq, code_seq, len);
num_mappings = bwt_map_exact_seeds_seq(code_seq, 18, 16,
bwt_optarg, bwt_index, mapping_list);
region_t *region;
for (size_t i = 0; i < num_mappings; i++) {
region = array_list_get(i, mapping_list);
printf("Region: chr = %lu, strand = %d, start = %lu, end = %lu\n",
region->chromosome_id, region->strand, region->start, region->end);
}
}
printf("Done.\n");
}
void apply_sw(sw_server_input_t* input, aligner_batch_t *batch) {
// printf("START: apply_sw\n");
int tid = omp_get_thread_num();
cal_t *cal = NULL;
array_list_t *cal_list = NULL, *mapping_list = NULL;//, *old_list = NULL, *new_list = NULL;
fastq_batch_t *fq_batch = batch->fq_batch;
size_t start, end;
genome_t *genome = input->genome_p;
size_t flank_length = input->flank_length;
// SIMD support for Smith-Waterman
float score, min_score = input->min_score;
// size_t curr_depth = 0;
sw_output_t *sw_output;
// sw_simd_input_t *sw_sinput = sw_simd_input_new(SIMD_DEPTH);
// sw_simd_output_t *sw_soutput = sw_simd_output_new(SIMD_DEPTH);
//sw_simd_context_t *context = sw_simd_context_new(input->match, input->mismatch,
// input->gap_open, input->gap_extend);
// for tracking the current read, cal being processed using sw_channel_t
//sw_channel_t *channel;
//sw_channel_t sw_channels[SIMD_DEPTH];
//memset(sw_channels, 0, sizeof(sw_channels));
//size_t header_len, read_len;
//size_t strands[SIMD_DEPTH], chromosomes[SIMD_DEPTH], starts[SIMD_DEPTH];
size_t index, num_cals;
size_t total = 0, valids = 0;
size_t num_seqs = batch->num_targets;
// set to zero
batch->num_done = batch->num_to_do;
batch->num_to_do = 0;
size_t sw_total = batch->num_done;
/*
// for all seqs pending to process !!
size_t sw_total = 0;
for (size_t i = 0; i < num_seqs; i++) {
sw_total += array_list_size(batch->mapping_lists[batch->targets[i]]);
}
printf("number of sw to run: %d (vs num_done = %d)\n", sw_total, batch->num_done);
*/
sw_optarg_t *sw_optarg = &input->sw_optarg;
/*
sw_optarg_t sw_optarg; //= sw_optarg_new(gap_open, gap_extend, matrix_filename);
sw_optarg.gap_open = input->gap_open;
sw_optarg.gap_extend = input->gap_extend;
sw_optarg.subst_matrix['A']['A'] = input->match; sw_optarg.subst_matrix['C']['A'] = input->mismatch; sw_optarg.subst_matrix['T']['A'] = input->mismatch; sw_optarg.subst_matrix['G']['A'] = input->mismatch;
sw_optarg.subst_matrix['A']['C'] = input->mismatch; sw_optarg.subst_matrix['C']['C'] = input->match; sw_optarg.subst_matrix['T']['C'] = input->mismatch; sw_optarg.subst_matrix['G']['C'] = input->mismatch;
sw_optarg.subst_matrix['A']['G'] = input->mismatch; sw_optarg.subst_matrix['C']['T'] = input->mismatch; sw_optarg.subst_matrix['T']['T'] = input->match; sw_optarg.subst_matrix['G']['T'] = input->mismatch;
sw_optarg.subst_matrix['A']['T'] = input->mismatch; sw_optarg.subst_matrix['C']['G'] = input->mismatch; sw_optarg.subst_matrix['T']['G'] = input->mismatch; sw_optarg.subst_matrix['G']['G'] = input->match;
*/
sw_multi_output_t *output = sw_multi_output_new(sw_total);
char *q[sw_total], *r[sw_total];
uint8_t strands[sw_total], chromosomes[sw_total];
size_t starts[sw_total];
size_t sw_count = 0, read_indices[sw_total];
int read_len;
// debugging: to kown how many reads are not mapped by SW score
// int unmapped_by_score[fq_batch->num_reads];
// memset(unmapped_by_score, 0, fq_batch->num_reads * sizeof(int));
// printf("num of sw to do: %i\n", sw_total);
// initialize query and reference sequences to Smith-Waterman
for (size_t i = 0; i < num_seqs; i++) {
index = batch->targets[i];
cal_list = batch->mapping_lists[index];
num_cals = array_list_size(cal_list);
// printf("sw_server: read #%i with %i cals\n", index, num_cals);
// processing each CAL from this read
for(size_t j = 0; j < num_cals; j++) {
// get cal and read index
cal = array_list_get(j, cal_list);
read_indices[sw_count] = index;
// query sequence, revcomp if necessary
read_len = fq_batch->data_indices[index + 1] - fq_batch->data_indices[index];
q[sw_count] = (char *) calloc((read_len + 1), sizeof(char));
memcpy(q[sw_count], &(fq_batch->seq[fq_batch->data_indices[index]]), read_len);
if (cal->strand == 1) {
seq_reverse_complementary(q[sw_count], read_len);
}
//q[sw_count] = &(fq_batch->seq[fq_batch->data_indices[index]]);
// reference sequence
//printf("\tSW: %d.[chromosome:%d]-[strand:%d]-[start:%d, end:%d]\n", j, cal->chromosome_id, cal->strand, cal->start, cal->end);
start = cal->start - flank_length;
end = cal->end + flank_length;
r[sw_count] = calloc(1, end - start + 2);
genome_read_sequence_by_chr_index(r[sw_count], cal->strand,
cal->chromosome_id - 1, &start, &end, genome);
// save some stuff, we'll use them after...
