static int initialize_output_files(char *output_directory, size_t output_directory_len, cp_hashtable **output_files) {
// Initialize collections of file descriptors
*output_files = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
50,
cp_hash_int,
(cp_compare_fn) int_cmp,
NULL,
(cp_destructor_fn) free_file_key1,
NULL,
(cp_destructor_fn) free_file_descriptor
);
char all_variants_filename[output_directory_len + 18];
sprintf(all_variants_filename, "%s/all_variants.txt", output_directory);
FILE *all_variants_file = fopen(all_variants_filename, "a");
if (!all_variants_file) { // Can't store results
return 1;
}
char *key = (char*) calloc (13, sizeof(char));
strncat(key, "all_variants", 12);
cp_hashtable_put(*output_files, key, all_variants_file);
char summary_filename[output_directory_len + 13];
sprintf(summary_filename, "%s/summary.txt", output_directory);
FILE *summary_file = fopen(summary_filename, "a");
if (!summary_file) { // Can't store results
return 2;
}
key = (char*) calloc (8, sizeof(char));
strncat(key, "summary", 7);
cp_hashtable_put(*output_files, key, summary_file);
char snp_phenotype_filename[output_directory_len + 20];
sprintf(snp_phenotype_filename, "%s/snp_phenotypes.txt", output_directory);
FILE *snp_phenotype_file = fopen(snp_phenotype_filename, "a");
if (!snp_phenotype_filename) {
return 3;
}
key = (char*) calloc (15, sizeof(char));
strncat(key, "snp_phenotypes", 14);
cp_hashtable_put(*output_files, key, snp_phenotype_file);
char mutation_phenotype_filename[output_directory_len + 25];
sprintf(mutation_phenotype_filename, "%s/mutation_phenotypes.txt", output_directory);
FILE *mutation_phenotype_file = fopen(mutation_phenotype_filename, "a");
if (!mutation_phenotype_filename) {
return 3;
}
key = (char*) calloc (20, sizeof(char));
strncat(key, "mutation_phenotypes", 19);
cp_hashtable_put(*output_files, key, mutation_phenotype_file);
return 0;
}
cp_hashtable *load_hasthable_codes() {
cp_hashtable *t = cp_hashtable_create(400,
cp_hash_istring,
(cp_compare_fn)strcasecmp);
/*const unsigned char COMBINATORIAL = (NUCLEOTIDES_NUM * NUCLEOTIDES_NUM * NUCLEOTIDES_NUM) + (NUCLEOTIDES_NUM * NUCLEOTIDES_NUM) + NUCLEOTIDES_NUM;
unsigned char *id_array = (unsigned char *)malloc(sizeof(unsigned char)*COMBINATORIAL);
*/
size_t id = 0;
char combination[4];
combination[3] = '\0';
for(unsigned int nt_1 = 0; nt_1 < NUCLEOTIDES_NUM; nt_1++){
combination[0] = NUCLEOTIDES[nt_1];
for(unsigned int nt_2 = 0; nt_2 < NUCLEOTIDES_NUM; nt_2++){
combination[1] = NUCLEOTIDES[nt_2];
for(unsigned int nt_3 = 0; nt_3 < NUCLEOTIDES_NUM; nt_3++){
combination[2] = NUCLEOTIDES[nt_3];
cp_hashtable_put(t, strdup(combination), (void *)id);
id++;
}
}
}
// printf("Table size %d\n", t->table_size);
combination[2] = '\0';
for(unsigned int nt_1 = 0; nt_1 < NUCLEOTIDES_NUM; nt_1++){
combination[0] = NUCLEOTIDES[nt_1];
for(unsigned int nt_2 = 0; nt_2 < NUCLEOTIDES_NUM; nt_2++){
combination[1] = NUCLEOTIDES[nt_2];
cp_hashtable_put(t, strdup(combination), (void *)id);
id++;
}
}
//printf("Table size %d\n", t->table_size);
combination[1] = '\0';
for(unsigned int nt = 0; nt < NUCLEOTIDES_NUM; nt++){
combination[0] = NUCLEOTIDES[nt];
cp_hashtable_put(t, strdup(combination), (void *)id);
id++;
}
return t;
}
cp_hashtable* associate_samples_and_positions(vcf_file_t* file) {
LOG_DEBUG_F("** %zu sample names read\n", file->samples_names->size);
array_list_t *sample_names = file->samples_names;
