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_template_utils_setup(void) {
source = gt_template_new();
alignment = gt_alignment_new();
target = gt_template_new();
output_attributes = gt_output_map_attributes_new();
}
