mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-29 08:08:12 +08:00
r183: reorganized the major workflow
This commit is contained in:
Heng Li
+67
-139
@@ -1,5 +1,6 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include <assert.h>
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#include <zlib.h>
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#include "Assembly.h"
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#include "Process_Read.h"
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@@ -482,7 +483,6 @@ void* Overlap_calculate_heap_merge(void* arg)
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fprintf(stderr, "total recorrected bases: %lld\n", asm_opt.num_recorrected_bases);
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}
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pthread_mutex_unlock(&statistics);
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free(arg);
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return NULL;
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}
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@@ -578,9 +578,6 @@ void* Output_related_reads(void* arg)
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destoryHaplotypeEvdience(&hap);
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destory_Round2_alignment(&second_round);
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free(arg);
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return NULL;
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}
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@@ -694,7 +691,6 @@ void* Save_corrected_reads(void* arg)
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destory_UC_Read(&g_read);
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free(first_round_read);
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free(second_round_read);
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free(arg);
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return NULL;
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}
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@@ -722,84 +718,37 @@ void Output_corrected_reads()
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fclose(output_file);
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}
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void Overlap_calculate_multipe_thr()
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void ha_overlap_and_correct(int round)
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{
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double start_time = Get_T();
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int i, *args;
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pthread_t *_r_threads;
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MALLOC(_r_threads, asm_opt.thread_num);
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args = (int*)alloca(sizeof(int) * asm_opt.thread_num);
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fprintf(stderr, "Begin calculating overlaps... \n");
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pthread_t *_r_threads;
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_r_threads = (pthread_t *)malloc(sizeof(pthread_t)*asm_opt.thread_num);
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int i = 0;
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for (i = 0; i < asm_opt.thread_num; i++)
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{
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int *arg = (int*)malloc(sizeof(*arg));
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*arg = i;
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if(!asm_opt.required_read_name)
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{
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pthread_create(_r_threads + i, NULL, Overlap_calculate_heap_merge, (void*)arg);
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}
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else
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{
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pthread_create(_r_threads + i, NULL, Output_related_reads, (void*)arg);
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}
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ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, &R_INF); // build the index
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for (i = 0; i < asm_opt.thread_num; i++) {
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args[i] = i;
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if (!asm_opt.required_read_name)
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pthread_create(_r_threads + i, NULL, Overlap_calculate_heap_merge, (void*)&args[i]);
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else
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pthread_create(_r_threads + i, NULL, Output_related_reads, (void*)&args[i]);
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}
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for (i = 0; i < asm_opt.thread_num; i++)
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for (i = 0; i < asm_opt.thread_num; i++)
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pthread_join(_r_threads[i], NULL);
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free(_r_threads);
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if(asm_opt.required_read_name)
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{
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exit(1);
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}
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ha_pt_destroy(ha_idx);
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ha_idx = 0;
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fprintf(stderr, "All overlaps have been calculated.\n");
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if (asm_opt.required_read_name) exit(0); // for debugging only
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fprintf(stderr, "%-30s%18.2f\n\n", "Overlap calculation time:", Get_T() - start_time);
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start_time = Get_T();
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_r_threads = (pthread_t *)malloc(sizeof(pthread_t)*asm_opt.thread_num);
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for (i = 0; i < asm_opt.thread_num; i++)
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{
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int *arg = (int*)malloc(sizeof(*arg));
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*arg = i;
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pthread_create(_r_threads + i, NULL, Save_corrected_reads, (void*)arg);
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for (i = 0; i < asm_opt.thread_num; i++) {
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args[i] = i;
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pthread_create(_r_threads + i, NULL, Save_corrected_reads, (void*)&args[i]);
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}
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for (i = 0; i < asm_opt.thread_num; i++)
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for (i = 0; i < asm_opt.thread_num; i++)
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pthread_join(_r_threads[i], NULL);
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free(_r_threads);
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fprintf(stderr, "%-30s%18.2f\n\n", "Corrected read saving time:", Get_T() - start_time);
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///only the last round can output read to disk
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if (asm_opt.roundID == asm_opt.number_of_round - 1)
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{
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start_time = Get_T();
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Output_corrected_reads();
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fprintf(stderr, "%-30s%18.2f\n\n", "Output time:", Get_T() - start_time);
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}
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free(_r_threads);
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}
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void update_overlaps(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf,
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UC_Read* g_read, UC_Read* overlap_read, int is_match, int is_exact)
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{
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@@ -1159,7 +1108,6 @@ void* Final_overlap_calculate_heap_merge(void* arg)
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}
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}
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pthread_mutex_unlock(&statistics);
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free(arg);
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return NULL;
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}
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@@ -1331,80 +1279,60 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
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fprintf(stderr, "[M::%s] took %0.2fs, revise edges #: %lld\n\n", __func__, Get_T()-startTime, revises);
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}
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void generate_overlaps(int last_round)