cp_hashtable *sample_ids = cp_hashtable_create(sample_names->size * 2,
cp_hash_string,
(cp_compare_fn) strcasecmp
);
int *index;
char *name;
for (int i = 0; i < sample_names->size; i++) {
name = sample_names->items[i];
index = (int*) malloc (sizeof(int)); *index = i;
if (cp_hashtable_get(sample_ids, name)) {
LOG_FATAL_F("Sample %s appears more than once. File can not be analyzed.\n", name);
}
cp_hashtable_put(sample_ids, name, index);
}
// char **keys = (char**) cp_hashtable_get_keys(sample_ids);
// int num_keys = cp_hashtable_count(sample_ids);
// for (int i = 0; i < num_keys; i++) {
// printf("%s\t%d\n", keys[i], *((int*) cp_hashtable_get(sample_ids, keys[i])));
// }
return sample_ids;
}
static long get_thread_serial(long tno)
{
long *num;
if (thread_id == NULL) return 0;
num = cp_hashtable_get(thread_id, &tno);
if (num == NULL)
{
long *key;
num = malloc(sizeof(long));
if (num == NULL)
{
cp_error(CP_MEMORY_ALLOCATION_FAILURE, "can\'t allocate thread mapping number");
return -1L;
}
key = malloc(sizeof(long));
if (key == NULL)
{
cp_error(CP_MEMORY_ALLOCATION_FAILURE, "can\'t allocate thread mapping key");
return -1L;
}
*num = ++thread_count;
*key = tno;
cp_hashtable_put(thread_id, key, num);
}
return *num;
}
void *writer(void *prm)
{
int i, num;
long count = (long) prm;
char kbuf[30];
char *entry;
cp_mutex_lock(&start_mutex);
while (!running)
cp_cond_wait(&start_cond, &start_mutex);
cp_mutex_unlock(&start_mutex);
for (i = 0; i < count; i++)
{
sprintf(kbuf, "ENTRY %d", i);
entry = strdup(kbuf);
num = i % COUNT;
if (!silent)
printf("writing (%d): %s\n", num, entry);
cp_mutex_lock(&lock[i % COUNT]);
cp_hashtable_put(t[num], entry, entry);
cp_list_append(tl[num], entry);
cp_cond_broadcast(&cond[i % COUNT]);
cp_mutex_unlock(&lock[i % COUNT]);
}
return NULL;
}
int load_mime_types(char *filename)
{
FILE *fp;
char mimebuf[LINELEN];
int rc = 0;
char *name;
char *ext;
char *curr;
mimemap =
cp_hashtable_create_by_option(COLLECTION_MODE_NOSYNC |
COLLECTION_MODE_COPY |
COLLECTION_MODE_DEEP,
500,
cp_hash_string,
cp_hash_compare_string,
(cp_copy_fn) strdup,
(cp_destructor_fn) free,
(cp_copy_fn) strdup,
(cp_destructor_fn) free);
fp = fopen(filename, "r");
if (fp == NULL)
{
cp_error(CP_INVALID_VALUE, "can\'t open %s", filename);
cp_hashtable_destroy(mimemap);
return -1;
}
while (fgets(mimebuf, LINELEN, fp))
{
if (mimebuf[0] == '#') continue;
name = curr = mimebuf;
while (*curr && !isspace(*curr)) curr++;
if (*curr == '\0') continue; /* no extension for this type */
*curr++ = '\0';
while (1)
{
while (*curr && isspace(*curr)) curr++;
ext = curr;
while (*curr && !isspace(*curr)) curr++;
if (strlen(ext))
{
*curr++ = '\0';
cp_hashtable_put(mimemap, ext, name);
}
else
break;
}
}
fclose(fp);
return rc;
}
int cp_log_init(char *filename, int verbosity)
{
int i, err_code_count;
unsigned long thread_no;
#ifdef SIGHUP
struct sigaction act;
#endif
log_filename = strdup(filename);
logfile = fopen(filename, "a+");
if (logfile == NULL)
return CP_LOG_FILE_OPEN_FAILURE;
loglevel = verbosity;
err_code_count = sizeof(error_messages) / sizeof(error_code_legend);
error_message_lookup =
cp_hashtable_create_by_mode(COLLECTION_MODE_NOSYNC,
err_code_count * 2,
cp_hash_int,
cp_hash_compare_int);
for (i = 0; i < err_code_count; i++)
{
error_code_legend *entry = &error_messages[i];
cp_hashtable_put(error_message_lookup, &entry->code, entry->msg);
