int sw_stage(void *data) {
batch_t *batch = (batch_t *) data;
if (batch->mapping_mode == RNA_MODE) {
return apply_sw_rna(batch->sw_input, batch);
} else {
return apply_sw(batch->sw_input, batch);
}
}
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);
}