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void ha_overlap_final(void)
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{
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double start_time = Get_T();
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asm_opt.roundID = asm_opt.number_of_round - last_round;
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fprintf(stderr, "Begin calculting final overlaps ...\n");
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int i, *args;
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pthread_t *_r_threads;
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ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, asm_opt.roundID == 0? 0 : 1, &R_INF);
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MALLOC(_r_threads, asm_opt.thread_num);
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args = (int*)alloca(sizeof(int) * asm_opt.thread_num);
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pthread_t *_r_threads;
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_r_threads = (pthread_t *)malloc(sizeof(pthread_t) * asm_opt.thread_num);
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int i = 0;
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for (i = 0; i < asm_opt.thread_num; i++)
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{
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int *arg = (int*)malloc(sizeof(*arg));
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*arg = i;
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pthread_create(_r_threads + i, NULL, Final_overlap_calculate_heap_merge, (void*)arg);
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}
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for (i = 0; i < asm_opt.thread_num; i++)
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pthread_join(_r_threads[i], NULL);
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free(_r_threads);
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///rescue_edges(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads, 4, 0.985);
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ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, &R_INF);
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for (i = 0; i < asm_opt.thread_num; i++) {
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args[i] = i;
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pthread_create(_r_threads + i, NULL, Final_overlap_calculate_heap_merge, (void*)&args[i]);
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}
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for (i = 0; i < asm_opt.thread_num; i++)
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pthread_join(_r_threads[i], NULL);
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free(_r_threads);
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ha_pt_destroy(ha_idx);
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ha_idx = 0;
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fprintf(stderr, "Final overlaps have been calculated.\n");
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fprintf(stderr, "%-30s%18.2f\n\n", "Final overlaps calculation time:", Get_T() - start_time);
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Output_PAF();
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trio_partition();
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build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
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R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
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asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name,
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asm_opt.large_pop_bubble_size, 0, 1);
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///rescue_edges(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads, 4, 0.985);
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fprintf(stderr, "[M::%s::%.3f*%.2f] ==> final overlap\n", __func__, yak_realtime(), yak_cputime() / yak_realtime());
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}
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void Correct_Reads(int last_round)
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int ha_assemble(void)
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{
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if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name))
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{
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build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
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R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
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asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, 0);
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exit(0);
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}
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else
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{
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///fprintf(stderr, "Cannot find overlap file. Please run the whole hifiasm.\n");
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}
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clear_opt(&asm_opt, last_round);
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if(last_round == 0)
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{
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generate_overlaps(last_round);
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return;
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}
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fprintf(stderr, "Error correction: Start the %d-th round ...\n", asm_opt.roundID);
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ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, asm_opt.roundID == 0? 0 : 1, &R_INF);
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Overlap_calculate_multipe_thr();
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ha_pt_destroy(ha_idx);
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fprintf(stderr, "Error correction: The %d-th round has been completed.\n", asm_opt.roundID);
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Correct_Reads(last_round - 1);
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int r, ovlp_loaded = 0;
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if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
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ovlp_loaded = 1;
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fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded overlaps from disk\n", __func__, yak_realtime(), yak_cputime() / yak_realtime());
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}
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if (!ovlp_loaded) {
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// construct hash table for high occurrence k-mers
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if (!asm_opt.no_kmer_flt)
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ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF);
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// error correction
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assert(asm_opt.number_of_round > 0);
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for (r = 0; r < asm_opt.number_of_round; ++r) {
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clear_opt(&asm_opt, asm_opt.number_of_round - r); // this update asm_opt.roundID and a few other fields
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ha_overlap_and_correct(r);
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fprintf(stderr, "[M::%s::%.3f*%.2f] ==> corrected reads for round %d\n", __func__, yak_realtime(), yak_cputime() / yak_realtime(), r + 1);
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}
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Output_corrected_reads();
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fprintf(stderr, "[M::%s::%.3f*%.2f] ==> written corrected reads to disk\n", __func__, yak_realtime(), yak_cputime() / yak_realtime());
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// overlap between corrected reads
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clear_opt(&asm_opt, 0);
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ha_overlap_final();
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fprintf(stderr, "[M::%s::%.3f*%.2f] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cputime() / yak_realtime());
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ha_ft_destroy(ha_flt_tab);
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Output_PAF();
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trio_partition();
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}
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build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
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R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
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asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, !ovlp_loaded);
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destory_All_reads(&R_INF);
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return 0;
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}
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