}
thread_id =
cp_hashtable_create_by_option(COLLECTION_MODE_DEEP, 10,
cp_hash_long, cp_hash_compare_long,
NULL, free, NULL, free);
thread_count = 0;
// thread_no = (unsigned long) pthread_self();
thread_no = (unsigned long) cp_thread_self();
get_thread_serial(thread_no); /* establish this as thread number one */
log_closing = 0;
#ifdef SIGHUP
act.sa_handler = cp_log_default_signal_handler;
sigemptyset(&act.sa_mask);
act.sa_flags = 0;
sigaction(SIGHUP, &act, NULL);
#endif
// signal(SIGHUP, cp_log_default_signal_handler);
return 0;
}
static void parse_effect_response(int tid, char *output_directory, size_t output_directory_len, cp_hashtable *output_files,
list_t *output_list, cp_hashtable *summary_count, cp_hashtable *gene_list) {
int *SO_found = (int*) malloc (sizeof(int)); // Whether the SO code field has been found
int *count;
char tmp_consequence_type[128];
int num_lines;
char **split_batch = split(effect_line[tid], "\n", &num_lines);
for (int i = 0; i < num_lines; i++) {
int num_columns;
char *copy_buf = strdup(split_batch[i]);
char **split_result = split(copy_buf, "\t", &num_columns);
free(copy_buf);
// Find consequence type name (always after SO field)
*SO_found = 0;
if (num_columns == 25) {
// LOG_DEBUG_F("gene = %s\tSO = %d\tCT = %s\n", split_result[17], atoi(split_result[18] + 3), split_result[19]);
if (!cp_hashtable_contains(gene_list, split_result[17])) {
cp_hashtable_put(gene_list, strdup(split_result[17]), NULL);
}
*SO_found = atoi(split_result[18] + 3);
memset(tmp_consequence_type, 0, 128 * sizeof(char));
strncat(tmp_consequence_type, split_result[19], strlen(split_result[19]));
} else {
if (strlen(split_batch[i]) == 0) { // Last line in batch could be only a newline
for (int s = 0; s < num_columns; s++) {
free(split_result[s]);
}
free(split_result);
continue;
}
LOG_INFO_F("[%d] Non-valid line found (%d fields): '%s'\n", tid, num_columns, split_batch[i]);
for (int s = 0; s < num_columns; s++) {
free(split_result[s]);
}
free(split_result);
continue;
}
for (int s = 0; s < num_columns; s++) {
free(split_result[s]);
}
free(split_result);
if (!*SO_found) { // SO:000000 is not valid
LOG_INFO_F("[%d] Non-valid SO found (0)\n", tid);
continue;
}
// LOG_DEBUG_F("[%d] SO found = %d\n", tid, *SO_found);
size_t consequence_type_len = strlen(tmp_consequence_type);
// If file does not exist, create its descriptor and summary counter
FILE *aux_file = cp_hashtable_get(output_files, SO_found);
if (!aux_file) {
#pragma omp critical
{
// This construction avoids 2 threads trying to insert the same CT
aux_file = cp_hashtable_get(output_files, SO_found);
if (!aux_file) {
char filename[output_directory_len + consequence_type_len + 6];
memset(filename, 0, (output_directory_len + consequence_type_len + 6) * sizeof(char));
strncat(filename, output_directory, output_directory_len);
strncat(filename, "/", 1);
strncat(filename, tmp_consequence_type, consequence_type_len);
strncat(filename, ".txt", 4);
aux_file = fopen(filename, "a");
// Add to hashtables (file descriptors and summary counters)
int *SO_stored = (int*) malloc (sizeof(int));
*SO_stored = *SO_found;
cp_hashtable_put(output_files, SO_stored, aux_file);
LOG_INFO_F("[%d] New consequence type found = %s\n", tid, tmp_consequence_type);
}
}
}
// Write line[tid] to file corresponding to its consequence type
if (aux_file) {
#pragma omp critical
{
// TODO move critical one level below?
