void gt_write_stream(gt_output_file* output, gt_input_file** inputs, uint64_t num_inputs, bool append_extra, bool clean_id, bool interleave, uint64_t threads, bool write_map, bool remove_scores){
// prepare attributes
gt_output_fasta_attributes* attributes = 0;
gt_output_map_attributes* map_attributes = 0;
if(!write_map){
attributes = gt_output_fasta_attributes_new();
gt_output_fasta_attributes_set_print_extra(attributes, append_extra);
gt_output_fasta_attributes_set_print_casava(attributes, !clean_id);
// check qualities
if(!gt_input_file_has_qualities(inputs[0])){
gt_output_fasta_attributes_set_format(attributes, F_FASTA);
}
}else{
map_attributes = gt_output_map_attributes_new();
gt_output_map_attributes_set_print_extra(map_attributes, append_extra);
gt_output_map_attributes_set_print_casava(map_attributes, !clean_id);
gt_output_map_attributes_set_print_scores(map_attributes, !remove_scores);
}
// generic parser attributes
gt_generic_parser_attributes* parser_attributes = gt_input_generic_parser_attributes_new(false); // do not force pairs
pthread_mutex_t input_mutex = PTHREAD_MUTEX_INITIALIZER;
if(interleave){
// main loop, interleave
#pragma omp parallel num_threads(threads)
{
register uint64_t i = 0;
register uint64_t c = 0;
gt_buffered_output_file* buffered_output = gt_buffered_output_file_new(output);
gt_buffered_input_file** buffered_input = malloc(num_inputs * sizeof(gt_buffered_input_file*));
for(i=0; i<num_inputs; i++){
buffered_input[i] = gt_buffered_input_file_new(inputs[i]);
}
// attache first input to output
gt_buffered_input_file_attach_buffered_output(buffered_input[0], buffered_output);
gt_template* template = gt_template_new();
gt_status status;
i=0;
while( gt_input_generic_parser_synch_blocks_a(&input_mutex, buffered_input, num_inputs, parser_attributes) == GT_STATUS_OK ){
for(i=0; i<num_inputs; i++){
if( (status = gt_input_generic_parser_get_template(buffered_input[i], template, parser_attributes)) == GT_STATUS_OK){
if(write_map){
gt_output_map_bofprint_template(buffered_output, template, map_attributes);
}else{
void gt_stats_fill(gt_input_file* input_file, gt_stats* target_all_stats, gt_stats* target_best_stats, uint64_t num_threads, bool paired_end){
// Stats info
gt_stats** all_stats = malloc(num_threads*sizeof(gt_stats*));
all_stats[0] = target_all_stats;
gt_stats** best_stats = malloc(num_threads*sizeof(gt_stats*));
best_stats[0] = target_best_stats;
gt_stats_analysis params_all = GT_STATS_ANALYSIS_DEFAULT();
params_all.best_map = false;
gt_stats_analysis params_best = GT_STATS_ANALYSIS_DEFAULT();
params_best.best_map = true;
//params_all.indel_profile = true
// Parallel reading+process
#pragma omp parallel num_threads(num_threads)
{
uint64_t tid = omp_get_thread_num();
gt_buffered_input_file* buffered_input = gt_buffered_input_file_new(input_file);
gt_status error_code;
gt_template *template = gt_template_new();
/*
* CORE functions
*/
void gt_stats_parallel_generate_stats() {
// Stats info
gt_stats_analysis stats_analysis = GT_STATS_ANALYSIS_DEFAULT();
gt_stats** stats = malloc(parameters.num_threads*sizeof(gt_stats*));
// Select analysis
stats_analysis.best_map = parameters.best_map;
stats_analysis.maps_profile = parameters.maps_profile|parameters.mismatch_quality|parameters.mismatch_transitions;
stats_analysis.nucleotide_stats = true;
stats_analysis.split_map_stats = parameters.splitmaps_profile;
stats_analysis.indel_profile = parameters.indel_profile;
// Open file
gt_input_file* input_file = (parameters.name_input_file==NULL) ?
gt_input_stream_open(stdin) : gt_input_file_open(parameters.name_input_file,parameters.mmap_input);
gt_sequence_archive* sequence_archive = NULL;
if (stats_analysis.indel_profile) {
sequence_archive = gt_sequence_archive_new();
register gt_input_file* const reference_file = gt_input_file_open(parameters.name_reference_file,false);
fprintf(stderr,"Loading reference file ...");
if (gt_input_multifasta_parser_get_archive(reference_file,sequence_archive)!=GT_IFP_OK) {
fprintf(stderr,"\n");
gt_fatal_error_msg("Error parsing reference file '%s'\n",parameters.name_reference_file);
}
gt_input_file_close(reference_file);
fprintf(stderr," done! \n");
}
// Parallel reading+process
#pragma omp parallel num_threads(parameters.num_threads)
{
uint64_t tid = omp_get_thread_num();
gt_buffered_input_file* buffered_input = gt_buffered_input_file_new(input_file);
gt_status error_code;
gt_template *template = gt_template_new();