strands[sw_count] = cal->strand;
chromosomes[sw_count] = cal->chromosome_id;
starts[sw_count] = start;
// printf("read #%i (sw #%i): query: %s (%i)\nref : %s (%i)\n\n", index, sw_count, q[sw_count], strlen(q[sw_count]), r[sw_count], strlen(r[sw_count]));
// increase counter
sw_count++;
}
// free cal_list
array_list_free(cal_list, (void *)cal_free);
batch->mapping_lists[index] = NULL;
}
// run Smith-Waterman
// printf("before smith_waterman: number of sw = %i\n", sw_total);
smith_waterman_mqmr(q, r, sw_total, sw_optarg, 1, output);
// printf("after smith_waterman\n");
/*
// debugging
{
FILE *fd = fopen("sw.out", "w");
sw_multi_output_save(sw_total, output, fd);
fclose(fd);
}
*/
size_t num_targets = 0;
// filter alignments by min_score
for (size_t i = 0; i < sw_total; i++) {
// score = output->score_p[i] / (strlen(output->query_map_p[i]) * input->match);
// if (score >= min_score) {
/*
printf("--------------------------------------------------------------\n");
printf("Smith-Waterman results:\n");
printf("id\t%s\n", &(batch->fq_batch->header[batch->fq_batch->header_indices[read_indices[i]]]));
printf("ref\n%s\n", r[i]);
printf("query\n%s\n", q[i]);
printf("map\n%s\n", output->ref_map_p[i]);
printf("ref: chr = %d, strand = %d, start = %d, len = %d\n", chromosomes[i], strands[i], starts[i], strlen(r[i]));
printf("query-map-start = %d, ref-map-start = %d\n",
output->query_start_p[i], output->ref_start_p[i]);
printf("score = %0.2f (min. score = %0.2f)\n", output->score_p[i], min_score);
printf("--------------------------------------------------------------\n");
*/
if (output->score_p[i] >= min_score) {
// valid mappings,
//insert in the list for further processing
index = read_indices[i];
if (batch->mapping_lists[index] == NULL) {
mapping_list = array_list_new(1000,
1.25f,
COLLECTION_MODE_ASYNCHRONIZED);
array_list_set_flag(0, mapping_list);
batch->mapping_lists[index] = mapping_list;
batch->targets[num_targets++] = index;
}
sw_output = sw_output_new(strands[i],
chromosomes[i],
starts[i],
strlen(r[i]),
strlen(output->query_map_p[i]),
output->query_start_p[i],
output->ref_start_p[i],
output->score_p[i],
score,
output->query_map_p[i],
output->ref_map_p[i]);
array_list_insert(sw_output, mapping_list);
batch->num_to_do++;
// debugging
//unmapped_by_score[index] = 1;
}
// free query and reference
free(q[i]);
free(r[i]);
}
batch->num_targets = num_targets;
/*
// debugging
for (size_t i = 0; i < fq_batch->num_reads; i++) {
if (unmapped_by_score[i] == 0) {
unmapped_by_score_counter[tid]++;
//printf("by score: %s\n", &(batch->fq_batch->header[batch->fq_batch->header_indices[index]]));
}
}
*/
// update counter
thr_sw_items[tid] += sw_count;
// free
sw_multi_output_free(output);
// printf("END: apply_sw, (%d Smith-Waterman, %d valids)\n", total, valids);
}