count = (int*) cp_hashtable_get(summary_count, tmp_consequence_type);
if (count == NULL) {
char *consequence_type = (char*) calloc (consequence_type_len+1, sizeof(char));
strncat(consequence_type, tmp_consequence_type, consequence_type_len);
assert(!strcmp(consequence_type, tmp_consequence_type));
count = (int*) malloc (sizeof(int));
*count = 0;
cp_hashtable_put(summary_count, consequence_type, count);
// LOG_DEBUG_F("[%d] Initialized summary count for %s\n", tmp_consequence_type);
}
// Increment counter for summary
(*count)++;
}
// LOG_DEBUG_F("[%d] before writing %s\n", tid, tmp_consequence_type);
list_item_t *output_item = list_item_new(tid, *SO_found, strdup(split_batch[i]));
list_insert_item(output_item, output_list);
// LOG_DEBUG_F("[%d] after writing %s\n", tid, tmp_consequence_type);
}
}
for (int i = 0; i < num_lines; i++) {
free(split_batch[i]);
}
free(split_batch);
}
int initialize_ws_output(shared_options_data_t *shared_options, effect_options_data_t *options_data){
int num_threads = shared_options->num_threads;
char *outdir = shared_options->output_directory;
// Initialize output text list
output_list = (list_t*) malloc (sizeof(list_t));
list_init("output", num_threads, shared_options->max_batches * shared_options->batch_lines, output_list);
// Initialize collections of file descriptors
output_files = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
50,
cp_hash_int,
(cp_compare_fn) int_cmp,
NULL,
(cp_destructor_fn) free_file_key1,
NULL,
(cp_destructor_fn) free_file_descriptor
);
char all_variants_filename[strlen(outdir) + 18];
sprintf(all_variants_filename, "%s/all_variants.txt", outdir);
all_variants_file = fopen(all_variants_filename, "a");
if (!all_variants_file) { // Can't store results
return 1;
}
char *key = (char*) calloc (13, sizeof(char));
strncat(key, "all_variants", 12);
cp_hashtable_put(output_files, key, all_variants_file);
char summary_filename[strlen(outdir) + 13];
sprintf(summary_filename, "%s/summary.txt", outdir);
summary_file = fopen(summary_filename, "a");
if (!summary_file) { // Can't store results
return 2;
}
key = (char*) calloc (8, sizeof(char));
strncat(key, "summary", 7);
cp_hashtable_put(output_files, key, summary_file);
char snp_phenotype_filename[strlen(outdir) + 20];
sprintf(snp_phenotype_filename, "%s/snp_phenotypes.txt", outdir);
snp_phenotype_file = fopen(snp_phenotype_filename, "a");
if (!snp_phenotype_filename) {
return 3;
}
key = (char*) calloc (15, sizeof(char));
strncat(key, "snp_phenotypes", 14);
cp_hashtable_put(output_files, key, snp_phenotype_file);
char mutation_phenotype_filename[strlen(outdir) + 25];
sprintf(mutation_phenotype_filename, "%s/mutation_phenotypes.txt", outdir);
mutation_phenotype_file = fopen(mutation_phenotype_filename, "a");
if (!mutation_phenotype_filename) {
return 3;
}
key = (char*) calloc (20, sizeof(char));
strncat(key, "mutation_phenotypes", 19);
cp_hashtable_put(output_files, key, mutation_phenotype_file);
// Initialize summary counters and genes list
summary_count = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
64,
cp_hash_istring,
(cp_compare_fn) strcasecmp,
NULL,
(cp_destructor_fn) free_file_key2,
NULL,
(cp_destructor_fn) free_summary_counter
);
gene_list = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
64,
cp_hash_istring,
(cp_compare_fn) strcasecmp,
NULL,
(cp_destructor_fn) free_file_key2,
NULL,
NULL
);
// Create a buffer for each thread
line = (char**) calloc (num_threads, sizeof(char*));
output_line = (char**) calloc (num_threads, sizeof(char*));
max_line_size = (int*) calloc (num_threads, sizeof(int));
snp_line = (char**) calloc (num_threads, sizeof(char*));
snp_output_line = (char**) calloc (num_threads, sizeof(char*));
snp_max_line_size = (int*) calloc (num_threads, sizeof(int));
mutation_line = (char**) calloc (num_threads, sizeof(char*));
mutation_output_line = (char**) calloc (num_threads, sizeof(char*));
mutation_max_line_size = (int*) calloc (num_threads, sizeof(int));
for (int i = 0; i < num_threads; i++) {
max_line_size[i] = snp_max_line_size[i] = mutation_max_line_size[i] = 512;
line[i] = (char*) calloc (max_line_size[i], sizeof(char));
output_line[i] = (char*) calloc (max_line_size[i], sizeof(char));
snp_line[i] = (char*) calloc (snp_max_line_size[i], sizeof(char));
snp_output_line[i] = (char*) calloc (snp_max_line_size[i], sizeof(char));
mutation_line[i] = (char*) calloc (mutation_max_line_size[i], sizeof(char));
mutation_output_line[i] = (char*) calloc (mutation_max_line_size[i], sizeof(char));
}
return 0;
}
static size_t write_effect_ws_results(char *contents, size_t size, size_t nmemb, void *userdata) {
int tid = omp_get_thread_num();
int i = 0;
int data_read_len = 0, next_line_len = 0;
// Whether the SO code field (previous to the consequence type name) has been found
int *SO_found = (int*) malloc (sizeof(int));
// Whether the buffer was consumed with a line read just partially
int premature_end = 0;
size_t realsize = size * nmemb;
int *count;
char *data = contents;
char tmp_consequence_type[128];
char *aux_buffer;
char *output_text;
LOG_DEBUG_F("Effect WS invoked, response size = %zu bytes\n", realsize);
while (data_read_len < realsize) {
assert((line + tid) != NULL);
assert((max_line_size + tid) != NULL);
LOG_DEBUG_F("[%d] loop iteration #%d\n", tid, i);
// Get length of data to copy
next_line_len = strcspn(data, "\n");
// If the line[tid] is too long for the current buffers, reallocate a little more than the needed memory
if (strlen(line[tid]) + next_line_len + 1 > max_line_size[tid]) {
// LOG_DEBUG_F("Line too long (%d elements, but %zu needed) in batch #%d\n",
// max_line_size[tid], strlen(line[tid]) + next_line_len, batch_num);
// char *out_buf = (char*) calloc (next_line_len+1, sizeof(char));
// snprintf(out_buf, next_line_len, "%s", data);
// LOG_INFO_F("[%d] too big data is: '%s'\n", tid, out_buf);
char *aux_1 = (char*) realloc (line[tid], (max_line_size[tid] + next_line_len + 1) * sizeof(char));
char *aux_2 = (char*) realloc (output_line[tid], (max_line_size[tid] + next_line_len + 1) * sizeof(char));
if (!aux_1 || !aux_2) {
LOG_ERROR("Can't resize buffers\n");
// Can't resize buffers -> can't keep reading the file
if (!aux_1) { free(line[tid]); }
if (!aux_2) { free(output_line[tid]); }
return data_read_len;
}
line[tid] = aux_1;
output_line[tid] = aux_2;
max_line_size[tid] += next_line_len + 1;
// LOG_DEBUG_F("[%d] buffers realloc'd (%d)\n", tid, max_line_size[tid]);
}
// LOG_DEBUG_F("[%d] position = %d, read = %d, max_size = %zu\n", i, next_line_len, data_read_len, realsize);
if (data_read_len + next_line_len >= realsize) {
// Save current state (line[tid] partially read)
strncat(line[tid], data, next_line_len);
chomp(line[tid]);
line[tid][strlen(line[tid])] = '\0';
premature_end = 1;
// LOG_DEBUG_F("widow line[tid] = '%s'\n", line[tid]);
data_read_len = realsize;
break;
}
strncat(line[tid], data, next_line_len);
strncat(output_line[tid], line[tid], strlen(line[tid]));
// LOG_DEBUG_F("[%d] copy to buffer (%zu)\n", tid, strlen(line[tid]));
int num_substrings;
char *copy_buf = strdup(line[tid]);
// char *copy_buf = strdup(trim(line[tid]));
char **split_result = split(copy_buf, "\t", &num_substrings);
free(copy_buf);
// Find consequence type name (always after SO field)
*SO_found = 0;
if (num_substrings == 25) {
// LOG_DEBUG_F("gene = %s\tSO = %d\tCT = %s\n", split_result[17], atoi(split_result[18] + 3), split_result[19]);
if (!cp_hashtable_contains(gene_list, split_result[17])) {
cp_hashtable_put(gene_list, strdup(split_result[17]), NULL);
}
*SO_found = atoi(split_result[18] + 3);
memset(tmp_consequence_type, 0, 128 * sizeof(char));
strncat(tmp_consequence_type, split_result[19], strlen(split_result[19]));
} else {
LOG_INFO_F("[%d] Non-valid line found (%d fields): '%s'\n", tid, num_substrings, line[tid]);
memset(line[tid], 0, strlen(line[tid]));
memset(output_line[tid], 0, strlen(output_line[tid]));
// #pragma omp critical
// {
// printf("********\n");
// LOG_INFO_F("[%d] Non-valid line found (%d fields): '%s'\n", tid, num_substrings, line[tid]);
for (int s = 0; s < num_substrings; s++) {
// printf("%s^", split_result[s]);
free(split_result[s]);
}
// printf("********\n\n");
free(split_result);
// }
continue;
}
for (int s = 0; s < num_substrings; s++) {
free(split_result[s]);
}
free(split_result);
if (!*SO_found) { // SO:000000 is not valid
LOG_INFO_F("[%d] Non-valid SO found (0)\n", tid);
memset(line[tid], 0, strlen(line[tid]));
memset(output_line[tid], 0, strlen(output_line[tid]));
continue;
}
// LOG_DEBUG_F("[%d] SO found = %d\n", tid, *SO_found);
size_t consequence_type_len = strlen(tmp_consequence_type);
// If file does not exist, create its descriptor and summary counter
FILE *aux_file = cp_hashtable_get(output_files, SO_found);
if (!aux_file) {
#pragma omp critical
{
// This construction avoids 2 threads trying to insert the same CT
aux_file = cp_hashtable_get(output_files, SO_found);
if (!aux_file) {
char filename[output_directory_len + consequence_type_len + 6];
memset(filename, 0, (output_directory_len + consequence_type_len + 6) * sizeof(char));
strncat(filename, output_directory, output_directory_len);
strncat(filename, "/", 1);
strncat(filename, tmp_consequence_type, consequence_type_len);
strncat(filename, ".txt", 4);
aux_file = fopen(filename, "a");
// Add to hashtables (file descriptors and summary counters)
int *SO_stored = (int*) malloc (sizeof(int));
*SO_stored = *SO_found;
cp_hashtable_put(output_files, SO_stored, aux_file);
LOG_INFO_F("[%d] new CT = %s\n", tid, tmp_consequence_type);
}
}
}
// Write line[tid] to file corresponding to its consequence type
if (aux_file) {
#pragma omp critical
{
// TODO move critical one level below?
count = (int*) cp_hashtable_get(summary_count, tmp_consequence_type);
if (count == NULL) {
char *consequence_type = (char*) calloc (consequence_type_len+1, sizeof(char));
strncat(consequence_type, tmp_consequence_type, consequence_type_len);
assert(!strcmp(consequence_type, tmp_consequence_type));
count = (int*) malloc (sizeof(int));
*count = 0;
cp_hashtable_put(summary_count, consequence_type, count);
// LOG_DEBUG_F("[%d] Initialized summary count for %s\n", tmp_consequence_type);
}
// Increment counter for summary
(*count)++;
}
// LOG_DEBUG_F("[%d] before writing %s\n", tid, tmp_consequence_type);
output_text = strdup(output_line[tid]);
list_item_t *output_item = list_item_new(tid, *SO_found, output_text);
list_insert_item(output_item, output_list);
// LOG_DEBUG_F("[%d] after writing %s\n", tid, tmp_consequence_type);
}
data += next_line_len+1;
data_read_len += next_line_len+1;
memset(line[tid], 0, strlen(line[tid]));
memset(output_line[tid], 0, strlen(output_line[tid]));
i++;
}
// Empty buffer for next callback invocation
if (!premature_end) {
memset(line[tid], 0, strlen(line[tid]));
memset(output_line[tid], 0, strlen(line[tid]));
}
free(SO_found);
return data_read_len;
}